Starting phenix.real_space_refine on Tue Mar 19 17:17:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6s_33646/03_2024/7y6s_33646.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6s_33646/03_2024/7y6s_33646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6s_33646/03_2024/7y6s_33646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6s_33646/03_2024/7y6s_33646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6s_33646/03_2024/7y6s_33646.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6s_33646/03_2024/7y6s_33646.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 15744 2.51 5 N 3933 2.21 5 O 5070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24852 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 7766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7766 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 38, 'TRANS': 965} Chain breaks: 9 Chain: "B" Number of atoms: 7766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7766 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 38, 'TRANS': 965} Chain breaks: 9 Chain: "C" Number of atoms: 7766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7766 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 38, 'TRANS': 965} Chain breaks: 9 Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "d" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 13.00, per 1000 atoms: 0.52 Number of scatterers: 24852 At special positions: 0 Unit cell: (171.72, 174.9, 154.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 5070 8.00 N 3933 7.00 C 15744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " 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=2.03 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 B1122 " - pdb=" SG CYS B1133 " 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 ALPHA1-2 " MAN E 4 " - " MAN E 5 " " MAN Q 4 " - " MAN Q 5 " " MAN c 4 " - " MAN c 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " MAN E 6 " - " MAN E 7 " " BMA Q 3 " - " MAN Q 4 " " MAN Q 6 " - " MAN Q 7 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " ALPHA1-6 " BMA E 3 " - " MAN E 6 " " BMA Q 3 " - " MAN Q 6 " " BMA c 3 " - " MAN c 6 " 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 G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " 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 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 2 " " NAG O 1 " - " FUC O 3 " " NAG P 1 " - " FUC P 4 " " NAG R 1 " - " FUC R 2 " " NAG a 1 " - " FUC a 3 " " NAG b 1 " - " FUC b 4 " " NAG d 1 " - " FUC d 2 " " NAG m 1 " - " FUC m 3 " NAG-ASN " NAG A1501 " - " ASN A 667 " " NAG A1502 " - " ASN A 787 " " NAG A1503 " - " ASN A1009 " " NAG A1504 " - " ASN A1249 " " NAG B1501 " - " ASN B 667 " " NAG B1502 " - " ASN B 787 " " NAG B1503 " - " ASN B1009 " " NAG B1504 " - " ASN B1249 " " NAG C1501 " - " ASN C 667 " " NAG C1502 " - " ASN C 787 " " NAG C1503 " - " ASN C1009 " " NAG C1504 " - " ASN C1249 " " NAG D 1 " - " ASN A 216 " " NAG E 1 " - " ASN A 264 " " NAG F 1 " - " ASN A 300 " " NAG G 1 " - " ASN A 324 " " NAG H 1 " - " ASN A 344 " " NAG I 1 " - " ASN A 425 " " NAG J 1 " - " ASN A 726 " " NAG K 1 " - " ASN A 688 " " NAG L 1 " - " ASN A 743 " " NAG M 1 " - " ASN A 781 " " NAG N 1 " - " ASN A 873 " " NAG O 1 " - " ASN A1232 " " NAG P 1 " - " ASN B 216 " " NAG Q 1 " - " ASN B 264 " " NAG R 1 " - " ASN B 300 " " NAG S 1 " - " ASN B 324 " " NAG T 1 " - " ASN B 344 " " NAG U 1 " - " ASN B 425 " " NAG V 1 " - " ASN B 726 " " NAG W 1 " - " ASN B 688 " " NAG X 1 " - " ASN B 743 " " NAG Y 1 " - " ASN B 781 " " NAG Z 1 " - " ASN B 873 " " NAG a 1 " - " ASN B1232 " " NAG b 1 " - " ASN C 216 " " NAG c 1 " - " ASN C 264 " " NAG d 1 " - " ASN C 300 " " NAG e 1 " - " ASN C 324 " " NAG f 1 " - " ASN C 344 " " NAG g 1 " - " ASN C 425 " " NAG h 1 " - " ASN C 726 " " NAG i 1 " - " ASN C 688 " " NAG j 1 " - " ASN C 743 " " NAG k 1 " - " ASN C 781 " " NAG l 1 " - " ASN C 873 " " NAG m 1 " - " ASN C1232 " Time building additional restraints: 11.59 Conformation dependent library (CDL) restraints added in 4.1 seconds 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5604 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 39 sheets defined 26.0% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 32 through 37 Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.508A pdb=" N CYS A 234 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 removed outlier: 3.621A pdb=" N VAL A 328 " --> pdb=" O ASP A 325 " (cutoff:3.500A) 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: 3.719A pdb=" N GLN A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 822 " --> pdb=" O ARG A 818 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN A 825 " --> pdb=" O GLN A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 852 removed outlier: 4.193A pdb=" N GLU A 834 " --> pdb=" O CYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 861 removed outlier: 3.848A pdb=" N LEU A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 910 through 914 Processing helix chain 'A' and resid 928 through 935 Processing helix chain 'A' and resid 946 through 961 Processing helix chain 'A' and resid 967 through 971 Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.587A pdb=" N ALA A 977 " --> pdb=" O PRO A 973 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1015 removed outlier: 4.146A pdb=" N LEU A 999 " --> pdb=" O ASN A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1055 removed outlier: 4.146A pdb=" N GLN A1045 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY A1046 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A1055 " --> pdb=" O GLN A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1058 No H-bonds generated for 'chain 'A' and resid 1056 through 1058' Processing helix chain 'A' and resid 1066 through 1074 Processing helix chain 'A' and resid 1075 through 1123 removed outlier: 3.707A pdb=" N VAL A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A1086 " --> pdb=" O GLN A1082 " (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 1237 through 1242 Processing helix chain 'A' and resid 1247 through 1253 Processing helix chain 'B' and resid 32 through 38 removed outlier: 3.851A pdb=" N LYS B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 238 removed outlier: 3.953A pdb=" N GLY B 236 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 238 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 329 removed outlier: 3.552A pdb=" N VAL B 328 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 475 Processing helix chain 'B' and resid 807 through 814 Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.650A pdb=" N GLN B 821 " --> pdb=" O SER B 817 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 822 " --> pdb=" O ARG B 818 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B 825 " --> pdb=" O GLN B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 852 Processing helix chain 'B' and resid 855 through 861 Processing helix chain 'B' and resid 895 through 904 removed outlier: 3.589A pdb=" N LYS B 904 " --> pdb=" O LEU B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 914 Processing helix chain 'B' and resid 928 through 935 Processing helix chain 'B' and resid 946 through 961 Processing helix chain 'B' and resid 967 through 971 Processing helix chain 'B' and resid 973 through 986 removed outlier: 3.509A pdb=" N ALA B 977 " --> pdb=" O PRO B 973 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 985 " --> pdb=" O ARG B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1014 removed outlier: 3.922A pdb=" N LEU B 999 " --> pdb=" O ASN B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1055 removed outlier: 4.135A pdb=" N GLN B1045 " --> pdb=" O VAL B1041 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY B1046 " --> pdb=" O VAL B1042 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B1055 " --> pdb=" O GLN B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1074 Processing helix chain 'B' and resid 1075 through 1122 removed outlier: 3.707A pdb=" N VAL B1081 " --> pdb=" O PRO B1077 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B1085 " --> pdb=" O VAL B1081 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B1086 " --> pdb=" O GLN B1082 " (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 1237 through 1242 removed outlier: 3.553A pdb=" N VAL B1241 " --> pdb=" O GLN B1237 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 325 through 329 removed outlier: 3.665A pdb=" N VAL C 328 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 476 Processing helix chain 'C' and resid 807 through 814 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 825 through 829 removed outlier: 6.739A pdb=" N ALA C 828 " --> pdb=" O GLN C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 852 removed outlier: 3.814A pdb=" N ALA C 836 " --> pdb=" O THR C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 861 removed outlier: 3.882A pdb=" N LEU C 861 " --> pdb=" O GLU C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 910 through 914 Processing helix chain 'C' and resid 928 through 935 Processing helix chain 'C' and resid 946 through 961 Processing helix chain 'C' and resid 967 through 971 Processing helix chain 'C' and resid 973 through 986 removed outlier: 3.653A pdb=" N ALA C 977 " --> pdb=" O PRO C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1015 removed outlier: 4.590A pdb=" N LEU C 999 " --> pdb=" O ASN C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1055 removed outlier: 4.058A pdb=" N GLN C1045 " --> pdb=" O VAL C1041 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY C1046 " --> pdb=" O VAL C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1074 Processing helix chain 'C' and resid 1075 through 1123 removed outlier: 3.670A pdb=" N VAL C1081 " --> pdb=" O PRO C1077 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C1086 " --> pdb=" O GLN C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1216 through 1218 No H-bonds generated for 'chain 'C' and resid 1216 through 1218' Processing helix chain 'C' and resid 1237 through 1242 removed outlier: 3.505A pdb=" N VAL C1241 " --> pdb=" O GLN C1237 " (cutoff:3.500A) Processing helix chain 'C' and resid 1247 through 1253 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.617A pdb=" N ALA A 74 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 192 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 184 removed outlier: 3.647A pdb=" N VAL A 175 " --> pdb=" O TYR A 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 268 removed outlier: 5.445A pdb=" N LEU B 684 " --> pdb=" O VAL B 697 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 694 " --> pdb=" O THR B 666 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 288 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 270 through 288 current: chain 'A' and resid 397 through 401 removed outlier: 3.870A pdb=" N LEU A 414 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL A 408 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 412 through 415 current: chain 'A' and resid 457 through 463 Processing sheet with id=AA6, first strand: chain 'A' and resid 294 through 298 removed outlier: 6.752A pdb=" N HIS A 338 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL A 422 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 336 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N PHE A 375 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE A 387 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 488 removed outlier: 3.682A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 502 removed outlier: 5.495A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR A 675 " --> pdb=" O THR C 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB1, first strand: chain 'A' and resid 780 through 798 removed outlier: 6.690A pdb=" N ASN A 781 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A1167 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER A 783 " --> pdb=" O ASP A1165 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP A1165 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE A1163 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASN A 787 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLY A1150 " --> pdb=" O ALA A1146 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ALA A1146 " --> pdb=" O GLY A1150 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A1152 " --> pdb=" O VAL A1144 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL A1144 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A1154 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER A1142 " --> pdb=" O LEU A1154 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR A1156 " --> pdb=" O ILE A1140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB3, first strand: chain 'A' and resid 881 through 884 removed outlier: 4.039A pdb=" N ASP A 884 " --> pdb=" O ARG A 889 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG A 889 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1220 through 1223 removed outlier: 4.185A pdb=" N ALA A1179 " --> pdb=" O ILE A1223 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N CYS A1173 " --> pdb=" O LEU A1233 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1187 through 1190 Processing sheet with id=AB6, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.188A pdb=" N TYR B 212 " --> pdb=" O CYS B 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.599A pdb=" N ALA B 74 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 192 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 123 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN B 151 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B 125 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AB9, first strand: chain 'B' and resid 267 through 268 removed outlier: 5.502A pdb=" N LEU C 684 " --> pdb=" O VAL C 697 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 271 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 271 through 288 current: chain 'B' and resid 397 through 401 removed outlier: 3.898A pdb=" N LEU B 414 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL B 408 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLY B 412 " --> pdb=" O VAL B 408 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 412 through 415 current: chain 'B' and resid 457 through 463 Processing sheet with id=AC2, first strand: chain 'B' and resid 293 through 298 removed outlier: 3.715A pdb=" N GLN B 295 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS B 338 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B 422 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 336 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN B 344 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N CYS B 373 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 483 through 488 removed outlier: 3.786A pdb=" N GLY B 715 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B 709 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE B 713 " --> pdb=" O VAL B 709 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 749 through 751 Processing sheet with id=AC5, first strand: chain 'B' and resid 780 through 798 removed outlier: 6.621A pdb=" N ASN B 781 " --> pdb=" O ILE B1167 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE B1167 " --> pdb=" O ASN B 781 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER B 783 " --> pdb=" O ASP B1165 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP B1165 " --> pdb=" O SER B 783 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE B1163 " --> pdb=" O PRO B 785 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN B 787 " --> pdb=" O SER B1161 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY B1150 " --> pdb=" O ALA B1146 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA B1146 " --> pdb=" O GLY B1150 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B1152 " --> pdb=" O VAL B1144 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL B1144 " --> pdb=" O LEU B1152 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B1154 " --> pdb=" O SER B1142 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER B1142 " --> pdb=" O LEU B1154 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR B1156 " --> pdb=" O ILE B1140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AC7, first strand: chain 'B' and resid 881 through 883 Processing sheet with id=AC8, first strand: chain 'B' and resid 1220 through 1223 removed outlier: 3.729A pdb=" N ALA B1179 " --> pdb=" O ILE B1223 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N CYS B1173 " --> pdb=" O LEU B1233 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1187 through 1190 Processing sheet with id=AD1, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.338A pdb=" N TYR C 212 " --> pdb=" O CYS C 230 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 73 through 74 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 73 through 74 current: chain 'C' and resid 106 through 110 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 148 through 152 current: chain 'C' and resid 172 through 175 Processing sheet with id=AD3, first strand: chain 'C' and resid 271 through 288 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 271 through 288 current: chain 'C' and resid 397 through 401 removed outlier: 3.723A pdb=" N LEU C 414 " --> pdb=" O VAL C 406 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL C 408 " --> pdb=" O GLY C 412 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLY C 412 " --> pdb=" O VAL C 408 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 411 through 415 current: chain 'C' and resid 457 through 463 Processing sheet with id=AD4, first strand: chain 'C' and resid 296 through 298 removed outlier: 7.112A pdb=" N HIS C 338 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL C 422 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 336 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N CYS C 373 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 483 through 488 removed outlier: 3.748A pdb=" N GLY C 715 " --> pdb=" O ALA C 707 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 749 through 751 Processing sheet with id=AD7, first strand: chain 'C' and resid 780 through 786 Processing sheet with id=AD8, first strand: chain 'C' and resid 789 through 798 removed outlier: 7.101A pdb=" N GLY C1150 " --> pdb=" O ALA C1146 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ALA C1146 " --> pdb=" O GLY C1150 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU C1152 " --> pdb=" O VAL C1144 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL C1144 " --> pdb=" O LEU C1152 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU C1154 " --> pdb=" O SER C1142 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER C1142 " --> pdb=" O LEU C1154 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N THR C1156 " --> pdb=" O ILE C1140 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 804 through 806 Processing sheet with id=AE1, first strand: chain 'C' and resid 881 through 882 Processing sheet with id=AE2, first strand: chain 'C' and resid 1220 through 1223 removed outlier: 3.659A pdb=" N ALA C1179 " --> pdb=" O ILE C1223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1187 through 1190 877 hydrogen bonds defined for protein. 2355 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: 9.88 Time building geometry restraints manager: 12.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7719 1.34 - 1.46: 6440 1.46 - 1.58: 11047 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 25341 Sorted by residual: bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.42e+00 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.22e+00 bond pdb=" C1 NAG B1501 " pdb=" O5 NAG B1501 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" CA SER B 506 " pdb=" CB SER B 506 " ideal model delta sigma weight residual 1.535 1.492 0.043 1.71e-02 3.42e+03 6.36e+00 ... (remaining 25336 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.95: 721 106.95 - 113.71: 14794 113.71 - 120.46: 9043 120.46 - 127.21: 9718 127.21 - 133.97: 203 Bond angle restraints: 34479 Sorted by residual: angle pdb=" C PHE C 725 " pdb=" N ASN C 726 " pdb=" CA ASN C 726 " ideal model delta sigma weight residual 122.53 129.95 -7.42 1.92e+00 2.71e-01 1.49e+01 angle pdb=" N ASN C 726 " pdb=" CA ASN C 726 " pdb=" CB ASN C 726 " ideal model delta sigma weight residual 110.42 105.22 5.20 1.53e+00 4.27e-01 1.16e+01 angle pdb=" C ASP C 434 " pdb=" N VAL C 435 " pdb=" CA VAL C 435 " ideal model delta sigma weight residual 121.97 127.01 -5.04 1.80e+00 3.09e-01 7.83e+00 angle pdb=" C ILE B 424 " pdb=" N ASN B 425 " pdb=" CA ASN B 425 " ideal model delta sigma weight residual 123.23 127.61 -4.38 1.57e+00 4.06e-01 7.77e+00 angle pdb=" CA SER B 506 " pdb=" C SER B 506 " pdb=" O SER B 506 " ideal model delta sigma weight residual 121.58 118.36 3.22 1.16e+00 7.43e-01 7.70e+00 ... (remaining 34474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.46: 15215 24.46 - 48.92: 774 48.92 - 73.39: 202 73.39 - 97.85: 156 97.85 - 122.31: 81 Dihedral angle restraints: 16428 sinusoidal: 7698 harmonic: 8730 Sorted by residual: 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 -86.00 -163.17 77.17 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS A 808 " pdb=" SG CYS A 808 " pdb=" SG CYS A 830 " pdb=" CB CYS A 830 " ideal model delta sinusoidal sigma weight residual -86.00 -128.21 42.21 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CA ILE B 424 " pdb=" C ILE B 424 " pdb=" N ASN B 425 " pdb=" CA ASN B 425 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 16425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 4299 0.188 - 0.377: 33 0.377 - 0.565: 2 0.565 - 0.753: 2 0.753 - 0.942: 2 Chirality restraints: 4338 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN B 726 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.22e+01 chirality pdb=" C1 NAG k 1 " pdb=" ND2 ASN C 781 " pdb=" C2 NAG k 1 " pdb=" O5 NAG k 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 726 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 4335 not shown) Planarity restraints: 4305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 425 " -0.034 2.00e-02 2.50e+03 3.32e-02 1.37e+01 pdb=" CG ASN B 425 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN B 425 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 425 " 0.034 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 726 " 0.033 2.00e-02 2.50e+03 3.10e-02 1.20e+01 pdb=" CG ASN C 726 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN C 726 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 726 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG h 1 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 425 " 0.002 2.00e-02 2.50e+03 2.90e-02 1.05e+01 pdb=" CG ASN A 425 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 425 " -0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN A 425 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.032 2.00e-02 2.50e+03 ... (remaining 4302 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 820 2.70 - 3.25: 25244 3.25 - 3.80: 39013 3.80 - 4.35: 50719 4.35 - 4.90: 84513 Nonbonded interactions: 200309 Sorted by model distance: nonbonded pdb=" OD1 ASP B 265 " pdb=" OH TYR C 675 " model vdw 2.147 2.440 nonbonded pdb=" ND2 ASN C 240 " pdb=" O PHE C 438 " model vdw 2.163 2.520 nonbonded pdb=" O PRO C 498 " pdb=" OG1 THR C 650 " model vdw 2.172 2.440 nonbonded pdb=" O PRO A 498 " pdb=" OG1 THR A 650 " model vdw 2.180 2.440 nonbonded pdb=" OG1 THR A1234 " pdb=" OD1 ASP A1236 " model vdw 2.181 2.440 ... (remaining 200304 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'P' selection = chain 'b' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'c' } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'j' and resid 1) selection = (chain 'l' and resid 1) } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.370 Check model and map are aligned: 0.360 Set scattering table: 0.250 Process input model: 68.020 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 : 0.005 0.073 25341 Z= 0.284 Angle : 0.756 8.541 34479 Z= 0.341 Chirality : 0.059 0.942 4338 Planarity : 0.004 0.053 4257 Dihedral : 19.821 122.311 10788 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.34 % Favored : 95.53 % Rotamer: Outliers : 0.31 % Allowed : 0.54 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 2952 helix: 0.67 (0.20), residues: 672 sheet: -1.01 (0.20), residues: 588 loop : -0.60 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 65 HIS 0.003 0.001 HIS C1139 PHE 0.021 0.001 PHE C 725 TYR 0.034 0.001 TYR B 403 ARG 0.008 0.001 ARG C 924 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 2.790 Fit side-chains REVERT: A 158 MET cc_start: 0.8700 (pmm) cc_final: 0.8480 (pmm) REVERT: A 435 VAL cc_start: 0.8529 (m) cc_final: 0.8275 (p) REVERT: A 492 LEU cc_start: 0.8917 (mm) cc_final: 0.8614 (tp) REVERT: A 952 MET cc_start: 0.9167 (mtp) cc_final: 0.8858 (mtm) REVERT: A 1107 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8658 (mt-10) REVERT: A 1136 ASP cc_start: 0.8597 (m-30) cc_final: 0.8197 (m-30) REVERT: A 1209 MET cc_start: 0.9370 (mtt) cc_final: 0.9127 (mtp) REVERT: B 214 MET cc_start: 0.8368 (mtp) cc_final: 0.7889 (tmm) REVERT: B 435 VAL cc_start: 0.8521 (m) cc_final: 0.8312 (p) REVERT: B 814 ASN cc_start: 0.9571 (t0) cc_final: 0.9333 (t0) REVERT: B 1244 ASP cc_start: 0.9152 (t70) cc_final: 0.8705 (t0) REVERT: C 1209 MET cc_start: 0.9270 (mtt) cc_final: 0.9047 (mtp) outliers start: 8 outliers final: 3 residues processed: 63 average time/residue: 0.3659 time to fit residues: 39.9467 Evaluate side-chains 49 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 121 optimal weight: 0.0770 chunk 235 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 272 optimal weight: 3.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN ** C1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25341 Z= 0.221 Angle : 0.671 9.881 34479 Z= 0.311 Chirality : 0.050 0.672 4338 Planarity : 0.004 0.064 4257 Dihedral : 16.497 113.268 5659 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 0.19 % Allowed : 5.28 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 2952 helix: 1.19 (0.20), residues: 693 sheet: -0.77 (0.20), residues: 585 loop : -0.57 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 65 HIS 0.003 0.001 HIS C1139 PHE 0.014 0.001 PHE A 347 TYR 0.018 0.001 TYR B 403 ARG 0.006 0.000 ARG C1235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 2.871 Fit side-chains REVERT: A 158 MET cc_start: 0.8691 (pmm) cc_final: 0.8436 (pmm) REVERT: A 435 VAL cc_start: 0.8481 (m) cc_final: 0.8190 (p) REVERT: A 492 LEU cc_start: 0.8915 (mm) cc_final: 0.8621 (tp) REVERT: A 814 ASN cc_start: 0.9480 (t0) cc_final: 0.9265 (t0) REVERT: A 952 MET cc_start: 0.9131 (mtp) cc_final: 0.8867 (mtm) REVERT: A 1107 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8619 (mt-10) REVERT: A 1136 ASP cc_start: 0.8593 (m-30) cc_final: 0.8275 (p0) REVERT: A 1209 MET cc_start: 0.9338 (mtt) cc_final: 0.9114 (mtp) REVERT: B 214 MET cc_start: 0.8334 (mtp) cc_final: 0.7784 (tmm) REVERT: B 814 ASN cc_start: 0.9511 (t0) cc_final: 0.9180 (t0) REVERT: B 952 MET cc_start: 0.9190 (tpp) cc_final: 0.8812 (tpp) REVERT: B 1244 ASP cc_start: 0.9220 (t70) cc_final: 0.8715 (t0) REVERT: C 1209 MET cc_start: 0.9261 (mtt) cc_final: 0.9059 (mtp) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.3272 time to fit residues: 30.7386 Evaluate side-chains 46 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 214 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 185 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 243 optimal weight: 8.9990 chunk 270 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 218 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25341 Z= 0.277 Angle : 0.657 10.593 34479 Z= 0.303 Chirality : 0.049 0.635 4338 Planarity : 0.004 0.067 4257 Dihedral : 13.617 107.609 5658 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 1.00 % Allowed : 8.05 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2952 helix: 1.54 (0.20), residues: 693 sheet: -0.68 (0.20), residues: 585 loop : -0.51 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 65 HIS 0.004 0.001 HIS B 161 PHE 0.014 0.001 PHE A 347 TYR 0.014 0.001 TYR B 403 ARG 0.006 0.000 ARG C1235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 45 time to evaluate : 2.718 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.8746 (pmm) cc_final: 0.8488 (pmm) REVERT: A 214 MET cc_start: 0.8506 (tpp) cc_final: 0.7707 (tmm) REVERT: A 231 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7634 (m) REVERT: A 435 VAL cc_start: 0.8534 (m) cc_final: 0.8187 (p) REVERT: A 492 LEU cc_start: 0.8946 (mm) cc_final: 0.8657 (tp) REVERT: A 814 ASN cc_start: 0.9481 (t0) cc_final: 0.9232 (t0) REVERT: A 939 MET cc_start: 0.9366 (ttt) cc_final: 0.9139 (ttm) REVERT: A 952 MET cc_start: 0.9150 (mtp) cc_final: 0.8902 (mtm) REVERT: A 1107 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8651 (mt-10) REVERT: A 1136 ASP cc_start: 0.8567 (m-30) cc_final: 0.8328 (p0) REVERT: A 1209 MET cc_start: 0.9359 (mtt) cc_final: 0.9144 (mtp) REVERT: B 158 MET cc_start: 0.6425 (ppp) cc_final: 0.6142 (ppp) REVERT: B 214 MET cc_start: 0.8326 (mtp) cc_final: 0.7830 (tmm) REVERT: B 814 ASN cc_start: 0.9473 (t0) cc_final: 0.9109 (t0) REVERT: B 952 MET cc_start: 0.9241 (tpp) cc_final: 0.8736 (tpp) REVERT: B 1244 ASP cc_start: 0.9240 (t70) cc_final: 0.8693 (t0) outliers start: 26 outliers final: 13 residues processed: 67 average time/residue: 0.3049 time to fit residues: 37.5627 Evaluate side-chains 56 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 273 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 25341 Z= 0.312 Angle : 0.656 10.061 34479 Z= 0.302 Chirality : 0.049 0.638 4338 Planarity : 0.004 0.064 4257 Dihedral : 12.382 105.820 5658 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 1.31 % Allowed : 9.63 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2952 helix: 1.67 (0.20), residues: 684 sheet: -0.62 (0.21), residues: 576 loop : -0.53 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 65 HIS 0.003 0.001 HIS B 951 PHE 0.014 0.001 PHE A 347 TYR 0.011 0.001 TYR B 403 ARG 0.011 0.000 ARG A 994 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 41 time to evaluate : 2.679 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.8784 (pmm) cc_final: 0.8518 (pmm) REVERT: A 214 MET cc_start: 0.8513 (tpp) cc_final: 0.7778 (tmm) REVERT: A 231 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.7660 (m) REVERT: A 435 VAL cc_start: 0.8552 (m) cc_final: 0.8198 (p) REVERT: A 492 LEU cc_start: 0.8973 (mm) cc_final: 0.8670 (tp) REVERT: A 757 CYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8131 (m) REVERT: A 939 MET cc_start: 0.9355 (ttt) cc_final: 0.9133 (ttm) REVERT: A 952 MET cc_start: 0.9183 (mtp) cc_final: 0.8927 (mtm) REVERT: A 1107 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8657 (mt-10) REVERT: A 1136 ASP cc_start: 0.8552 (m-30) cc_final: 0.8308 (p0) REVERT: A 1209 MET cc_start: 0.9358 (mtt) cc_final: 0.9114 (mtp) REVERT: B 46 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.7531 (p) REVERT: B 158 MET cc_start: 0.6383 (ppp) cc_final: 0.5992 (ppp) REVERT: B 214 MET cc_start: 0.8327 (mtp) cc_final: 0.7828 (tmm) REVERT: B 441 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8390 (pt) REVERT: B 639 THR cc_start: 0.7627 (OUTLIER) cc_final: 0.7402 (p) REVERT: B 814 ASN cc_start: 0.9476 (t0) cc_final: 0.9096 (t0) REVERT: B 952 MET cc_start: 0.9277 (tpp) cc_final: 0.8762 (tpp) REVERT: B 1244 ASP cc_start: 0.9226 (t70) cc_final: 0.8662 (t0) REVERT: C 427 THR cc_start: 0.9509 (OUTLIER) cc_final: 0.9173 (p) outliers start: 34 outliers final: 21 residues processed: 71 average time/residue: 0.2803 time to fit residues: 37.6393 Evaluate side-chains 68 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 41 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 0.2980 chunk 164 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 260 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25341 Z= 0.262 Angle : 0.629 10.098 34479 Z= 0.289 Chirality : 0.048 0.608 4338 Planarity : 0.003 0.062 4257 Dihedral : 11.885 106.285 5658 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 1.77 % Allowed : 10.40 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 2952 helix: 1.82 (0.20), residues: 684 sheet: -0.57 (0.21), residues: 582 loop : -0.51 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 65 HIS 0.002 0.001 HIS C 110 PHE 0.012 0.001 PHE A 347 TYR 0.010 0.001 TYR C 675 ARG 0.003 0.000 ARG C1112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 42 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8789 (pmm) cc_final: 0.8514 (pmm) REVERT: A 214 MET cc_start: 0.8520 (tpp) cc_final: 0.7803 (tmm) REVERT: A 231 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7549 (m) REVERT: A 435 VAL cc_start: 0.8539 (m) cc_final: 0.8196 (p) REVERT: A 492 LEU cc_start: 0.8962 (mm) cc_final: 0.8671 (tp) REVERT: A 757 CYS cc_start: 0.8633 (OUTLIER) cc_final: 0.7995 (m) REVERT: A 939 MET cc_start: 0.9359 (ttt) cc_final: 0.9137 (ttm) REVERT: A 952 MET cc_start: 0.9166 (mtp) cc_final: 0.8911 (mtm) REVERT: A 1107 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8622 (mt-10) REVERT: A 1136 ASP cc_start: 0.8552 (m-30) cc_final: 0.8302 (p0) REVERT: A 1209 MET cc_start: 0.9356 (mtt) cc_final: 0.9128 (mtp) REVERT: B 46 VAL cc_start: 0.7776 (OUTLIER) cc_final: 0.7547 (p) REVERT: B 158 MET cc_start: 0.6425 (ppp) cc_final: 0.6036 (ppp) REVERT: B 214 MET cc_start: 0.8321 (mtp) cc_final: 0.7813 (tmm) REVERT: B 814 ASN cc_start: 0.9472 (t0) cc_final: 0.9061 (t0) REVERT: B 952 MET cc_start: 0.9290 (tpp) cc_final: 0.8773 (tpp) REVERT: B 1244 ASP cc_start: 0.9236 (t70) cc_final: 0.8669 (t0) REVERT: C 158 MET cc_start: 0.8441 (pmm) cc_final: 0.8003 (pmm) REVERT: C 1107 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8871 (tm-30) outliers start: 46 outliers final: 31 residues processed: 86 average time/residue: 0.2854 time to fit residues: 46.0352 Evaluate side-chains 75 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 41 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 290 optimal weight: 0.5980 chunk 240 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 GLN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25341 Z= 0.205 Angle : 0.621 10.144 34479 Z= 0.282 Chirality : 0.048 0.603 4338 Planarity : 0.003 0.059 4257 Dihedral : 11.684 105.504 5657 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.81 % Allowed : 10.87 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2952 helix: 1.90 (0.20), residues: 684 sheet: -0.53 (0.21), residues: 582 loop : -0.48 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 65 HIS 0.002 0.000 HIS C 110 PHE 0.011 0.001 PHE A 347 TYR 0.010 0.001 TYR C 675 ARG 0.002 0.000 ARG B1207 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 43 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8775 (pmm) cc_final: 0.8501 (pmm) REVERT: A 214 MET cc_start: 0.8522 (tpp) cc_final: 0.7801 (tmm) REVERT: A 231 THR cc_start: 0.7749 (OUTLIER) cc_final: 0.7536 (m) REVERT: A 435 VAL cc_start: 0.8531 (m) cc_final: 0.8236 (p) REVERT: A 492 LEU cc_start: 0.8955 (mm) cc_final: 0.8672 (tp) REVERT: A 757 CYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7983 (m) REVERT: A 814 ASN cc_start: 0.9458 (t0) cc_final: 0.9146 (t0) REVERT: A 939 MET cc_start: 0.9352 (ttt) cc_final: 0.9138 (ttm) REVERT: A 952 MET cc_start: 0.9160 (mtp) cc_final: 0.8912 (mtm) REVERT: A 1107 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8568 (mt-10) REVERT: A 1136 ASP cc_start: 0.8545 (m-30) cc_final: 0.8304 (p0) REVERT: A 1144 VAL cc_start: 0.9719 (OUTLIER) cc_final: 0.9500 (p) REVERT: A 1209 MET cc_start: 0.9362 (mtt) cc_final: 0.9138 (mtp) REVERT: B 46 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7545 (p) REVERT: B 158 MET cc_start: 0.6428 (ppp) cc_final: 0.6174 (ppp) REVERT: B 214 MET cc_start: 0.8307 (mtp) cc_final: 0.7805 (tmm) REVERT: B 441 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8320 (pt) REVERT: B 814 ASN cc_start: 0.9455 (t0) cc_final: 0.9026 (t0) REVERT: B 952 MET cc_start: 0.9301 (tpp) cc_final: 0.8766 (tpp) REVERT: B 1244 ASP cc_start: 0.9222 (t70) cc_final: 0.8640 (t0) REVERT: C 158 MET cc_start: 0.8389 (pmm) cc_final: 0.8043 (pmm) REVERT: C 427 THR cc_start: 0.9485 (OUTLIER) cc_final: 0.9189 (p) REVERT: C 1107 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8844 (tm-30) outliers start: 47 outliers final: 35 residues processed: 87 average time/residue: 0.2897 time to fit residues: 45.8109 Evaluate side-chains 83 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 42 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 165 optimal weight: 0.2980 chunk 211 optimal weight: 0.0020 chunk 164 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 289 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 ASN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 988 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25341 Z= 0.145 Angle : 0.602 10.127 34479 Z= 0.273 Chirality : 0.047 0.564 4338 Planarity : 0.003 0.075 4257 Dihedral : 11.153 104.913 5657 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.81 % Allowed : 11.14 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2952 helix: 2.00 (0.20), residues: 693 sheet: -0.47 (0.21), residues: 588 loop : -0.42 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 65 HIS 0.002 0.000 HIS A 429 PHE 0.010 0.001 PHE A 347 TYR 0.011 0.001 TYR B 675 ARG 0.015 0.000 ARG A 994 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 48 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8744 (pmm) cc_final: 0.8472 (pmm) REVERT: A 214 MET cc_start: 0.8547 (tpp) cc_final: 0.7749 (tmm) REVERT: A 231 THR cc_start: 0.7690 (OUTLIER) cc_final: 0.7476 (m) REVERT: A 435 VAL cc_start: 0.8498 (m) cc_final: 0.8242 (p) REVERT: A 492 LEU cc_start: 0.8929 (mm) cc_final: 0.8671 (tp) REVERT: A 757 CYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8037 (m) REVERT: A 814 ASN cc_start: 0.9438 (t0) cc_final: 0.9125 (t0) REVERT: A 952 MET cc_start: 0.9141 (mtp) cc_final: 0.8899 (mtm) REVERT: A 1136 ASP cc_start: 0.8550 (m-30) cc_final: 0.8283 (p0) REVERT: A 1209 MET cc_start: 0.9332 (mtt) cc_final: 0.9116 (mtp) REVERT: B 46 VAL cc_start: 0.7715 (OUTLIER) cc_final: 0.7504 (p) REVERT: B 214 MET cc_start: 0.8263 (mtp) cc_final: 0.7765 (tmm) REVERT: B 814 ASN cc_start: 0.9412 (t0) cc_final: 0.8960 (t0) REVERT: B 952 MET cc_start: 0.9302 (tpp) cc_final: 0.8805 (tpp) REVERT: B 1244 ASP cc_start: 0.9206 (t70) cc_final: 0.8646 (t0) REVERT: C 158 MET cc_start: 0.8375 (pmm) cc_final: 0.8164 (pmm) outliers start: 47 outliers final: 32 residues processed: 92 average time/residue: 0.3148 time to fit residues: 51.8769 Evaluate side-chains 77 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 42 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 172 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 196 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 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 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25341 Z= 0.218 Angle : 0.616 10.218 34479 Z= 0.279 Chirality : 0.047 0.547 4338 Planarity : 0.003 0.055 4257 Dihedral : 10.966 104.539 5657 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.89 % Allowed : 11.60 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2952 helix: 2.06 (0.20), residues: 684 sheet: -0.46 (0.21), residues: 588 loop : -0.41 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 65 HIS 0.002 0.000 HIS A 161 PHE 0.009 0.001 PHE A 347 TYR 0.010 0.001 TYR B 675 ARG 0.009 0.000 ARG A 994 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 41 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8761 (pmm) cc_final: 0.8482 (pmm) REVERT: A 214 MET cc_start: 0.8543 (tpp) cc_final: 0.7803 (tmm) REVERT: A 231 THR cc_start: 0.7650 (OUTLIER) cc_final: 0.7436 (m) REVERT: A 435 VAL cc_start: 0.8517 (m) cc_final: 0.8261 (p) REVERT: A 492 LEU cc_start: 0.8949 (mm) cc_final: 0.8682 (tp) REVERT: A 757 CYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8084 (m) REVERT: A 814 ASN cc_start: 0.9439 (t0) cc_final: 0.9121 (t0) REVERT: A 952 MET cc_start: 0.9160 (mtp) cc_final: 0.8909 (mtm) REVERT: A 1209 MET cc_start: 0.9323 (mtt) cc_final: 0.9102 (mtp) REVERT: B 46 VAL cc_start: 0.7727 (OUTLIER) cc_final: 0.7520 (p) REVERT: B 158 MET cc_start: 0.6421 (ppp) cc_final: 0.6153 (ppp) REVERT: B 214 MET cc_start: 0.8267 (mtp) cc_final: 0.7828 (tmm) REVERT: B 441 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8243 (pt) REVERT: B 814 ASN cc_start: 0.9421 (t0) cc_final: 0.8967 (t0) REVERT: B 952 MET cc_start: 0.9306 (tpp) cc_final: 0.8808 (tpp) REVERT: B 1244 ASP cc_start: 0.9222 (t70) cc_final: 0.8643 (t0) REVERT: C 158 MET cc_start: 0.8377 (pmm) cc_final: 0.8172 (pmm) REVERT: C 427 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.9123 (p) outliers start: 49 outliers final: 36 residues processed: 85 average time/residue: 0.2995 time to fit residues: 46.9100 Evaluate side-chains 82 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 41 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 961 MET Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 269 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 211 optimal weight: 0.1980 chunk 82 optimal weight: 6.9990 chunk 243 optimal weight: 8.9990 chunk 254 optimal weight: 6.9990 chunk 268 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 GLN A 996 GLN A1109 GLN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25341 Z= 0.171 Angle : 0.601 10.047 34479 Z= 0.272 Chirality : 0.047 0.538 4338 Planarity : 0.003 0.054 4257 Dihedral : 10.585 104.186 5657 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.77 % Allowed : 11.91 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2952 helix: 2.11 (0.20), residues: 684 sheet: -0.40 (0.21), residues: 588 loop : -0.38 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 65 HIS 0.003 0.000 HIS A 429 PHE 0.009 0.001 PHE A 347 TYR 0.011 0.001 TYR B 675 ARG 0.007 0.000 ARG A 994 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 42 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8746 (pmm) cc_final: 0.8468 (pmm) REVERT: A 214 MET cc_start: 0.8552 (tpp) cc_final: 0.7756 (tmm) REVERT: A 231 THR cc_start: 0.7645 (OUTLIER) cc_final: 0.7432 (m) REVERT: A 435 VAL cc_start: 0.8621 (m) cc_final: 0.8347 (p) REVERT: A 492 LEU cc_start: 0.8947 (mm) cc_final: 0.8695 (tp) REVERT: A 757 CYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8094 (m) REVERT: A 814 ASN cc_start: 0.9430 (t0) cc_final: 0.9104 (t0) REVERT: A 952 MET cc_start: 0.9146 (mtp) cc_final: 0.8899 (mtm) REVERT: A 1136 ASP cc_start: 0.8546 (m-30) cc_final: 0.8283 (p0) REVERT: A 1209 MET cc_start: 0.9326 (mtt) cc_final: 0.9116 (mtp) REVERT: B 46 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7498 (p) REVERT: B 158 MET cc_start: 0.6279 (ppp) cc_final: 0.6018 (ppp) REVERT: B 214 MET cc_start: 0.8263 (mtp) cc_final: 0.7759 (tmm) REVERT: B 441 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8220 (pt) REVERT: B 814 ASN cc_start: 0.9408 (t0) cc_final: 0.8899 (t0) REVERT: B 952 MET cc_start: 0.9300 (tpp) cc_final: 0.8797 (tpp) REVERT: B 1244 ASP cc_start: 0.9207 (t70) cc_final: 0.8645 (t0) REVERT: C 427 THR cc_start: 0.9443 (OUTLIER) cc_final: 0.9128 (p) outliers start: 46 outliers final: 37 residues processed: 85 average time/residue: 0.2801 time to fit residues: 43.9029 Evaluate side-chains 84 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 42 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 961 MET Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.8980 chunk 284 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 chunk 198 optimal weight: 8.9990 chunk 298 optimal weight: 0.3980 chunk 275 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 979 GLN A1109 GLN B1128 GLN C 71 HIS ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25341 Z= 0.145 Angle : 0.595 10.050 34479 Z= 0.269 Chirality : 0.046 0.513 4338 Planarity : 0.003 0.053 4257 Dihedral : 10.182 103.671 5657 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.66 % Allowed : 12.29 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2952 helix: 2.12 (0.20), residues: 693 sheet: -0.25 (0.21), residues: 612 loop : -0.36 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 65 HIS 0.005 0.000 HIS C 157 PHE 0.009 0.001 PHE A 347 TYR 0.011 0.001 TYR B 675 ARG 0.004 0.000 ARG A 994 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 42 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8723 (pmm) cc_final: 0.8439 (pmm) REVERT: A 214 MET cc_start: 0.8563 (tpp) cc_final: 0.7752 (tmm) REVERT: A 231 THR cc_start: 0.7608 (OUTLIER) cc_final: 0.7388 (m) REVERT: A 435 VAL cc_start: 0.8632 (m) cc_final: 0.8371 (p) REVERT: A 492 LEU cc_start: 0.8933 (mm) cc_final: 0.8690 (tp) REVERT: A 757 CYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8099 (m) REVERT: A 814 ASN cc_start: 0.9404 (t0) cc_final: 0.9065 (t0) REVERT: A 1136 ASP cc_start: 0.8544 (m-30) cc_final: 0.8191 (m-30) REVERT: B 158 MET cc_start: 0.6396 (ppp) cc_final: 0.6125 (ppp) REVERT: B 214 MET cc_start: 0.8236 (mtp) cc_final: 0.7724 (tmm) REVERT: B 441 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8176 (pt) REVERT: B 814 ASN cc_start: 0.9379 (t0) cc_final: 0.8871 (t0) REVERT: B 952 MET cc_start: 0.9304 (tpp) cc_final: 0.8798 (tpp) REVERT: B 1244 ASP cc_start: 0.9176 (t70) cc_final: 0.8623 (t0) REVERT: C 427 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.9115 (p) outliers start: 43 outliers final: 35 residues processed: 82 average time/residue: 0.2869 time to fit residues: 42.9125 Evaluate side-chains 82 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 43 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 961 MET Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 219 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN C 71 HIS ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.048187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.037625 restraints weight = 151069.604| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 4.78 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.274 25341 Z= 0.227 Angle : 0.730 59.199 34479 Z= 0.379 Chirality : 0.048 0.709 4338 Planarity : 0.003 0.053 4257 Dihedral : 10.180 103.691 5657 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.62 % Allowed : 12.41 % Favored : 85.97 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.16), residues: 2952 helix: 2.10 (0.20), residues: 693 sheet: -0.25 (0.21), residues: 612 loop : -0.36 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 65 HIS 0.003 0.000 HIS C 157 PHE 0.009 0.001 PHE A 347 TYR 0.011 0.001 TYR B 675 ARG 0.004 0.000 ARG A 994 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3519.90 seconds wall clock time: 66 minutes 22.68 seconds (3982.68 seconds total)