Starting phenix.real_space_refine on Thu Sep 18 12:04:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ay6_43981/09_2025/9ay6_43981.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ay6_43981/09_2025/9ay6_43981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ay6_43981/09_2025/9ay6_43981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ay6_43981/09_2025/9ay6_43981.map" model { file = "/net/cci-nas-00/data/ceres_data/9ay6_43981/09_2025/9ay6_43981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ay6_43981/09_2025/9ay6_43981.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 105 5.16 5 C 10331 2.51 5 N 2812 2.21 5 O 3393 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16641 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3568 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "C" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3541 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 2 Chain: "D" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "E" Number of atoms: 3603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3603 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 20, 'TRANS': 436} Chain breaks: 2 Chain: "F" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1147 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain: "H" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "L" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 585 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'TRANS': 116} Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 117 Planarities with less than four sites: {'UNK:plan-1': 117} Unresolved non-hydrogen planarities: 117 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: 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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 Time building chain proxies: 3.70, per 1000 atoms: 0.22 Number of scatterers: 16641 At special positions: 0 Unit cell: (132.715, 152.57, 122.265, 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 105 16.00 O 3393 8.00 N 2812 7.00 C 10331 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 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 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.27 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 444 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 149 " 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 330 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 444 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 377 " - pdb=" SG CYS E 444 " distance=2.03 Simple disulfide: pdb=" SG CYS E 384 " - pdb=" SG CYS E 417 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA V 3 " - " MAN V 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA V 3 " - " MAN V 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " BMA 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG 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 k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 289 " " NAG A 604 " - " ASN A 354 " " NAG A 605 " - " ASN A 397 " " NAG A 606 " - " ASN A 197 " " NAG A 607 " - " ASN A 391 " " NAG A 608 " - " ASN A 88 " " NAG B 701 " - " ASN B 611 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 152 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 241 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 338 " " NAG C 608 " - " ASN C 385 " " NAG C 609 " - " ASN C 276 " " NAG C 610 " - " ASN C 354 " " NAG D 701 " - " ASN D 611 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 137 " " NAG E 603 " - " ASN E 152 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 289 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 354 " " NAG E 609 " - " ASN E 338 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG G 1 " - " ASN A 148 " " NAG I 1 " - " ASN A 152 " " NAG J 1 " - " ASN A 241 " " NAG K 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 295 " " NAG O 1 " - " ASN A 301 " " NAG P 1 " - " ASN A 331 " " NAG Q 1 " - " ASN A 362 " " NAG R 1 " - " ASN A 385 " " NAG S 1 " - " ASN A 447 " " NAG T 1 " - " ASN C 148 " " NAG U 1 " - " ASN C 197 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN C 289 " " NAG X 1 " - " ASN C 295 " " NAG Y 1 " - " ASN C 331 " " NAG Z 1 " - " ASN C 362 " " NAG a 1 " - " ASN C 447 " " NAG b 1 " - " ASN C 391 " " NAG c 1 " - " ASN E 148 " " NAG d 1 " - " ASN E 241 " " NAG e 1 " - " ASN E 262 " " NAG f 1 " - " ASN E 276 " " NAG g 1 " - " ASN E 362 " " NAG h 1 " - " ASN E 295 " " NAG i 1 " - " ASN E 331 " " NAG j 1 " - " ASN E 447 " " NAG k 1 " - " ASN E 391 " " NAG l 1 " - " ASN E 461 " " NAG m 1 " - " ASN E 385 " Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 681.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3788 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 30 sheets defined 31.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.166A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.766A pdb=" N HIS A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.670A pdb=" N THR A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.511A pdb=" N GLN A 427 " --> pdb=" O ASN A 424 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 428 " --> pdb=" O MET A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 428' Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.771A pdb=" N GLU A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.552A pdb=" N ALA B 533 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER B 534 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 546 removed outlier: 3.533A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 558 Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.934A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 424 through 428 removed outlier: 3.614A pdb=" N ARG C 428 " --> pdb=" O MET C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 462 Processing helix chain 'C' and resid 473 through 483 removed outlier: 4.285A pdb=" N ASN C 477 " --> pdb=" O ASP C 473 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP C 478 " --> pdb=" O MET C 474 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 535 removed outlier: 3.951A pdb=" N MET D 535 " --> pdb=" O ALA D 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 532 through 535' Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 548 through 557 Processing helix chain 'D' and resid 562 through 567 Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.648A pdb=" N ILE D 622 " --> pdb=" O LEU D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 Processing helix chain 'E' and resid 57 through 63 removed outlier: 3.584A pdb=" N TYR E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.153A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 194 through 199 removed outlier: 3.735A pdb=" N THR E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 removed outlier: 3.972A pdb=" N ASN E 280 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 352 removed outlier: 3.981A pdb=" N LYS E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N HIS E 351 " --> pdb=" O GLN E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.692A pdb=" N THR E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 424 through 428 removed outlier: 3.788A pdb=" N GLN E 427 " --> pdb=" O ASN E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 483 removed outlier: 3.575A pdb=" N ASN E 477 " --> pdb=" O ASP E 473 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR E 483 " --> pdb=" O ARG E 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.965A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 558 removed outlier: 4.036A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ILE F 548 " --> pdb=" O LEU F 544 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA F 558 " --> pdb=" O ASN F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 568 Processing helix chain 'F' and resid 568 through 596 removed outlier: 3.554A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'H' and resid 76 through 80 Processing sheet with id=AA1, first strand: chain 'A' and resid 493 through 497 removed outlier: 3.665A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 169 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.526A pdb=" N ALA A 200 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR A 434 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR A 202 " --> pdb=" O TYR A 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 302 removed outlier: 6.136A pdb=" N GLN A 293 " --> pdb=" O SER A 333 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 329 through 333 current: chain 'A' and resid 380 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 380 through 384 current: chain 'A' and resid 464 through 469 Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 498 removed outlier: 5.549A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'C' and resid 161 through 169 Processing sheet with id=AB5, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.747A pdb=" N THR C 202 " --> pdb=" O TYR C 434 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 304 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 318 through 321 current: chain 'C' and resid 380 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 380 through 384 current: chain 'C' and resid 464 through 468 Processing sheet with id=AB7, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.645A pdb=" N GLN C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 494 through 498 removed outlier: 5.879A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AC2, first strand: chain 'E' and resid 161 through 169 Processing sheet with id=AC3, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.708A pdb=" N THR E 202 " --> pdb=" O TYR E 434 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 270 through 271 Processing sheet with id=AC5, first strand: chain 'E' and resid 373 through 377 removed outlier: 7.017A pdb=" N CYS E 296 " --> pdb=" O SER E 446 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N SER E 446 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ARG E 298 " --> pdb=" O CYS E 444 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N CYS E 444 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN E 300 " --> pdb=" O ILE E 442 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ILE E 442 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 304 through 310 removed outlier: 6.818A pdb=" N GLN E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 392 through 394 removed outlier: 6.281A pdb=" N ARG E 359 " --> pdb=" O PHE E 467 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'H' and resid 51 through 52 removed outlier: 6.870A pdb=" N UNK H 34 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N UNK H 48 " --> pdb=" O UNK H 32 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N UNK H 32 " --> pdb=" O UNK H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AD2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.563A pdb=" N UNK L 11 " --> pdb=" O UNK L 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'L' and resid 31 through 37 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 44 through 45 current: chain 'L' and resid 102 through 106 538 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5230 1.34 - 1.46: 3216 1.46 - 1.58: 8334 1.58 - 1.70: 0 1.70 - 1.81: 138 Bond restraints: 16918 Sorted by residual: bond pdb=" C1 NAG l 1 " pdb=" O5 NAG l 1 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.79e+00 bond pdb=" N ILE C 395 " pdb=" CA ILE C 395 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.22e+00 bond pdb=" C1 NAG m 2 " pdb=" O5 NAG m 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.18e+00 bond pdb=" C1 NAG h 2 " pdb=" O5 NAG h 2 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.32e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.25e+00 ... (remaining 16913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 21181 1.33 - 2.66: 1527 2.66 - 3.99: 191 3.99 - 5.33: 85 5.33 - 6.66: 23 Bond angle restraints: 23007 Sorted by residual: angle pdb=" N GLN B 630 " pdb=" CA GLN B 630 " pdb=" C GLN B 630 " ideal model delta sigma weight residual 112.72 108.23 4.49 1.28e+00 6.10e-01 1.23e+01 angle pdb=" N SER D 615 " pdb=" CA SER D 615 " pdb=" CB SER D 615 " ideal model delta sigma weight residual 114.17 110.34 3.83 1.14e+00 7.69e-01 1.13e+01 angle pdb=" N ALA A 58 " pdb=" CA ALA A 58 " pdb=" CB ALA A 58 " ideal model delta sigma weight residual 114.17 110.41 3.76 1.14e+00 7.69e-01 1.09e+01 angle pdb=" C UNK H 49 " pdb=" CA UNK H 49 " pdb=" CB UNK H 49 " ideal model delta sigma weight residual 110.08 116.01 -5.93 1.90e+00 2.77e-01 9.73e+00 angle pdb=" C UNK L 99 " pdb=" CA UNK L 99 " pdb=" CB UNK L 99 " ideal model delta sigma weight residual 110.08 115.97 -5.89 1.90e+00 2.77e-01 9.62e+00 ... (remaining 23002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.15: 11097 22.15 - 44.31: 311 44.31 - 66.46: 47 66.46 - 88.62: 51 88.62 - 110.77: 25 Dihedral angle restraints: 11531 sinusoidal: 5706 harmonic: 5825 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 142.98 -49.98 1 1.00e+01 1.00e-02 3.43e+01 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 93.00 141.61 -48.61 1 1.00e+01 1.00e-02 3.25e+01 dihedral pdb=" CA CYS A 228 " pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " ideal model delta sinusoidal sigma weight residual -73.00 -1.18 -71.82 1 2.00e+01 2.50e-03 1.65e+01 ... (remaining 11528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 2884 0.130 - 0.259: 56 0.259 - 0.389: 7 0.389 - 0.518: 0 0.518 - 0.648: 1 Chirality restraints: 2948 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-02 2.50e+03 2.83e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.65e+01 chirality pdb=" C1 NAG C 607 " pdb=" ND2 ASN C 338 " pdb=" C2 NAG C 607 " pdb=" O5 NAG C 607 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 2945 not shown) Planarity restraints: 2880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " -0.281 2.00e-02 2.50e+03 2.36e-01 6.93e+02 pdb=" C7 NAG Z 2 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " 0.398 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 1 " -0.171 2.00e-02 2.50e+03 1.40e-01 2.47e+02 pdb=" C7 NAG Z 1 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG Z 1 " -0.126 2.00e-02 2.50e+03 pdb=" N2 NAG Z 1 " 0.225 2.00e-02 2.50e+03 pdb=" O7 NAG Z 1 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 2 " 0.117 2.00e-02 2.50e+03 9.64e-02 1.16e+02 pdb=" C7 NAG Y 2 " -0.031 2.00e-02 2.50e+03 pdb=" C8 NAG Y 2 " 0.087 2.00e-02 2.50e+03 pdb=" N2 NAG Y 2 " -0.155 2.00e-02 2.50e+03 pdb=" O7 NAG Y 2 " -0.018 2.00e-02 2.50e+03 ... (remaining 2877 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2257 2.76 - 3.29: 16300 3.29 - 3.83: 26644 3.83 - 4.36: 30960 4.36 - 4.90: 52070 Nonbonded interactions: 128231 Sorted by model distance: nonbonded pdb=" OG1 THR B 627 " pdb=" OE1 GLN B 630 " model vdw 2.225 3.040 nonbonded pdb=" N UNK L 13 " pdb=" O UNK L 117 " model vdw 2.235 3.120 nonbonded pdb=" OD1 ASN E 280 " pdb=" NH1 ARG E 455 " model vdw 2.252 3.120 nonbonded pdb=" OE2 GLU E 145 " pdb=" NH1 ARG E 418 " model vdw 2.259 3.120 nonbonded pdb=" OD1 ASN D 607 " pdb=" OG SER D 649 " model vdw 2.275 3.040 ... (remaining 128226 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 35 through 179 or resid 189 through 397 or resid 411 throu \ gh 608)) selection = (chain 'C' and (resid 35 through 270 or (resid 271 and (name N or name CA or nam \ e C or name O or name CB )) or resid 272 through 608)) selection = (chain 'E' and (resid 35 through 270 or (resid 271 and (name N or name CA or nam \ e C or name O or name CB )) or resid 272 through 397 or resid 411 through 503 or \ resid 602 through 609)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = (chain 'F' and resid 521 through 701) } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'j' and resid 1) selection = (chain 'l' and resid 1) selection = (chain 'm' and resid 1) } ncs_group { reference = chain 'H' selection = (chain 'L' and resid 16 through 117) } ncs_group { reference = chain 'V' selection = chain 'e' } ncs_group { reference = chain 'g' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.690 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 : 0.006 0.242 17048 Z= 0.277 Angle : 0.900 40.665 23369 Z= 0.434 Chirality : 0.052 0.648 2948 Planarity : 0.007 0.236 2819 Dihedral : 13.032 110.774 7659 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.20), residues: 1763 helix: 1.30 (0.25), residues: 434 sheet: -0.31 (0.25), residues: 402 loop : -0.27 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 585 TYR 0.014 0.001 TYR A 191 PHE 0.015 0.002 PHE A 53 TRP 0.013 0.001 TRP A 96 HIS 0.004 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00528 (16918) covalent geometry : angle 0.79800 (23007) SS BOND : bond 0.04581 ( 28) SS BOND : angle 5.92679 ( 56) hydrogen bonds : bond 0.15010 ( 538) hydrogen bonds : angle 6.20935 ( 1446) link_ALPHA1-3 : bond 0.00271 ( 3) link_ALPHA1-3 : angle 1.90080 ( 9) link_ALPHA1-6 : bond 0.00214 ( 2) link_ALPHA1-6 : angle 1.89405 ( 6) link_BETA1-4 : bond 0.01008 ( 36) link_BETA1-4 : angle 3.36171 ( 108) link_NAG-ASN : bond 0.00383 ( 61) link_NAG-ASN : angle 2.37452 ( 183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 481 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8500 (ptm) cc_final: 0.8276 (ptm) REVERT: A 97 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8545 (mmmt) REVERT: A 102 GLU cc_start: 0.8536 (tp30) cc_final: 0.8160 (mm-30) REVERT: A 142 MET cc_start: 0.8741 (mmm) cc_final: 0.8196 (mmt) REVERT: A 172 ASP cc_start: 0.8849 (m-30) cc_final: 0.8300 (m-30) REVERT: A 232 LYS cc_start: 0.8210 (mttt) cc_final: 0.7734 (ttpt) REVERT: B 522 PHE cc_start: 0.8671 (t80) cc_final: 0.8078 (t80) REVERT: B 529 THR cc_start: 0.8630 (t) cc_final: 0.8331 (m) REVERT: B 530 MET cc_start: 0.7642 (mtp) cc_final: 0.7080 (mtp) REVERT: B 535 MET cc_start: 0.7595 (mtp) cc_final: 0.7391 (mtp) REVERT: B 550 GLN cc_start: 0.7384 (mp10) cc_final: 0.6934 (mp10) REVERT: B 584 GLU cc_start: 0.8509 (tp30) cc_final: 0.8067 (tm-30) REVERT: B 626 MET cc_start: 0.7637 (mmm) cc_final: 0.7354 (tpp) REVERT: B 645 LEU cc_start: 0.9173 (mt) cc_final: 0.8892 (mp) REVERT: B 647 GLU cc_start: 0.8508 (tt0) cc_final: 0.8156 (tt0) REVERT: B 651 ASN cc_start: 0.9326 (t0) cc_final: 0.8808 (t0) REVERT: B 660 LEU cc_start: 0.8497 (tp) cc_final: 0.8259 (tt) REVERT: C 104 MET cc_start: 0.9315 (ttt) cc_final: 0.8994 (tpp) REVERT: C 159 ASP cc_start: 0.8239 (p0) cc_final: 0.7986 (p0) REVERT: C 376 ASN cc_start: 0.9121 (t0) cc_final: 0.7625 (p0) REVERT: C 474 MET cc_start: 0.8503 (mmm) cc_final: 0.8164 (mmt) REVERT: C 483 TYR cc_start: 0.8806 (p90) cc_final: 0.8604 (p90) REVERT: D 641 ILE cc_start: 0.8821 (mt) cc_final: 0.8615 (mp) REVERT: D 648 GLU cc_start: 0.7965 (tp30) cc_final: 0.7763 (tp30) REVERT: E 35 TRP cc_start: 0.7800 (m100) cc_final: 0.7253 (m100) REVERT: E 99 ASN cc_start: 0.8598 (p0) cc_final: 0.8246 (t0) REVERT: E 145 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7662 (tp30) REVERT: E 161 LYS cc_start: 0.8644 (mmtm) cc_final: 0.8414 (ptmm) REVERT: E 369 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7671 (mm-30) REVERT: E 376 ASN cc_start: 0.8893 (t0) cc_final: 0.7865 (p0) REVERT: E 425 MET cc_start: 0.8220 (mtp) cc_final: 0.7477 (mmm) REVERT: F 565 LEU cc_start: 0.6445 (mt) cc_final: 0.5900 (mt) outliers start: 0 outliers final: 0 residues processed: 481 average time/residue: 0.1392 time to fit residues: 96.4898 Evaluate side-chains 281 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN A 421 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN C 195 ASN D 551 GLN D 564 HIS E 329 HIS ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.114119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.095026 restraints weight = 36715.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097431 restraints weight = 23810.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099068 restraints weight = 17865.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100114 restraints weight = 14749.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100855 restraints weight = 12970.284| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 17048 Z= 0.295 Angle : 0.859 11.041 23369 Z= 0.404 Chirality : 0.049 0.456 2948 Planarity : 0.004 0.050 2819 Dihedral : 10.352 84.592 4259 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.46 % Allowed : 9.12 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.20), residues: 1763 helix: 1.15 (0.24), residues: 452 sheet: -0.23 (0.25), residues: 425 loop : -0.36 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 298 TYR 0.025 0.002 TYR A 217 PHE 0.020 0.002 PHE D 522 TRP 0.021 0.002 TRP C 112 HIS 0.007 0.001 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.00670 (16918) covalent geometry : angle 0.79732 (23007) SS BOND : bond 0.00472 ( 28) SS BOND : angle 1.11015 ( 56) hydrogen bonds : bond 0.05485 ( 538) hydrogen bonds : angle 5.37260 ( 1446) link_ALPHA1-3 : bond 0.00206 ( 3) link_ALPHA1-3 : angle 2.66899 ( 9) link_ALPHA1-6 : bond 0.00446 ( 2) link_ALPHA1-6 : angle 2.02881 ( 6) link_BETA1-4 : bond 0.00700 ( 36) link_BETA1-4 : angle 2.72543 ( 108) link_NAG-ASN : bond 0.00679 ( 61) link_NAG-ASN : angle 3.00240 ( 183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 287 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.8747 (m-90) cc_final: 0.8404 (m100) REVERT: A 97 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8601 (mmmt) REVERT: A 102 GLU cc_start: 0.8763 (tp30) cc_final: 0.8330 (mm-30) REVERT: A 172 ASP cc_start: 0.8787 (m-30) cc_final: 0.8300 (m-30) REVERT: B 530 MET cc_start: 0.8029 (mtp) cc_final: 0.7737 (mtp) REVERT: B 535 MET cc_start: 0.7435 (mtp) cc_final: 0.7095 (mtp) REVERT: B 536 THR cc_start: 0.7963 (p) cc_final: 0.7562 (t) REVERT: B 629 LEU cc_start: 0.7882 (mt) cc_final: 0.7662 (mt) REVERT: B 660 LEU cc_start: 0.8714 (tp) cc_final: 0.8435 (tt) REVERT: C 113 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8722 (t0) REVERT: C 376 ASN cc_start: 0.9098 (t0) cc_final: 0.7688 (p0) REVERT: C 473 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7892 (p0) REVERT: C 483 TYR cc_start: 0.8834 (p90) cc_final: 0.8597 (p90) REVERT: D 535 MET cc_start: 0.8588 (mpp) cc_final: 0.8377 (mpp) REVERT: D 536 THR cc_start: 0.8302 (p) cc_final: 0.7857 (t) REVERT: D 584 GLU cc_start: 0.8339 (tt0) cc_final: 0.7846 (tt0) REVERT: D 626 MET cc_start: 0.7924 (tmm) cc_final: 0.7482 (tmm) REVERT: D 631 TRP cc_start: 0.8348 (t-100) cc_final: 0.7746 (t-100) REVERT: D 655 LYS cc_start: 0.8545 (pttp) cc_final: 0.8187 (pttt) REVERT: E 99 ASN cc_start: 0.8778 (p0) cc_final: 0.8233 (t0) REVERT: E 376 ASN cc_start: 0.8924 (t0) cc_final: 0.7877 (p0) REVERT: E 425 MET cc_start: 0.8046 (mtp) cc_final: 0.7551 (mmm) REVERT: F 554 ASN cc_start: 0.8712 (m-40) cc_final: 0.8292 (p0) REVERT: F 634 GLU cc_start: 0.8185 (tp30) cc_final: 0.7886 (tp30) REVERT: F 656 ASN cc_start: 0.9182 (m-40) cc_final: 0.8673 (t0) outliers start: 55 outliers final: 32 residues processed: 319 average time/residue: 0.1341 time to fit residues: 63.8653 Evaluate side-chains 275 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 553 SER Chi-restraints excluded: chain F residue 620 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN C 195 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 HIS E 397 ASN ** E 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 552 GLN F 564 HIS F 577 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.117127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097374 restraints weight = 36672.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099995 restraints weight = 23184.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.101731 restraints weight = 17301.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.102903 restraints weight = 14214.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.103619 restraints weight = 12397.673| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17048 Z= 0.149 Angle : 0.708 13.759 23369 Z= 0.336 Chirality : 0.046 0.402 2948 Planarity : 0.004 0.042 2819 Dihedral : 8.905 78.704 4259 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.64 % Allowed : 12.45 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.20), residues: 1763 helix: 1.58 (0.25), residues: 444 sheet: -0.08 (0.25), residues: 424 loop : -0.29 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 143 TYR 0.024 0.001 TYR D 643 PHE 0.012 0.001 PHE A 53 TRP 0.039 0.002 TRP E 35 HIS 0.006 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00328 (16918) covalent geometry : angle 0.63884 (23007) SS BOND : bond 0.00335 ( 28) SS BOND : angle 1.23970 ( 56) hydrogen bonds : bond 0.04579 ( 538) hydrogen bonds : angle 4.95631 ( 1446) link_ALPHA1-3 : bond 0.00774 ( 3) link_ALPHA1-3 : angle 2.07392 ( 9) link_ALPHA1-6 : bond 0.00659 ( 2) link_ALPHA1-6 : angle 1.94100 ( 6) link_BETA1-4 : bond 0.00707 ( 36) link_BETA1-4 : angle 2.34502 ( 108) link_NAG-ASN : bond 0.00671 ( 61) link_NAG-ASN : angle 2.95522 ( 183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 277 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8633 (tp30) cc_final: 0.8227 (mm-30) REVERT: A 104 MET cc_start: 0.9392 (ttm) cc_final: 0.9132 (ttp) REVERT: A 142 MET cc_start: 0.8859 (mmm) cc_final: 0.8409 (mmt) REVERT: A 172 ASP cc_start: 0.8674 (m-30) cc_final: 0.8208 (m-30) REVERT: A 246 GLN cc_start: 0.7947 (pm20) cc_final: 0.7529 (tp-100) REVERT: B 522 PHE cc_start: 0.8900 (t80) cc_final: 0.8600 (t80) REVERT: B 535 MET cc_start: 0.7617 (mtp) cc_final: 0.7260 (mtp) REVERT: B 543 ASN cc_start: 0.8318 (t0) cc_final: 0.7850 (t0) REVERT: B 567 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8545 (mmtm) REVERT: C 104 MET cc_start: 0.9354 (tpp) cc_final: 0.9029 (tpp) REVERT: C 217 TYR cc_start: 0.8733 (m-80) cc_final: 0.8377 (m-80) REVERT: C 376 ASN cc_start: 0.9107 (t0) cc_final: 0.7712 (p0) REVERT: C 473 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7780 (p0) REVERT: C 483 TYR cc_start: 0.8803 (p90) cc_final: 0.8532 (p90) REVERT: D 530 MET cc_start: 0.7504 (mtp) cc_final: 0.7256 (mtt) REVERT: D 551 GLN cc_start: 0.7932 (pt0) cc_final: 0.7682 (pt0) REVERT: D 584 GLU cc_start: 0.8228 (tt0) cc_final: 0.7808 (tt0) REVERT: D 626 MET cc_start: 0.8270 (tmm) cc_final: 0.7641 (tmm) REVERT: D 631 TRP cc_start: 0.8217 (t-100) cc_final: 0.7971 (t-100) REVERT: D 643 TYR cc_start: 0.9172 (m-80) cc_final: 0.8863 (m-80) REVERT: D 655 LYS cc_start: 0.8623 (pttp) cc_final: 0.8289 (pttt) REVERT: E 99 ASN cc_start: 0.8711 (p0) cc_final: 0.8224 (t0) REVERT: E 107 ASP cc_start: 0.8288 (t0) cc_final: 0.7967 (t0) REVERT: E 376 ASN cc_start: 0.8920 (t0) cc_final: 0.7856 (p0) REVERT: E 425 MET cc_start: 0.7878 (mtp) cc_final: 0.7394 (mmm) REVERT: F 554 ASN cc_start: 0.8612 (m-40) cc_final: 0.8218 (p0) REVERT: F 656 ASN cc_start: 0.9140 (m-40) cc_final: 0.8735 (t0) outliers start: 42 outliers final: 25 residues processed: 304 average time/residue: 0.1366 time to fit residues: 62.7291 Evaluate side-chains 267 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 351 HIS Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 146 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN C 72 HIS C 195 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** E 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN F 552 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.096113 restraints weight = 36565.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.098629 restraints weight = 22765.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.100370 restraints weight = 16799.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.101512 restraints weight = 13665.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102340 restraints weight = 11865.357| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17048 Z= 0.179 Angle : 0.725 18.377 23369 Z= 0.337 Chirality : 0.047 0.625 2948 Planarity : 0.003 0.041 2819 Dihedral : 8.042 73.515 4259 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.08 % Allowed : 13.33 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.20), residues: 1763 helix: 1.71 (0.25), residues: 441 sheet: -0.05 (0.25), residues: 432 loop : -0.26 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 298 TYR 0.019 0.001 TYR D 643 PHE 0.020 0.002 PHE F 522 TRP 0.048 0.002 TRP E 35 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00405 (16918) covalent geometry : angle 0.64039 (23007) SS BOND : bond 0.00402 ( 28) SS BOND : angle 1.18948 ( 56) hydrogen bonds : bond 0.04406 ( 538) hydrogen bonds : angle 4.76977 ( 1446) link_ALPHA1-3 : bond 0.00789 ( 3) link_ALPHA1-3 : angle 2.20192 ( 9) link_ALPHA1-6 : bond 0.00718 ( 2) link_ALPHA1-6 : angle 2.01387 ( 6) link_BETA1-4 : bond 0.00639 ( 36) link_BETA1-4 : angle 2.28585 ( 108) link_NAG-ASN : bond 0.00666 ( 61) link_NAG-ASN : angle 3.42566 ( 183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8205 (pt0) cc_final: 0.7761 (pp20) REVERT: A 102 GLU cc_start: 0.8732 (tp30) cc_final: 0.8325 (mm-30) REVERT: A 104 MET cc_start: 0.9419 (ttm) cc_final: 0.8404 (tpp) REVERT: A 142 MET cc_start: 0.8912 (mmm) cc_final: 0.7944 (mmt) REVERT: A 172 ASP cc_start: 0.8677 (m-30) cc_final: 0.8253 (m-30) REVERT: A 246 GLN cc_start: 0.7926 (pm20) cc_final: 0.7592 (tp-100) REVERT: B 535 MET cc_start: 0.7503 (mtp) cc_final: 0.7179 (mtp) REVERT: B 536 THR cc_start: 0.7881 (p) cc_final: 0.7584 (t) REVERT: B 606 THR cc_start: 0.9351 (m) cc_final: 0.9010 (p) REVERT: C 104 MET cc_start: 0.9318 (tpp) cc_final: 0.8910 (tpp) REVERT: C 153 MET cc_start: 0.8617 (tpp) cc_final: 0.8249 (ttm) REVERT: C 217 TYR cc_start: 0.8767 (m-80) cc_final: 0.8281 (m-80) REVERT: C 246 GLN cc_start: 0.7525 (pm20) cc_final: 0.7225 (pm20) REVERT: C 376 ASN cc_start: 0.9133 (t0) cc_final: 0.7752 (p0) REVERT: C 483 TYR cc_start: 0.8866 (p90) cc_final: 0.8519 (p90) REVERT: D 530 MET cc_start: 0.7499 (mtp) cc_final: 0.7245 (mtt) REVERT: D 626 MET cc_start: 0.8268 (tmm) cc_final: 0.7571 (tmm) REVERT: D 631 TRP cc_start: 0.8165 (t-100) cc_final: 0.7678 (t-100) REVERT: D 655 LYS cc_start: 0.8604 (pttp) cc_final: 0.8240 (pttt) REVERT: E 83 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6742 (mt-10) REVERT: E 99 ASN cc_start: 0.8742 (p0) cc_final: 0.8364 (t0) REVERT: E 107 ASP cc_start: 0.8279 (t0) cc_final: 0.8004 (t0) REVERT: E 125 LEU cc_start: 0.9325 (mt) cc_final: 0.8975 (mt) REVERT: E 376 ASN cc_start: 0.8932 (t0) cc_final: 0.7866 (p0) REVERT: E 425 MET cc_start: 0.7967 (mtp) cc_final: 0.7474 (mmm) REVERT: F 554 ASN cc_start: 0.8617 (m-40) cc_final: 0.8387 (p0) REVERT: F 634 GLU cc_start: 0.8142 (tp30) cc_final: 0.7795 (tp30) REVERT: F 656 ASN cc_start: 0.9110 (OUTLIER) cc_final: 0.8627 (t0) outliers start: 49 outliers final: 31 residues processed: 286 average time/residue: 0.1371 time to fit residues: 59.3506 Evaluate side-chains 268 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 351 HIS Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 656 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 38 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 21 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 HIS E 329 HIS ** E 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.115411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096174 restraints weight = 36465.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.098818 restraints weight = 22334.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.100558 restraints weight = 16282.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.101773 restraints weight = 13207.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102593 restraints weight = 11409.513| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17048 Z= 0.156 Angle : 0.697 18.489 23369 Z= 0.326 Chirality : 0.045 0.544 2948 Planarity : 0.003 0.042 2819 Dihedral : 7.400 68.456 4259 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.14 % Allowed : 13.77 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.20), residues: 1763 helix: 1.66 (0.25), residues: 441 sheet: 0.04 (0.25), residues: 432 loop : -0.28 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 475 TYR 0.011 0.001 TYR D 643 PHE 0.011 0.001 PHE F 522 TRP 0.052 0.002 TRP E 35 HIS 0.006 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00355 (16918) covalent geometry : angle 0.61457 (23007) SS BOND : bond 0.00513 ( 28) SS BOND : angle 1.03978 ( 56) hydrogen bonds : bond 0.04204 ( 538) hydrogen bonds : angle 4.63398 ( 1446) link_ALPHA1-3 : bond 0.00867 ( 3) link_ALPHA1-3 : angle 2.20038 ( 9) link_ALPHA1-6 : bond 0.00845 ( 2) link_ALPHA1-6 : angle 1.95560 ( 6) link_BETA1-4 : bond 0.00629 ( 36) link_BETA1-4 : angle 2.14797 ( 108) link_NAG-ASN : bond 0.00444 ( 61) link_NAG-ASN : angle 3.32638 ( 183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 249 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7986 (p) REVERT: A 49 GLU cc_start: 0.8184 (pt0) cc_final: 0.7841 (pp20) REVERT: A 102 GLU cc_start: 0.8677 (tp30) cc_final: 0.8327 (mm-30) REVERT: A 104 MET cc_start: 0.9437 (ttm) cc_final: 0.8426 (tpp) REVERT: A 142 MET cc_start: 0.8966 (mmm) cc_final: 0.8031 (mmt) REVERT: A 172 ASP cc_start: 0.8664 (m-30) cc_final: 0.8260 (m-30) REVERT: A 246 GLN cc_start: 0.7882 (pm20) cc_final: 0.7522 (tp-100) REVERT: A 283 ASN cc_start: 0.9145 (m-40) cc_final: 0.8875 (m110) REVERT: B 535 MET cc_start: 0.7606 (mtp) cc_final: 0.7278 (mtp) REVERT: B 536 THR cc_start: 0.7933 (p) cc_final: 0.7701 (t) REVERT: B 606 THR cc_start: 0.9306 (m) cc_final: 0.8970 (p) REVERT: C 104 MET cc_start: 0.9276 (tpp) cc_final: 0.8855 (tpp) REVERT: C 217 TYR cc_start: 0.8821 (m-80) cc_final: 0.8294 (m-80) REVERT: C 246 GLN cc_start: 0.7554 (pm20) cc_final: 0.7269 (pm20) REVERT: C 376 ASN cc_start: 0.9127 (t0) cc_final: 0.7751 (p0) REVERT: C 483 TYR cc_start: 0.8871 (p90) cc_final: 0.8501 (p90) REVERT: D 557 ARG cc_start: 0.8223 (tpp80) cc_final: 0.7792 (tpp80) REVERT: D 631 TRP cc_start: 0.8120 (t-100) cc_final: 0.7757 (t-100) REVERT: E 99 ASN cc_start: 0.8808 (p0) cc_final: 0.8372 (t0) REVERT: E 107 ASP cc_start: 0.8202 (t0) cc_final: 0.7991 (t0) REVERT: E 158 ARG cc_start: 0.7478 (mtp-110) cc_final: 0.7240 (ttp-110) REVERT: E 202 THR cc_start: 0.9399 (m) cc_final: 0.9006 (p) REVERT: E 376 ASN cc_start: 0.8935 (t0) cc_final: 0.7879 (p0) REVERT: E 425 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7523 (mmm) REVERT: F 552 GLN cc_start: 0.6855 (pp30) cc_final: 0.6008 (tp40) REVERT: F 656 ASN cc_start: 0.9100 (OUTLIER) cc_final: 0.8637 (t0) outliers start: 50 outliers final: 34 residues processed: 279 average time/residue: 0.1295 time to fit residues: 54.8915 Evaluate side-chains 268 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 656 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 67 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.109928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.090847 restraints weight = 37158.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.093147 restraints weight = 23509.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.094756 restraints weight = 17693.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095830 restraints weight = 14561.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.096265 restraints weight = 12741.151| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 17048 Z= 0.338 Angle : 0.892 18.847 23369 Z= 0.415 Chirality : 0.050 0.574 2948 Planarity : 0.004 0.045 2819 Dihedral : 7.874 65.012 4259 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.90 % Allowed : 14.84 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.20), residues: 1763 helix: 1.25 (0.25), residues: 448 sheet: -0.31 (0.24), residues: 436 loop : -0.51 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 298 TYR 0.017 0.002 TYR C 191 PHE 0.016 0.002 PHE C 168 TRP 0.066 0.003 TRP E 35 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00777 (16918) covalent geometry : angle 0.81650 (23007) SS BOND : bond 0.00646 ( 28) SS BOND : angle 1.32902 ( 56) hydrogen bonds : bond 0.04916 ( 538) hydrogen bonds : angle 5.07338 ( 1446) link_ALPHA1-3 : bond 0.00646 ( 3) link_ALPHA1-3 : angle 2.44247 ( 9) link_ALPHA1-6 : bond 0.00947 ( 2) link_ALPHA1-6 : angle 1.77676 ( 6) link_BETA1-4 : bond 0.00655 ( 36) link_BETA1-4 : angle 2.46134 ( 108) link_NAG-ASN : bond 0.00824 ( 61) link_NAG-ASN : angle 3.65269 ( 183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 233 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8320 (p) REVERT: A 49 GLU cc_start: 0.8277 (pt0) cc_final: 0.7928 (pp20) REVERT: A 102 GLU cc_start: 0.8852 (tp30) cc_final: 0.8574 (mm-30) REVERT: A 104 MET cc_start: 0.9511 (ttm) cc_final: 0.9006 (ttm) REVERT: A 142 MET cc_start: 0.8936 (mmm) cc_final: 0.8127 (mmt) REVERT: A 172 ASP cc_start: 0.8778 (m-30) cc_final: 0.8384 (m-30) REVERT: B 535 MET cc_start: 0.7729 (mtp) cc_final: 0.7302 (mtp) REVERT: B 536 THR cc_start: 0.8146 (p) cc_final: 0.7911 (t) REVERT: B 567 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8560 (mmtt) REVERT: B 581 LEU cc_start: 0.9212 (tt) cc_final: 0.8967 (tp) REVERT: B 606 THR cc_start: 0.9332 (m) cc_final: 0.8973 (p) REVERT: B 629 LEU cc_start: 0.7891 (mt) cc_final: 0.7632 (mt) REVERT: C 246 GLN cc_start: 0.7559 (pm20) cc_final: 0.7219 (pm20) REVERT: C 376 ASN cc_start: 0.9224 (t0) cc_final: 0.7806 (p0) REVERT: C 389 LEU cc_start: 0.9619 (mt) cc_final: 0.9366 (mt) REVERT: D 557 ARG cc_start: 0.8507 (tpp80) cc_final: 0.8234 (tpp80) REVERT: D 631 TRP cc_start: 0.7911 (t-100) cc_final: 0.7474 (t-100) REVERT: D 655 LYS cc_start: 0.8624 (pttp) cc_final: 0.8184 (pttt) REVERT: E 99 ASN cc_start: 0.8870 (p0) cc_final: 0.8471 (t0) REVERT: E 158 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7517 (ttp-110) REVERT: E 376 ASN cc_start: 0.8923 (t0) cc_final: 0.7799 (p0) REVERT: E 425 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7414 (mmm) REVERT: E 501 LYS cc_start: 0.7904 (tttm) cc_final: 0.7433 (pttp) REVERT: F 656 ASN cc_start: 0.9159 (OUTLIER) cc_final: 0.8851 (t0) outliers start: 62 outliers final: 38 residues processed: 265 average time/residue: 0.1410 time to fit residues: 55.8162 Evaluate side-chains 249 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 656 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 115 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 42 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 194 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 616 ASN E 431 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.095545 restraints weight = 36332.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098065 restraints weight = 22594.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.099784 restraints weight = 16735.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.100966 restraints weight = 13613.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.101689 restraints weight = 11781.875| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17048 Z= 0.132 Angle : 0.713 17.722 23369 Z= 0.334 Chirality : 0.047 0.837 2948 Planarity : 0.004 0.047 2819 Dihedral : 7.149 61.588 4259 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.89 % Allowed : 16.48 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.20), residues: 1763 helix: 1.46 (0.25), residues: 442 sheet: -0.06 (0.25), residues: 422 loop : -0.49 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 617 TYR 0.010 0.001 TYR A 191 PHE 0.014 0.001 PHE A 53 TRP 0.078 0.002 TRP E 35 HIS 0.004 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00290 (16918) covalent geometry : angle 0.64270 (23007) SS BOND : bond 0.00340 ( 28) SS BOND : angle 0.96341 ( 56) hydrogen bonds : bond 0.04118 ( 538) hydrogen bonds : angle 4.67150 ( 1446) link_ALPHA1-3 : bond 0.00939 ( 3) link_ALPHA1-3 : angle 2.10279 ( 9) link_ALPHA1-6 : bond 0.01120 ( 2) link_ALPHA1-6 : angle 1.71101 ( 6) link_BETA1-4 : bond 0.00664 ( 36) link_BETA1-4 : angle 2.07806 ( 108) link_NAG-ASN : bond 0.00501 ( 61) link_NAG-ASN : angle 3.12989 ( 183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8673 (tp30) cc_final: 0.8326 (mm-30) REVERT: A 104 MET cc_start: 0.9457 (ttm) cc_final: 0.8930 (ttm) REVERT: A 142 MET cc_start: 0.8989 (mmm) cc_final: 0.8054 (mmt) REVERT: A 172 ASP cc_start: 0.8683 (m-30) cc_final: 0.8347 (m-30) REVERT: A 246 GLN cc_start: 0.8037 (pm20) cc_final: 0.7755 (pm20) REVERT: B 536 THR cc_start: 0.8029 (p) cc_final: 0.7723 (t) REVERT: B 606 THR cc_start: 0.9266 (m) cc_final: 0.8908 (p) REVERT: B 635 ILE cc_start: 0.8631 (pt) cc_final: 0.8345 (mm) REVERT: C 376 ASN cc_start: 0.9132 (t0) cc_final: 0.7794 (p0) REVERT: C 389 LEU cc_start: 0.9572 (mt) cc_final: 0.9353 (mt) REVERT: D 655 LYS cc_start: 0.8602 (pttp) cc_final: 0.8152 (pttt) REVERT: E 99 ASN cc_start: 0.8792 (p0) cc_final: 0.8449 (t0) REVERT: E 158 ARG cc_start: 0.7643 (mtp-110) cc_final: 0.7440 (ttp-110) REVERT: E 202 THR cc_start: 0.9386 (m) cc_final: 0.9010 (p) REVERT: E 376 ASN cc_start: 0.8896 (t0) cc_final: 0.7843 (p0) REVERT: E 425 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7373 (mmm) REVERT: F 656 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8628 (t0) outliers start: 46 outliers final: 32 residues processed: 268 average time/residue: 0.1266 time to fit residues: 51.5582 Evaluate side-chains 256 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 656 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 145 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 74 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 HIS C 424 ASN D 616 ASN E 329 HIS ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.111366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.092369 restraints weight = 36905.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094801 restraints weight = 23240.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.096445 restraints weight = 17262.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.097556 restraints weight = 14144.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098001 restraints weight = 12328.792| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17048 Z= 0.226 Angle : 0.783 20.531 23369 Z= 0.364 Chirality : 0.052 1.377 2948 Planarity : 0.004 0.046 2819 Dihedral : 7.190 59.410 4259 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.02 % Allowed : 16.79 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.20), residues: 1763 helix: 1.35 (0.25), residues: 449 sheet: -0.13 (0.25), residues: 417 loop : -0.56 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 298 TYR 0.011 0.002 TYR A 191 PHE 0.017 0.002 PHE D 522 TRP 0.072 0.002 TRP E 35 HIS 0.005 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00523 (16918) covalent geometry : angle 0.71489 (23007) SS BOND : bond 0.00459 ( 28) SS BOND : angle 1.03573 ( 56) hydrogen bonds : bond 0.04334 ( 538) hydrogen bonds : angle 4.76158 ( 1446) link_ALPHA1-3 : bond 0.00796 ( 3) link_ALPHA1-3 : angle 2.09060 ( 9) link_ALPHA1-6 : bond 0.01017 ( 2) link_ALPHA1-6 : angle 1.98337 ( 6) link_BETA1-4 : bond 0.00620 ( 36) link_BETA1-4 : angle 2.21950 ( 108) link_NAG-ASN : bond 0.00586 ( 61) link_NAG-ASN : angle 3.24242 ( 183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8757 (tp30) cc_final: 0.8426 (mm-30) REVERT: A 104 MET cc_start: 0.9500 (ttm) cc_final: 0.9020 (ttm) REVERT: A 142 MET cc_start: 0.9011 (mmm) cc_final: 0.8574 (mmt) REVERT: A 172 ASP cc_start: 0.8754 (m-30) cc_final: 0.8384 (m-30) REVERT: A 246 GLN cc_start: 0.8042 (pm20) cc_final: 0.7775 (pm20) REVERT: B 535 MET cc_start: 0.7614 (mtp) cc_final: 0.7232 (mtp) REVERT: B 536 THR cc_start: 0.8131 (p) cc_final: 0.7864 (t) REVERT: B 606 THR cc_start: 0.9270 (m) cc_final: 0.8928 (p) REVERT: B 635 ILE cc_start: 0.8732 (pt) cc_final: 0.8480 (mm) REVERT: C 376 ASN cc_start: 0.9161 (t0) cc_final: 0.7788 (p0) REVERT: D 655 LYS cc_start: 0.8654 (pttp) cc_final: 0.8271 (pttt) REVERT: E 99 ASN cc_start: 0.8806 (p0) cc_final: 0.8384 (t0) REVERT: E 158 ARG cc_start: 0.7722 (mtp-110) cc_final: 0.7500 (ttp-110) REVERT: E 202 THR cc_start: 0.9367 (m) cc_final: 0.8977 (p) REVERT: E 376 ASN cc_start: 0.8942 (t0) cc_final: 0.7845 (p0) REVERT: E 425 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7363 (mmm) REVERT: F 656 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8803 (t0) outliers start: 48 outliers final: 36 residues processed: 255 average time/residue: 0.1368 time to fit residues: 52.6606 Evaluate side-chains 254 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 656 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 181 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 155 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B 616 ASN C 195 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 ASN D 616 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.096171 restraints weight = 36559.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.098694 restraints weight = 22557.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.100410 restraints weight = 16545.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101565 restraints weight = 13450.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.102268 restraints weight = 11653.628| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17048 Z= 0.134 Angle : 0.705 16.137 23369 Z= 0.331 Chirality : 0.047 0.935 2948 Planarity : 0.004 0.047 2819 Dihedral : 6.767 59.738 4259 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.26 % Allowed : 18.11 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.20), residues: 1763 helix: 1.41 (0.25), residues: 449 sheet: -0.06 (0.25), residues: 425 loop : -0.49 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 298 TYR 0.011 0.001 TYR B 643 PHE 0.012 0.001 PHE A 53 TRP 0.060 0.002 TRP E 35 HIS 0.004 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00303 (16918) covalent geometry : angle 0.64229 (23007) SS BOND : bond 0.00311 ( 28) SS BOND : angle 0.83826 ( 56) hydrogen bonds : bond 0.03933 ( 538) hydrogen bonds : angle 4.56166 ( 1446) link_ALPHA1-3 : bond 0.00906 ( 3) link_ALPHA1-3 : angle 1.89605 ( 9) link_ALPHA1-6 : bond 0.01081 ( 2) link_ALPHA1-6 : angle 1.92006 ( 6) link_BETA1-4 : bond 0.00651 ( 36) link_BETA1-4 : angle 2.02737 ( 108) link_NAG-ASN : bond 0.00429 ( 61) link_NAG-ASN : angle 2.94489 ( 183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8084 (OUTLIER) cc_final: 0.7881 (p) REVERT: A 102 GLU cc_start: 0.8673 (tp30) cc_final: 0.8341 (mm-30) REVERT: A 104 MET cc_start: 0.9441 (ttm) cc_final: 0.8859 (ttm) REVERT: A 142 MET cc_start: 0.9028 (mmm) cc_final: 0.8173 (mmt) REVERT: A 172 ASP cc_start: 0.8659 (m-30) cc_final: 0.8322 (m-30) REVERT: B 535 MET cc_start: 0.7491 (mtp) cc_final: 0.7116 (mtp) REVERT: B 536 THR cc_start: 0.8003 (p) cc_final: 0.7742 (t) REVERT: B 606 THR cc_start: 0.9253 (m) cc_final: 0.8913 (p) REVERT: C 194 ILE cc_start: 0.9046 (tp) cc_final: 0.8823 (tp) REVERT: C 376 ASN cc_start: 0.9087 (t0) cc_final: 0.7754 (p0) REVERT: D 631 TRP cc_start: 0.7825 (t-100) cc_final: 0.7280 (t-100) REVERT: D 655 LYS cc_start: 0.8632 (pttp) cc_final: 0.8177 (pttt) REVERT: E 99 ASN cc_start: 0.8788 (p0) cc_final: 0.8379 (t0) REVERT: E 158 ARG cc_start: 0.7651 (mtp-110) cc_final: 0.7439 (ttp-110) REVERT: E 159 ASP cc_start: 0.8493 (p0) cc_final: 0.8284 (p0) REVERT: E 201 ILE cc_start: 0.9020 (tt) cc_final: 0.8665 (pt) REVERT: E 202 THR cc_start: 0.9351 (m) cc_final: 0.8892 (p) REVERT: E 376 ASN cc_start: 0.8886 (t0) cc_final: 0.7826 (p0) REVERT: E 425 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7363 (mmm) REVERT: F 626 MET cc_start: 0.7384 (tpp) cc_final: 0.7143 (tpp) REVERT: F 656 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8642 (t0) outliers start: 36 outliers final: 26 residues processed: 258 average time/residue: 0.1338 time to fit residues: 53.0596 Evaluate side-chains 251 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 656 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 33 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 124 optimal weight: 0.0040 chunk 170 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 149 optimal weight: 0.0470 chunk 160 optimal weight: 0.4980 chunk 110 optimal weight: 0.2980 chunk 119 optimal weight: 6.9990 chunk 14 optimal weight: 0.0050 overall best weight: 0.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 ASN D 543 ASN E 329 HIS F 616 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.117122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.098645 restraints weight = 36439.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101242 restraints weight = 22530.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102971 restraints weight = 16382.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.104134 restraints weight = 13258.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.104907 restraints weight = 11462.948| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17048 Z= 0.122 Angle : 0.697 16.722 23369 Z= 0.331 Chirality : 0.046 0.691 2948 Planarity : 0.004 0.049 2819 Dihedral : 6.398 59.306 4259 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.01 % Allowed : 18.99 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.20), residues: 1763 helix: 1.27 (0.25), residues: 455 sheet: 0.05 (0.25), residues: 436 loop : -0.45 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 502 TYR 0.008 0.001 TYR C 39 PHE 0.013 0.001 PHE A 53 TRP 0.051 0.002 TRP E 35 HIS 0.006 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00267 (16918) covalent geometry : angle 0.64307 (23007) SS BOND : bond 0.00246 ( 28) SS BOND : angle 1.00383 ( 56) hydrogen bonds : bond 0.03671 ( 538) hydrogen bonds : angle 4.48322 ( 1446) link_ALPHA1-3 : bond 0.00903 ( 3) link_ALPHA1-3 : angle 1.72503 ( 9) link_ALPHA1-6 : bond 0.01066 ( 2) link_ALPHA1-6 : angle 1.81646 ( 6) link_BETA1-4 : bond 0.00693 ( 36) link_BETA1-4 : angle 1.94701 ( 108) link_NAG-ASN : bond 0.00441 ( 61) link_NAG-ASN : angle 2.67799 ( 183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9361 (ttm) cc_final: 0.8606 (tpp) REVERT: A 142 MET cc_start: 0.9048 (mmm) cc_final: 0.8251 (mmt) REVERT: A 172 ASP cc_start: 0.8618 (m-30) cc_final: 0.8259 (m-30) REVERT: B 535 MET cc_start: 0.7605 (mtp) cc_final: 0.7236 (mtp) REVERT: B 536 THR cc_start: 0.7971 (p) cc_final: 0.7293 (t) REVERT: B 606 THR cc_start: 0.9203 (m) cc_final: 0.8881 (p) REVERT: B 629 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6897 (mp) REVERT: B 633 LYS cc_start: 0.8811 (mtpp) cc_final: 0.8610 (mttp) REVERT: C 95 MET cc_start: 0.8485 (ptm) cc_final: 0.8066 (ppp) REVERT: C 153 MET cc_start: 0.8610 (tpp) cc_final: 0.8368 (tpp) REVERT: C 246 GLN cc_start: 0.7594 (pm20) cc_final: 0.7332 (mt0) REVERT: C 376 ASN cc_start: 0.9040 (t0) cc_final: 0.7680 (p0) REVERT: D 550 GLN cc_start: 0.6740 (pp30) cc_final: 0.6488 (pp30) REVERT: D 605 CYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8121 (m) REVERT: D 631 TRP cc_start: 0.7873 (t-100) cc_final: 0.6796 (t-100) REVERT: D 655 LYS cc_start: 0.8569 (pttp) cc_final: 0.8229 (pttt) REVERT: E 99 ASN cc_start: 0.8774 (p0) cc_final: 0.8418 (t0) REVERT: E 201 ILE cc_start: 0.8779 (tt) cc_final: 0.8297 (pt) REVERT: E 202 THR cc_start: 0.9280 (m) cc_final: 0.8924 (p) REVERT: E 376 ASN cc_start: 0.8852 (t0) cc_final: 0.7861 (p0) REVERT: E 425 MET cc_start: 0.7792 (mtp) cc_final: 0.7413 (mmm) REVERT: F 656 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8595 (t0) outliers start: 32 outliers final: 23 residues processed: 272 average time/residue: 0.1353 time to fit residues: 55.8888 Evaluate side-chains 261 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 656 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 114 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 30 optimal weight: 0.0370 chunk 123 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 112 optimal weight: 0.0980 chunk 103 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.4264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN E 103 GLN F 640 GLN F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095671 restraints weight = 36877.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.098154 restraints weight = 22819.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.099847 restraints weight = 16779.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.100983 restraints weight = 13633.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.101694 restraints weight = 11826.535| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17048 Z= 0.171 Angle : 0.729 16.546 23369 Z= 0.345 Chirality : 0.046 0.626 2948 Planarity : 0.004 0.051 2819 Dihedral : 6.406 57.951 4259 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.26 % Allowed : 19.43 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.20), residues: 1763 helix: 1.34 (0.25), residues: 454 sheet: -0.02 (0.24), residues: 446 loop : -0.47 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 298 TYR 0.012 0.001 TYR B 643 PHE 0.014 0.001 PHE D 522 TRP 0.041 0.002 TRP F 610 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00399 (16918) covalent geometry : angle 0.67210 (23007) SS BOND : bond 0.00347 ( 28) SS BOND : angle 0.93993 ( 56) hydrogen bonds : bond 0.03917 ( 538) hydrogen bonds : angle 4.56818 ( 1446) link_ALPHA1-3 : bond 0.00757 ( 3) link_ALPHA1-3 : angle 1.80391 ( 9) link_ALPHA1-6 : bond 0.00997 ( 2) link_ALPHA1-6 : angle 2.02801 ( 6) link_BETA1-4 : bond 0.00600 ( 36) link_BETA1-4 : angle 2.02774 ( 108) link_NAG-ASN : bond 0.00533 ( 61) link_NAG-ASN : angle 2.83241 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2584.37 seconds wall clock time: 45 minutes 44.10 seconds (2744.10 seconds total)