Starting phenix.real_space_refine (version: dev) on Mon Sep 5 02:07:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6t_33647/09_2022/7y6t_33647.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6t_33647/09_2022/7y6t_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_33647/09_2022/7y6t_33647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6t_33647/09_2022/7y6t_33647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6t_33647/09_2022/7y6t_33647.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6t_33647/09_2022/7y6t_33647.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4709/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: 3 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: 1 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: 1 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: 1 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 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 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 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: 1 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 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: 1 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: 2 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: 3 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: 1 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: 1 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 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: 1 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: 1 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 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: 1 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 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: 1 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 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: 1 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: 2 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: 3 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: 1 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: 1 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 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: 1 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: 1 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: 1 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 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: 1 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: 2 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 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 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 chiralities: 7 Time building chain proxies: 15.76, per 1000 atoms: 0.56 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: 14.07 Conformation dependent library (CDL) restraints added in 3.5 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: 2.00 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: 12.43 Time building geometry restraints manager: 14.86 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 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.426 1.347 0.079 3.20e-02 9.77e+02 6.06e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.426 1.348 0.078 3.20e-02 9.77e+02 5.90e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.426 1.350 0.076 3.20e-02 9.77e+02 5.70e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.426 1.354 0.072 3.20e-02 9.77e+02 5.11e+00 bond pdb=" C1 NAG I 1 " pdb=" C2 NAG I 1 " ideal model delta sigma weight residual 1.526 1.568 -0.042 2.00e-02 2.50e+03 4.37e+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=" C3 NAG H 1 " pdb=" C4 NAG H 1 " pdb=" C5 NAG H 1 " ideal model delta sigma weight residual 110.18 117.29 -7.11 1.42e+00 4.96e-01 2.51e+01 angle pdb=" C2 NAG U 1 " pdb=" N2 NAG U 1 " pdb=" C7 NAG U 1 " ideal model delta sigma weight residual 123.12 129.17 -6.05 1.28e+00 6.08e-01 2.23e+01 angle pdb=" C2 NAG F 1 " pdb=" N2 NAG F 1 " pdb=" C7 NAG F 1 " ideal model delta sigma weight residual 123.12 129.17 -6.05 1.28e+00 6.08e-01 2.23e+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 ... (remaining 38931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 15779 21.69 - 43.39: 858 43.39 - 65.08: 100 65.08 - 86.78: 37 86.78 - 108.47: 19 Dihedral angle restraints: 16793 sinusoidal: 6806 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 16790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 4767 0.163 - 0.326: 35 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 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. 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 12.260 Check model and map are aligned: 0.400 Convert atoms to be neutral: 0.220 Process input model: 76.930 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 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 : 0.007 0.079 28576 Z= 0.484 Angle : 0.880 11.538 38936 Z= 0.496 Chirality : 0.059 0.815 4821 Planarity : 0.005 0.056 4875 Dihedral : 14.016 108.470 10312 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 40.38 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.18 % Favored : 90.38 % Rotamer Outliers : 0.41 % 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 *********************** 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 : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 0.4023 time to fit residues: 41.8146 Evaluate side-chains 41 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 3.203 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.3153 time to fit residues: 6.7216 ------------------------------------------------------------------------------- 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: 7.9990 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: 2.9990 chunk 163 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 849 ASN B 903 ASN 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 28576 Z= 0.242 Angle : 0.662 7.970 38936 Z= 0.372 Chirality : 0.054 0.810 4821 Planarity : 0.004 0.056 4875 Dihedral : 9.342 112.488 4522 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.80 % Favored : 90.85 % Rotamer Outliers : 0.27 % 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: -1.62 (0.14), residues: 3432 helix: 0.77 (0.19), residues: 743 sheet: -1.31 (0.19), residues: 714 loop : -1.77 (0.14), residues: 1975 *********************** 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 54 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 54 average time/residue: 0.3657 time to fit residues: 37.2061 Evaluate side-chains 43 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 3.548 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 5 average time/residue: 0.2599 time to fit residues: 6.7035 ------------------------------------------------------------------------------- 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: 6.9990 chunk 96 optimal weight: 9.9990 chunk 259 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 312 optimal weight: 6.9990 chunk 337 optimal weight: 10.0000 chunk 277 optimal weight: 30.0000 chunk 309 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 250 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** A1109 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 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 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** ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 28576 Z= 0.358 Angle : 0.715 8.809 38936 Z= 0.401 Chirality : 0.053 0.787 4821 Planarity : 0.005 0.065 4875 Dihedral : 9.393 112.001 4522 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 32.68 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.62 % Favored : 90.03 % Rotamer Outliers : 0.03 % 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: 0.45 (0.18), residues: 760 sheet: -1.48 (0.19), residues: 676 loop : -1.83 (0.14), residues: 1996 *********************** 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 46 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.3810 time to fit residues: 33.3021 Evaluate side-chains 40 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 3.218 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3571 time to fit residues: 5.6309 ------------------------------------------------------------------------------- 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: 0.7980 chunk 234 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 313 optimal weight: 0.9980 chunk 331 optimal weight: 20.0000 chunk 163 optimal weight: 4.9990 chunk 296 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 258 ASN ** 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** C1149 GLN 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 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1033 HIS ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 28576 Z= 0.210 Angle : 0.635 7.394 38936 Z= 0.354 Chirality : 0.052 0.807 4821 Planarity : 0.004 0.068 4875 Dihedral : 9.197 111.231 4522 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.62 % Favored : 91.00 % Rotamer Outliers : 0.10 % 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: 0.81 (0.19), residues: 763 sheet: -1.37 (0.19), residues: 691 loop : -1.77 (0.14), residues: 1978 *********************** 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 46 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.3927 time to fit residues: 34.8268 Evaluate side-chains 39 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 3.075 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3128 time to fit residues: 5.2025 ------------------------------------------------------------------------------- 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: 9.9990 chunk 188 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 282 optimal weight: 20.0000 chunk 229 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 chunk 297 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 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 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 170 ASN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** 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 849 ASN C 933 GLN ** C1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 0.7030 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 28576 Z= 0.383 Angle : 0.728 7.905 38936 Z= 0.406 Chirality : 0.052 0.793 4821 Planarity : 0.004 0.067 4875 Dihedral : 9.329 112.021 4522 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 33.97 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.85 % Favored : 89.83 % Rotamer Outliers : 0.03 % 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: -1.90 (0.14), residues: 3432 helix: 0.35 (0.18), residues: 761 sheet: -1.56 (0.19), residues: 701 loop : -1.84 (0.14), residues: 1970 *********************** 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 44 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 3.532 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.3737 time to fit residues: 31.6482 Evaluate side-chains 40 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 3.371 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3281 time to fit residues: 4.7681 ------------------------------------------------------------------------------- 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: 9.9990 chunk 65 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 331 optimal weight: 9.9990 chunk 275 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 27 optimal weight: 30.0000 chunk 109 optimal weight: 5.9990 chunk 174 optimal weight: 20.0000 overall best weight: 7.1788 ------------------------------------------------------------------------------- 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 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 GLN ** 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 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 ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN ** B 114 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 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 993 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 28576 Z= 0.378 Angle : 0.733 8.459 38936 Z= 0.409 Chirality : 0.052 0.787 4821 Planarity : 0.005 0.066 4875 Dihedral : 9.410 112.017 4522 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 34.94 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.26 % Favored : 89.36 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.14), residues: 3432 helix: 0.26 (0.18), residues: 748 sheet: -1.68 (0.19), residues: 691 loop : -1.88 (0.14), residues: 1993 *********************** 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 44 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 44 average time/residue: 0.3767 time to fit residues: 32.0983 Evaluate side-chains 39 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 3.335 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.3008 time to fit residues: 5.3137 ------------------------------------------------------------------------------- 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: 0.7980 chunk 37 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 242 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 279 optimal weight: 30.0000 chunk 185 optimal weight: 10.0000 chunk 330 optimal weight: 6.9990 chunk 206 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 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 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 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 903 ASN ** C1051 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 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 28576 Z= 0.241 Angle : 0.657 6.996 38936 Z= 0.367 Chirality : 0.052 0.802 4821 Planarity : 0.004 0.069 4875 Dihedral : 9.262 111.554 4522 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 27.72 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.32 % Favored : 90.30 % Rotamer Outliers : 0.03 % 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: -1.78 (0.14), residues: 3432 helix: 0.58 (0.18), residues: 761 sheet: -1.59 (0.19), residues: 686 loop : -1.79 (0.14), residues: 1985 *********************** 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 43 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.3971 time to fit residues: 32.8866 Evaluate side-chains 38 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 3.308 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3444 time to fit residues: 4.9537 ------------------------------------------------------------------------------- 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: 2.9990 chunk 132 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 chunk 225 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 259 optimal weight: 5.9990 chunk 300 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 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 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** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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** ** B1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 28576 Z= 0.243 Angle : 0.651 6.852 38936 Z= 0.364 Chirality : 0.052 0.800 4821 Planarity : 0.004 0.071 4875 Dihedral : 9.198 111.341 4522 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 26.75 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.27 % Favored : 90.41 % Rotamer Outliers : 0.00 % 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: -1.68 (0.14), residues: 3432 helix: 0.78 (0.19), residues: 750 sheet: -1.47 (0.19), residues: 691 loop : -1.79 (0.14), residues: 1991 *********************** 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 43 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 3.396 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.3883 time to fit residues: 32.4646 Evaluate side-chains 37 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 3.560 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5568 ------------------------------------------------------------------------------- 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: 5.9990 chunk 308 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 134 optimal weight: 0.0570 chunk 241 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 278 optimal weight: 20.0000 chunk 291 optimal weight: 6.9990 chunk 306 optimal weight: 30.0000 chunk 202 optimal weight: 8.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- 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 301 GLN ** 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 ** 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 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** ** 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: 0.7007 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 28576 Z= 0.253 Angle : 0.654 7.318 38936 Z= 0.365 Chirality : 0.052 0.799 4821 Planarity : 0.004 0.071 4875 Dihedral : 9.185 111.261 4522 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 27.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.59 % Favored : 90.15 % Rotamer Outliers : 0.03 % 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: -1.68 (0.14), residues: 3432 helix: 0.82 (0.19), residues: 748 sheet: -1.49 (0.19), residues: 690 loop : -1.79 (0.14), residues: 1994 *********************** 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 44 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 3.003 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.3862 time to fit residues: 32.5884 Evaluate side-chains 37 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 3.164 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1896 ------------------------------------------------------------------------------- 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: 0.9980 chunk 198 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 341 optimal weight: 0.9980 chunk 314 optimal weight: 20.0000 chunk 272 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 210 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 282 ASN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 ASN ** 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 147 ASN 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 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** ** 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: 0.6993 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 28576 Z= 0.202 Angle : 0.635 7.121 38936 Z= 0.352 Chirality : 0.052 0.817 4821 Planarity : 0.004 0.070 4875 Dihedral : 9.044 110.817 4522 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.28 % Favored : 91.46 % Rotamer Outliers : 0.00 % 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: -1.56 (0.14), residues: 3432 helix: 1.00 (0.19), residues: 754 sheet: -1.44 (0.19), residues: 697 loop : -1.74 (0.14), residues: 1981 ********************** 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 46 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.4145 time to fit residues: 36.0416 Evaluate side-chains 37 residues out of total 2949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 3.423 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1869 ------------------------------------------------------------------------------- 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: 0.9980 chunk 83 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 0.0970 chunk 272 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 279 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- 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 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 995 ASN ** 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 = 0.3129 r_free = 0.3129 target = 0.025702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.018444 restraints weight = 498550.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.019063 restraints weight = 332645.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.019510 restraints weight = 249479.915| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 28576 Z= 0.214 Angle : 0.624 7.197 38936 Z= 0.347 Chirality : 0.051 0.770 4821 Planarity : 0.004 0.071 4875 Dihedral : 8.996 110.781 4522 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.57 % Favored : 91.17 % Rotamer Outliers : 0.00 % 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: -1.51 (0.14), residues: 3432 helix: 1.06 (0.19), residues: 754 sheet: -1.42 (0.19), residues: 695 loop : -1.72 (0.14), residues: 1983 =============================================================================== Job complete usr+sys time: 3380.93 seconds wall clock time: 66 minutes 24.17 seconds (3984.17 seconds total)