Starting phenix.real_space_refine on Wed Mar 20 17:09:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6t_33647/03_2024/7y6t_33647.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6t_33647/03_2024/7y6t_33647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6t_33647/03_2024/7y6t_33647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6t_33647/03_2024/7y6t_33647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6t_33647/03_2024/7y6t_33647.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6t_33647/03_2024/7y6t_33647.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 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 115 5.16 5 C 17678 2.51 5 N 4487 2.21 5 O 5708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27988 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 8648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1124, 8648 Classifications: {'peptide': 1124} Link IDs: {'PTRANS': 45, 'TRANS': 1078} Chain breaks: 3 Chain: "C" Number of atoms: 8440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8440 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 43, 'TRANS': 1054} Chain breaks: 1 Chain: "B" Number of atoms: 9398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9398 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 47, 'TRANS': 1176} Chain: "D" 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: "E" 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: "F" 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "O" 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: "P" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 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: "Q" 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 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: "T" 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: "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: 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: "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: 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "a" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "b" 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: "c" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 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: "d" 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 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: "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: 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: "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: 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: "k" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.74, per 1000 atoms: 0.53 Number of scatterers: 27988 At special positions: 0 Unit cell: (165.36, 181.26, 165.36, 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 115 16.00 O 5708 8.00 N 4487 7.00 C 17678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.02 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.03 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 373 " distance=2.03 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 473 " distance=2.02 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 700 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 830 " distance=2.03 Simple disulfide: pdb=" SG CYS C 920 " - pdb=" SG CYS C 931 " distance=2.02 Simple disulfide: pdb=" SG CYS C1122 " - pdb=" SG CYS C1133 " distance=2.03 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 599 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 830 " distance=2.03 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 931 " distance=2.03 Simple disulfide: pdb=" SG CYS B1122 " - pdb=" SG CYS B1133 " distance=2.03 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1226 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 D 3 " - " MAN D 4 " " BMA O 3 " - " MAN O 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA O 3 " - " MAN O 5 " " BMA b 3 " - " MAN b 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " 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 N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " BETA1-6 " NAG M 1 " - " FUC M 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 4 " " NAG P 1 " - " FUC P 2 " " NAG S 1 " - " FUC S 2 " " NAG Z 1 " - " FUC Z 3 " " NAG a 1 " - " FUC a 4 " " NAG c 1 " - " FUC c 2 " " NAG f 1 " - " FUC f 2 " " NAG k 1 " - " FUC k 4 " NAG-ASN " NAG A1501 " - " ASN A 300 " " NAG A1502 " - " ASN A 425 " " NAG A1503 " - " ASN A 344 " " NAG A1504 " - " ASN A 667 " " NAG A1505 " - " ASN A1009 " " NAG A1506 " - " ASN A 381 " " NAG B1501 " - " ASN B 118 " " NAG B1502 " - " ASN B 514 " " NAG B1503 " - " ASN B 556 " " NAG B1504 " - " ASN B 667 " " NAG B1505 " - " ASN B 743 " " NAG B1506 " - " ASN B 787 " " NAG B1507 " - " ASN B1009 " " NAG C1501 " - " ASN C 118 " " NAG C1502 " - " ASN C 381 " " NAG C1503 " - " ASN C 667 " " NAG C1504 " - " ASN C 787 " " NAG C1505 " - " ASN C1009 " " NAG D 1 " - " ASN A 264 " " NAG E 1 " - " ASN A 324 " " NAG F 1 " - " ASN A 726 " " NAG H 1 " - " ASN A 743 " " NAG I 1 " - " ASN A 781 " " NAG J 1 " - " ASN A 787 " " NAG K 1 " - " ASN A 873 " " NAG L 1 " - " ASN A1232 " " NAG M 1 " - " ASN A 216 " " NAG N 1 " - " ASN C 216 " " NAG O 1 " - " ASN C 264 " " NAG P 1 " - " ASN C 300 " " NAG Q 1 " - " ASN C 324 " " NAG R 1 " - " ASN C 344 " " NAG S 1 " - " ASN C 351 " " NAG T 1 " - " ASN C 425 " " NAG U 1 " - " ASN C 726 " " NAG V 1 " - " ASN C 688 " " NAG W 1 " - " ASN C 743 " " NAG X 1 " - " ASN C 781 " " NAG Y 1 " - " ASN C 873 " " NAG Z 1 " - " ASN C1232 " " NAG a 1 " - " ASN B 216 " " NAG b 1 " - " ASN B 264 " " NAG c 1 " - " ASN B 300 " " NAG d 1 " - " ASN B 324 " " NAG e 1 " - " ASN B 344 " " NAG f 1 " - " ASN B 351 " " NAG g 1 " - " ASN B 425 " " NAG h 1 " - " ASN B 688 " " NAG i 1 " - " ASN B 781 " " NAG j 1 " - " ASN B 873 " " NAG k 1 " - " ASN B1232 " Time building additional restraints: 14.51 Conformation dependent library (CDL) restraints added in 4.9 seconds 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6388 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 49 sheets defined 25.6% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.894A pdb=" N LEU A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 807 through 814 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.928A pdb=" N LEU A 822 " --> pdb=" O ARG A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 852 Processing helix chain 'A' and resid 855 through 862 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.752A pdb=" N VAL A 913 " --> pdb=" O LEU A 910 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 914 " --> pdb=" O GLY A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 910 through 914' Processing helix chain 'A' and resid 916 through 923 removed outlier: 3.928A pdb=" N CYS A 920 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 937 Processing helix chain 'A' and resid 946 through 963 Processing helix chain 'A' and resid 967 through 971 removed outlier: 3.813A pdb=" N ALA A 971 " --> pdb=" O ALA A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 986 Processing helix chain 'A' and resid 992 through 1016 removed outlier: 3.795A pdb=" N LEU A 999 " --> pdb=" O ASN A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1022 removed outlier: 3.548A pdb=" N SER A1021 " --> pdb=" O LYS A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1056 removed outlier: 4.031A pdb=" N GLN A1045 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY A1046 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1074 removed outlier: 4.113A pdb=" N ILE A1070 " --> pdb=" O SER A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1122 removed outlier: 3.931A pdb=" N ARG A1085 " --> pdb=" O VAL A1081 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A1086 " --> pdb=" O GLN A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1197 removed outlier: 4.400A pdb=" N HIS A1197 " --> pdb=" O LEU A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'A' and resid 1236 through 1242 removed outlier: 3.786A pdb=" N ASP A1240 " --> pdb=" O ASP A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1254 Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 115 through 118 removed outlier: 3.689A pdb=" N ASN C 118 " --> pdb=" O GLY C 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 115 through 118' Processing helix chain 'C' and resid 231 through 238 removed outlier: 3.994A pdb=" N ILE C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.925A pdb=" N ALA C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 689 through 692 Processing helix chain 'C' and resid 807 through 813 Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.923A pdb=" N GLN C 825 " --> pdb=" O GLN C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 852 Processing helix chain 'C' and resid 855 through 862 Processing helix chain 'C' and resid 885 through 888 removed outlier: 3.634A pdb=" N GLY C 888 " --> pdb=" O PRO C 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 885 through 888' Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 910 through 914 removed outlier: 3.852A pdb=" N VAL C 913 " --> pdb=" O LEU C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 923 removed outlier: 3.732A pdb=" N GLY C 923 " --> pdb=" O ARG C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 936 Processing helix chain 'C' and resid 946 through 963 Processing helix chain 'C' and resid 967 through 971 removed outlier: 3.660A pdb=" N ALA C 970 " --> pdb=" O THR C 967 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA C 971 " --> pdb=" O ALA C 968 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 967 through 971' Processing helix chain 'C' and resid 973 through 986 removed outlier: 3.638A pdb=" N ALA C 977 " --> pdb=" O PRO C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1016 removed outlier: 4.146A pdb=" N LEU C 999 " --> pdb=" O ASN C 995 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C1016 " --> pdb=" O SER C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1055 removed outlier: 4.069A pdb=" N GLN C1045 " --> pdb=" O VAL C1041 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY C1046 " --> pdb=" O VAL C1042 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C1055 " --> pdb=" O GLN C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1058 No H-bonds generated for 'chain 'C' and resid 1056 through 1058' Processing helix chain 'C' and resid 1066 through 1074 Processing helix chain 'C' and resid 1075 through 1122 removed outlier: 3.675A pdb=" N LEU C1086 " --> pdb=" O GLN C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1193 through 1197 removed outlier: 3.962A pdb=" N HIS C1197 " --> pdb=" O LEU C1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 1236 through 1242 removed outlier: 3.853A pdb=" N ASP C1240 " --> pdb=" O ASP C1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 1247 through 1254 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 115 through 118 Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 232 through 238 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 466 through 475 Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.168A pdb=" N GLY B 526 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 527 " --> pdb=" O HIS B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 523 through 527' Processing helix chain 'B' and resid 575 through 580 removed outlier: 4.214A pdb=" N ASN B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 814 Processing helix chain 'B' and resid 816 through 827 removed outlier: 4.141A pdb=" N LEU B 822 " --> pdb=" O ARG B 818 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN B 825 " --> pdb=" O GLN B 821 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 827 " --> pdb=" O LEU B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 852 removed outlier: 4.005A pdb=" N LYS B 831 " --> pdb=" O THR B 827 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE B 833 " --> pdb=" O ALA B 829 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 834 " --> pdb=" O CYS B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 863 removed outlier: 3.974A pdb=" N THR B 863 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 918 through 922 Processing helix chain 'B' and resid 928 through 936 Processing helix chain 'B' and resid 946 through 962 Processing helix chain 'B' and resid 973 through 986 Processing helix chain 'B' and resid 992 through 1016 removed outlier: 3.589A pdb=" N GLN B 996 " --> pdb=" O LEU B 992 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B1016 " --> pdb=" O SER B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1054 removed outlier: 4.223A pdb=" N GLN B1045 " --> pdb=" O VAL B1041 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY B1046 " --> pdb=" O VAL B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1074 Processing helix chain 'B' and resid 1075 through 1123 Processing helix chain 'B' and resid 1193 through 1197 removed outlier: 3.856A pdb=" N HIS B1197 " --> pdb=" O LEU B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1216 through 1218 No H-bonds generated for 'chain 'B' and resid 1216 through 1218' Processing helix chain 'B' and resid 1236 through 1242 removed outlier: 3.598A pdb=" N ASP B1240 " --> pdb=" O ASP B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1247 through 1253 removed outlier: 3.668A pdb=" N ASP B1253 " --> pdb=" O ASN B1249 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 184 Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 150 removed outlier: 3.659A pdb=" N ASN A 147 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE A 125 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 285 removed outlier: 7.352A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N CYS A 283 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER A 443 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 398 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 285 removed outlier: 7.352A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N CYS A 283 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER A 443 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASP A 448 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TYR A 463 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 450 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE A 461 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU A 452 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 298 removed outlier: 6.622A pdb=" N CYS A 373 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 488 removed outlier: 4.321A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL A 709 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 502 removed outlier: 4.305A pdb=" N VAL A 694 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AB1, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB2, first strand: chain 'A' and resid 780 through 798 removed outlier: 5.816A pdb=" N PHE A 788 " --> pdb=" O PRO A1160 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET A 790 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A1158 " --> pdb=" O MET A 790 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 792 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR A1156 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 794 " --> pdb=" O LEU A1154 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A1154 " --> pdb=" O THR A 794 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR A 796 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU A1152 " --> pdb=" O TYR A 796 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN A 798 " --> pdb=" O GLY A1150 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY A1150 " --> pdb=" O GLN A 798 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A1141 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU A1158 " --> pdb=" O HIS A1139 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N HIS A1139 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB4, first strand: chain 'A' and resid 881 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1220 through 1223 removed outlier: 4.198A pdb=" N ALA A1179 " --> pdb=" O ILE A1223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1187 through 1190 Processing sheet with id=AB7, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.138A pdb=" N TYR C 212 " --> pdb=" O CYS C 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 181 through 184 Processing sheet with id=AB9, first strand: chain 'C' and resid 147 through 150 removed outlier: 3.567A pdb=" N ASN C 147 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE C 125 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 147 through 150 removed outlier: 3.567A pdb=" N ASN C 147 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE C 125 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 271 through 288 removed outlier: 5.349A pdb=" N LYS C 272 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL C 453 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL C 274 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE C 451 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASN C 276 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA C 449 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL C 447 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER C 443 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU C 284 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE C 441 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA C 286 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP C 439 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 406 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU C 414 " --> pdb=" O VAL C 406 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL C 408 " --> pdb=" O GLY C 412 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLY C 412 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 271 through 288 removed outlier: 5.349A pdb=" N LYS C 272 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL C 453 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL C 274 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE C 451 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASN C 276 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA C 449 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL C 447 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER C 443 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU C 284 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE C 441 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA C 286 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP C 439 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN C 454 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ILE C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 293 through 297 removed outlier: 5.248A pdb=" N ILE C 335 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N CYS C 373 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 483 through 488 removed outlier: 9.202A pdb=" N SER C 703 " --> pdb=" O SER C 718 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N SER C 718 " --> pdb=" O SER C 703 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN C 705 " --> pdb=" O VAL C 716 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL C 716 " --> pdb=" O GLN C 705 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA C 707 " --> pdb=" O VAL C 714 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 499 through 502 removed outlier: 4.257A pdb=" N VAL C 694 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU C 684 " --> pdb=" O VAL C 697 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 749 through 751 Processing sheet with id=AC8, first strand: chain 'C' and resid 781 through 786 Processing sheet with id=AC9, first strand: chain 'C' and resid 789 through 798 removed outlier: 6.750A pdb=" N GLY C1150 " --> pdb=" O ALA C1146 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ALA C1146 " --> pdb=" O GLY C1150 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C1152 " --> pdb=" O VAL C1144 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL C1144 " --> pdb=" O LEU C1152 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU C1154 " --> pdb=" O SER C1142 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER C1142 " --> pdb=" O LEU C1154 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR C1156 " --> pdb=" O ILE C1140 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 804 through 806 Processing sheet with id=AD2, first strand: chain 'C' and resid 879 through 883 Processing sheet with id=AD3, first strand: chain 'C' and resid 1220 through 1223 removed outlier: 3.951A pdb=" N ALA C1179 " --> pdb=" O ILE C1223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.959A pdb=" N TYR B 212 " --> pdb=" O CYS B 230 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AD6, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AD7, first strand: chain 'B' and resid 271 through 288 removed outlier: 5.128A pdb=" N LYS B 272 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL B 453 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL B 274 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 451 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASN B 276 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 449 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 447 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER B 443 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU B 284 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 441 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA B 286 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TRP B 439 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 414 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 408 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY B 412 " --> pdb=" O VAL B 408 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 271 through 288 removed outlier: 5.128A pdb=" N LYS B 272 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL B 453 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL B 274 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 451 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASN B 276 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 449 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 447 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER B 443 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU B 284 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 441 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA B 286 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TRP B 439 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLN B 454 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 294 through 298 removed outlier: 5.476A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN B 344 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR B 371 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 390 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N CYS B 373 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 483 through 488 removed outlier: 4.376A pdb=" N GLY B 715 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 709 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE B 713 " --> pdb=" O VAL B 709 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 510 through 513 removed outlier: 6.441A pdb=" N TYR B 619 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL B 590 " --> pdb=" O TYR B 619 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN B 621 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE B 588 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR B 623 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY B 625 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER B 584 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 510 through 513 Processing sheet with id=AE4, first strand: chain 'B' and resid 528 through 535 removed outlier: 6.383A pdb=" N SER B 520 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER B 532 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N SER B 518 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR B 534 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR B 516 " --> pdb=" O THR B 534 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 565 through 568 removed outlier: 3.848A pdb=" N VAL B 613 " --> pdb=" O GLY B 605 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 649 through 654 removed outlier: 4.028A pdb=" N VAL B 694 " --> pdb=" O THR B 666 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU B 684 " --> pdb=" O VAL B 697 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 749 through 751 Processing sheet with id=AE8, first strand: chain 'B' and resid 780 through 786 removed outlier: 4.036A pdb=" N GLY B 780 " --> pdb=" O ALA B1168 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 789 through 798 removed outlier: 6.533A pdb=" N LEU B1158 " --> pdb=" O HIS B1139 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N HIS B1139 " --> pdb=" O LEU B1158 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AF2, first strand: chain 'B' and resid 881 through 883 Processing sheet with id=AF3, first strand: chain 'B' and resid 1220 through 1223 removed outlier: 3.614A pdb=" N ALA B1179 " --> pdb=" O ILE B1223 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N CYS B1173 " --> pdb=" O LEU B1233 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1187 through 1191 removed outlier: 4.430A pdb=" N SER B1206 " --> pdb=" O GLU B1211 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLU B1211 " --> pdb=" O SER B1206 " (cutoff:3.500A) 1085 hydrogen bonds defined for protein. 2943 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: 13.22 Time building geometry restraints manager: 14.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6282 1.33 - 1.45: 7689 1.45 - 1.58: 14459 1.58 - 1.70: 1 1.70 - 1.83: 145 Bond restraints: 28576 Sorted by residual: bond pdb=" C1 BMA j 3 " pdb=" C2 BMA j 3 " ideal model delta sigma weight residual 1.519 1.595 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C1 BMA j 3 " pdb=" O5 BMA j 3 " ideal model delta sigma weight residual 1.410 1.474 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C1 NAG k 1 " pdb=" O5 NAG k 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.96e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.347 0.059 2.00e-02 2.50e+03 8.63e+00 bond pdb=" C1 NAG a 1 " pdb=" O5 NAG a 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.47e+00 ... (remaining 28571 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.47: 368 104.47 - 111.89: 14806 111.89 - 119.31: 9045 119.31 - 126.72: 14457 126.72 - 134.14: 260 Bond angle restraints: 38936 Sorted by residual: angle pdb=" N GLN C 127 " pdb=" CA GLN C 127 " pdb=" C GLN C 127 " ideal model delta sigma weight residual 110.80 99.26 11.54 2.13e+00 2.20e-01 2.93e+01 angle pdb=" C GLY C1008 " pdb=" N ASN C1009 " pdb=" CA ASN C1009 " ideal model delta sigma weight residual 122.38 113.99 8.39 1.81e+00 3.05e-01 2.15e+01 angle pdb=" N GLY A 294 " pdb=" CA GLY A 294 " pdb=" C GLY A 294 " ideal model delta sigma weight residual 113.18 103.12 10.06 2.37e+00 1.78e-01 1.80e+01 angle pdb=" N GLN B 127 " pdb=" CA GLN B 127 " pdb=" C GLN B 127 " ideal model delta sigma weight residual 110.80 102.05 8.75 2.13e+00 2.20e-01 1.69e+01 angle pdb=" C TRP A 439 " pdb=" N THR A 440 " pdb=" CA THR A 440 " ideal model delta sigma weight residual 122.29 115.56 6.73 1.65e+00 3.67e-01 1.66e+01 ... (remaining 38931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.49: 17028 24.49 - 48.97: 868 48.97 - 73.46: 196 73.46 - 97.94: 127 97.94 - 122.43: 92 Dihedral angle restraints: 18311 sinusoidal: 8324 harmonic: 9987 Sorted by residual: dihedral pdb=" CB CYS C 920 " pdb=" SG CYS C 920 " pdb=" SG CYS C 931 " pdb=" CB CYS C 931 " ideal model delta sinusoidal sigma weight residual 93.00 168.65 -75.65 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" CB CYS B 920 " pdb=" SG CYS B 920 " pdb=" SG CYS B 931 " pdb=" CB CYS B 931 " ideal model delta sinusoidal sigma weight residual -86.00 -152.82 66.82 1 1.00e+01 1.00e-02 5.82e+01 dihedral pdb=" CB CYS A 920 " pdb=" SG CYS A 920 " pdb=" SG CYS A 931 " pdb=" CB CYS A 931 " ideal model delta sinusoidal sigma weight residual 93.00 158.85 -65.85 1 1.00e+01 1.00e-02 5.67e+01 ... (remaining 18308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 4746 0.163 - 0.326: 56 0.326 - 0.489: 10 0.489 - 0.652: 6 0.652 - 0.815: 3 Chirality restraints: 4821 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 743 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 425 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 787 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 4818 not shown) Planarity restraints: 4926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 324 " 0.002 2.00e-02 2.50e+03 5.57e-02 3.88e+01 pdb=" CG ASN A 324 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN A 324 " -0.068 2.00e-02 2.50e+03 pdb=" ND2 ASN A 324 " 0.054 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 322 " 0.019 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C ASN A 322 " -0.068 2.00e-02 2.50e+03 pdb=" O ASN A 322 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE A 323 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 216 " 0.003 2.00e-02 2.50e+03 3.36e-02 1.41e+01 pdb=" CG ASN B 216 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B 216 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN B 216 " 0.041 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " -0.037 2.00e-02 2.50e+03 ... (remaining 4923 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 904 2.61 - 3.19: 31351 3.19 - 3.76: 50032 3.76 - 4.33: 69243 4.33 - 4.90: 103134 Nonbonded interactions: 254664 Sorted by model distance: nonbonded pdb=" NE2 GLN B1116 " pdb=" OD1 ASN B1120 " model vdw 2.044 2.520 nonbonded pdb=" O PRO B 498 " pdb=" OG1 THR B 650 " model vdw 2.054 2.440 nonbonded pdb=" O PRO A 498 " pdb=" OG1 THR A 650 " model vdw 2.056 2.440 nonbonded pdb=" OG1 THR B1234 " pdb=" OD1 ASP B1236 " model vdw 2.072 2.440 nonbonded pdb=" NE2 GLN A 59 " pdb=" OH TYR A 213 " model vdw 2.076 2.520 ... (remaining 254659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 509 or resid 636 through 1254 or resid 1501 thr \ ough 1505)) selection = (chain 'B' and (resid 31 through 509 or resid 636 through 1254 or resid 1501 thr \ ough 1505)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'O' selection = chain 'b' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'F' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } ncs_group { reference = (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 'P' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'i' and resid 1) } ncs_group { reference = chain 'N' selection = chain 'a' 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: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.460 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 80.400 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.200 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 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 : 0.008 0.076 28576 Z= 0.512 Angle : 0.974 11.538 38936 Z= 0.499 Chirality : 0.064 0.815 4821 Planarity : 0.005 0.056 4875 Dihedral : 19.089 122.427 11830 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 40.32 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.18 % Favored : 90.38 % Rotamer: Outliers : 0.41 % Allowed : 1.87 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3432 helix: 0.33 (0.18), residues: 745 sheet: -1.33 (0.19), residues: 713 loop : -1.73 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP C 259 HIS 0.012 0.002 HIS B 429 PHE 0.031 0.003 PHE A 360 TYR 0.025 0.003 TYR C 676 ARG 0.010 0.001 ARG B1085 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 939 MET cc_start: 0.7191 (mmp) cc_final: 0.6868 (mmp) REVERT: B 961 MET cc_start: 0.9446 (ptt) cc_final: 0.9231 (ptp) outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 0.3476 time to fit residues: 37.5189 Evaluate side-chains 41 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 0.9990 chunk 259 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 268 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 311 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN C 170 ASN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 ASN ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1149 GLN B 170 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 ASN ** B 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28576 Z= 0.221 Angle : 0.752 9.415 38936 Z= 0.369 Chirality : 0.053 0.599 4821 Planarity : 0.004 0.061 4875 Dihedral : 16.104 118.641 6040 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.80 % Favored : 90.82 % Rotamer: Outliers : 0.17 % Allowed : 7.90 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.14), residues: 3432 helix: 0.80 (0.19), residues: 747 sheet: -1.30 (0.20), residues: 704 loop : -1.76 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 259 HIS 0.008 0.001 HIS B 510 PHE 0.024 0.002 PHE B 91 TYR 0.031 0.002 TYR B 751 ARG 0.005 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 3.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.9479 (m-80) cc_final: 0.9250 (m-80) REVERT: B 939 MET cc_start: 0.6930 (mmp) cc_final: 0.6715 (mmp) outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.4452 time to fit residues: 45.0537 Evaluate side-chains 43 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 173 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 259 optimal weight: 20.0000 chunk 212 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 312 optimal weight: 0.5980 chunk 337 optimal weight: 9.9990 chunk 277 optimal weight: 30.0000 chunk 309 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 250 optimal weight: 7.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 ASN ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 933 GLN ** C1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28576 Z= 0.327 Angle : 0.791 9.646 38936 Z= 0.393 Chirality : 0.052 0.567 4821 Planarity : 0.004 0.066 4875 Dihedral : 14.082 112.147 6040 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 31.39 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.50 % Favored : 90.15 % Rotamer: Outliers : 0.03 % Allowed : 5.32 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3432 helix: 0.50 (0.18), residues: 760 sheet: -1.47 (0.19), residues: 700 loop : -1.82 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 259 HIS 0.007 0.001 HIS C 71 PHE 0.018 0.002 PHE C 128 TYR 0.025 0.002 TYR B 676 ARG 0.009 0.001 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 3.036 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 45 average time/residue: 0.3498 time to fit residues: 30.2134 Evaluate side-chains 39 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 308 optimal weight: 0.9990 chunk 234 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 313 optimal weight: 10.0000 chunk 331 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 chunk 296 optimal weight: 7.9990 chunk 89 optimal weight: 30.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN B 354 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 ASN ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1095 ASN ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28576 Z= 0.223 Angle : 0.725 9.961 38936 Z= 0.355 Chirality : 0.051 0.600 4821 Planarity : 0.004 0.068 4875 Dihedral : 12.736 107.875 6040 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 25.37 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.29 % Favored : 90.38 % Rotamer: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3432 helix: 0.75 (0.18), residues: 763 sheet: -1.40 (0.19), residues: 691 loop : -1.76 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 259 HIS 0.005 0.001 HIS A1192 PHE 0.024 0.002 PHE C 91 TYR 0.019 0.002 TYR C1202 ARG 0.010 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.9501 (m-80) cc_final: 0.9290 (m-80) REVERT: B 939 MET cc_start: 0.7068 (mmp) cc_final: 0.6713 (mmp) REVERT: B 1014 PHE cc_start: 0.9162 (m-80) cc_final: 0.8950 (m-80) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.3518 time to fit residues: 29.6814 Evaluate side-chains 39 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 276 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 282 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 169 optimal weight: 8.9990 chunk 297 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN C 170 ASN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 933 GLN ** C1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1149 GLN ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN B 577 GLN ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 995 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 28576 Z= 0.319 Angle : 0.767 10.066 38936 Z= 0.383 Chirality : 0.051 0.584 4821 Planarity : 0.004 0.067 4875 Dihedral : 12.135 107.636 6040 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 30.81 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.91 % Favored : 89.74 % Rotamer: Outliers : 0.03 % Allowed : 5.15 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.14), residues: 3432 helix: 0.53 (0.18), residues: 757 sheet: -1.56 (0.19), residues: 697 loop : -1.82 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 259 HIS 0.006 0.001 HIS C 71 PHE 0.018 0.002 PHE C 128 TYR 0.019 0.002 TYR C1202 ARG 0.006 0.001 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 2.889 Fit side-chains revert: symmetry clash REVERT: B 939 MET cc_start: 0.6841 (mmp) cc_final: 0.6632 (mmp) REVERT: B 1014 PHE cc_start: 0.9248 (m-80) cc_final: 0.9044 (m-80) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.3466 time to fit residues: 28.7699 Evaluate side-chains 40 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 111 optimal weight: 30.0000 chunk 298 optimal weight: 7.9990 chunk 65 optimal weight: 0.2980 chunk 194 optimal weight: 10.0000 chunk 81 optimal weight: 0.0270 chunk 331 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 109 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 overall best weight: 3.6644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 GLN ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 GLN ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28576 Z= 0.236 Angle : 0.726 9.752 38936 Z= 0.359 Chirality : 0.051 0.594 4821 Planarity : 0.004 0.070 4875 Dihedral : 11.725 107.049 6040 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 26.39 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.06 % Favored : 90.59 % Rotamer: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3432 helix: 0.79 (0.18), residues: 761 sheet: -1.47 (0.19), residues: 693 loop : -1.77 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 259 HIS 0.011 0.001 HIS B 429 PHE 0.022 0.002 PHE A 360 TYR 0.017 0.002 TYR A1105 ARG 0.014 0.001 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 3.324 Fit side-chains revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.9501 (m-80) cc_final: 0.9289 (m-80) outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 0.3585 time to fit residues: 29.3699 Evaluate side-chains 40 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 319 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 242 optimal weight: 20.0000 chunk 187 optimal weight: 20.0000 chunk 279 optimal weight: 30.0000 chunk 185 optimal weight: 20.0000 chunk 330 optimal weight: 8.9990 chunk 206 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 933 GLN ** C1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28576 Z= 0.259 Angle : 0.737 10.105 38936 Z= 0.365 Chirality : 0.051 0.581 4821 Planarity : 0.004 0.072 4875 Dihedral : 11.504 107.179 6040 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 27.55 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.29 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.14), residues: 3432 helix: 0.76 (0.18), residues: 750 sheet: -1.48 (0.19), residues: 688 loop : -1.79 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 259 HIS 0.009 0.001 HIS B 429 PHE 0.039 0.002 PHE C 360 TYR 0.024 0.002 TYR B 66 ARG 0.006 0.001 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 3.001 Fit side-chains revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.9509 (m-80) cc_final: 0.9308 (m-80) REVERT: B 939 MET cc_start: 0.7318 (mmp) cc_final: 0.7057 (mmp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.3500 time to fit residues: 28.4908 Evaluate side-chains 39 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 204 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 210 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 259 optimal weight: 20.0000 chunk 300 optimal weight: 0.0670 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 GLN ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 903 ASN ** C1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28576 Z= 0.193 Angle : 0.711 9.776 38936 Z= 0.347 Chirality : 0.051 0.591 4821 Planarity : 0.004 0.072 4875 Dihedral : 11.182 106.359 6040 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.33 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3432 helix: 0.99 (0.19), residues: 756 sheet: -1.44 (0.19), residues: 699 loop : -1.77 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 259 HIS 0.008 0.001 HIS B 270 PHE 0.037 0.001 PHE C 128 TYR 0.015 0.001 TYR B 66 ARG 0.006 0.000 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 3.438 Fit side-chains revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.9491 (m-80) cc_final: 0.9279 (m-80) REVERT: B 939 MET cc_start: 0.6972 (mmp) cc_final: 0.6734 (mmp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.3344 time to fit residues: 27.4008 Evaluate side-chains 38 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 316 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 308 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 241 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 278 optimal weight: 6.9990 chunk 291 optimal weight: 7.9990 chunk 306 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 933 GLN ** C1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 ASN ** B 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 28576 Z= 0.306 Angle : 0.760 9.802 38936 Z= 0.378 Chirality : 0.050 0.574 4821 Planarity : 0.004 0.072 4875 Dihedral : 11.102 107.738 6040 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 29.79 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.56 % Favored : 90.12 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3432 helix: 0.77 (0.19), residues: 755 sheet: -1.53 (0.19), residues: 696 loop : -1.79 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 259 HIS 0.010 0.002 HIS B 89 PHE 0.028 0.002 PHE C 360 TYR 0.019 0.002 TYR C1202 ARG 0.005 0.001 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 3.050 Fit side-chains revert: symmetry clash REVERT: B 939 MET cc_start: 0.6795 (mmp) cc_final: 0.6507 (mmp) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.3695 time to fit residues: 30.6681 Evaluate side-chains 37 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 325 optimal weight: 2.9990 chunk 198 optimal weight: 30.0000 chunk 154 optimal weight: 7.9990 chunk 226 optimal weight: 0.9980 chunk 341 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 chunk 272 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 210 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28576 Z= 0.219 Angle : 0.725 10.121 38936 Z= 0.356 Chirality : 0.051 0.592 4821 Planarity : 0.004 0.072 4875 Dihedral : 10.906 107.196 6040 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.62 % Favored : 91.08 % Rotamer: Outliers : 0.03 % Allowed : 0.44 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3432 helix: 0.97 (0.19), residues: 754 sheet: -1.45 (0.19), residues: 680 loop : -1.75 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 259 HIS 0.009 0.001 HIS C 951 PHE 0.034 0.002 PHE C 360 TYR 0.034 0.001 TYR A 212 ARG 0.005 0.000 ARG B 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 2.918 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.3477 time to fit residues: 28.8050 Evaluate side-chains 37 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 250 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 272 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 279 optimal weight: 40.0000 chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 933 GLN ** C1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.025369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.018223 restraints weight = 512763.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.018835 restraints weight = 337803.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.019281 restraints weight = 252857.434| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28576 Z= 0.280 Angle : 0.751 9.794 38936 Z= 0.372 Chirality : 0.050 0.578 4821 Planarity : 0.004 0.072 4875 Dihedral : 10.819 108.600 6040 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 29.50 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.59 % Favored : 90.12 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.14), residues: 3432 helix: 0.83 (0.19), residues: 754 sheet: -1.56 (0.19), residues: 675 loop : -1.77 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 259 HIS 0.008 0.001 HIS B 429 PHE 0.031 0.002 PHE C 360 TYR 0.030 0.002 TYR A 212 ARG 0.005 0.001 ARG B 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3574.53 seconds wall clock time: 69 minutes 56.58 seconds (4196.58 seconds total)