Starting phenix.real_space_refine (version: dev) on Sun Sep 4 13:53:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6s_33646/09_2022/7y6s_33646.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6s_33646/09_2022/7y6s_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_33646/09_2022/7y6s_33646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6s_33646/09_2022/7y6s_33646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6s_33646/09_2022/7y6s_33646.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6s_33646/09_2022/7y6s_33646.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 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 Convert atoms to be neutral 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4709/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: 2 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: 5 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: 1 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "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 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: 1 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: 2 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: 5 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: 1 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: 1 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 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: 1 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 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: 1 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 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: 1 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 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: 1 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: 2 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: 5 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: 1 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: 1 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 chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "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 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 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 chiralities: 4 Time building chain proxies: 13.89, per 1000 atoms: 0.56 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: 13.07 Conformation dependent library (CDL) restraints added in 3.7 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: 1.93 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: 10.68 Time building geometry restraints manager: 13.88 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=" 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 bond pdb=" N SER B 506 " pdb=" CA SER B 506 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.33e-02 5.65e+03 4.68e+00 bond pdb=" N THR B 639 " pdb=" CA THR B 639 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.43e+00 bond pdb=" N VAL B 638 " pdb=" CA VAL B 638 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.426 1.479 -0.053 3.20e-02 9.77e+02 2.78e+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=" C2 NAG J 1 " pdb=" N2 NAG J 1 " pdb=" C7 NAG J 1 " ideal model delta sigma weight residual 123.12 129.53 -6.41 1.28e+00 6.08e-01 2.50e+01 angle pdb=" C2 NAG V 1 " pdb=" N2 NAG V 1 " pdb=" C7 NAG V 1 " ideal model delta sigma weight residual 123.12 129.34 -6.22 1.28e+00 6.08e-01 2.35e+01 angle pdb=" C2 NAG V 2 " pdb=" N2 NAG V 2 " pdb=" C7 NAG V 2 " ideal model delta sigma weight residual 123.12 129.16 -6.04 1.28e+00 6.08e-01 2.22e+01 angle pdb=" C2 NAG h 1 " pdb=" N2 NAG h 1 " pdb=" C7 NAG h 1 " ideal model delta sigma weight residual 123.12 129.12 -6.00 1.28e+00 6.08e-01 2.19e+01 angle pdb=" C2 NAG l 2 " pdb=" N2 NAG l 2 " pdb=" C7 NAG l 2 " ideal model delta sigma weight residual 123.12 129.05 -5.93 1.28e+00 6.08e-01 2.14e+01 ... (remaining 34474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.95: 13942 20.95 - 41.91: 742 41.91 - 62.86: 115 62.86 - 83.82: 38 83.82 - 104.77: 34 Dihedral angle restraints: 14871 sinusoidal: 6141 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=" C2 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" C4 NAG G 1 " pdb=" C5 NAG G 1 " ideal model delta sinusoidal sigma weight residual 50.00 -54.77 104.77 1 2.00e+01 2.50e-03 3.01e+01 dihedral pdb=" C2 NAG e 1 " pdb=" C3 NAG e 1 " pdb=" C4 NAG e 1 " pdb=" C5 NAG e 1 " ideal model delta sinusoidal sigma weight residual 50.00 -54.66 104.66 1 2.00e+01 2.50e-03 3.01e+01 ... (remaining 14868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 4317 0.188 - 0.377: 15 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 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. 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: 2.450 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: 0.030 Extract box with map and model: 11.930 Check model and map are aligned: 0.390 Convert atoms to be neutral: 0.230 Process input model: 70.250 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 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 : 0.003 0.053 25341 Z= 0.208 Angle : 0.602 8.541 34479 Z= 0.333 Chirality : 0.053 0.942 4338 Planarity : 0.004 0.053 4257 Dihedral : 14.295 104.770 9231 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.34 % Favored : 95.53 % Rotamer Outliers : 0.31 % 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 *********************** 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 : 2.899 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 63 average time/residue: 0.3587 time to fit residues: 39.6978 Evaluate side-chains 44 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 2.937 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2141 time to fit residues: 4.8647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 77 optimal weight: 5.9990 chunk 153 optimal weight: 0.4980 chunk 121 optimal weight: 0.0470 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: 0.6280 ------------------------------------------------------------------------------- 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** ** C1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 25341 Z= 0.179 Angle : 0.558 7.348 34479 Z= 0.310 Chirality : 0.051 0.944 4338 Planarity : 0.004 0.063 4257 Dihedral : 9.660 104.909 4098 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.10 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.31 (0.15), residues: 2952 helix: 1.20 (0.20), residues: 693 sheet: -0.66 (0.20), residues: 609 loop : -0.59 (0.15), residues: 1650 *********************** 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 42 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 3.157 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.3195 time to fit residues: 25.8636 Evaluate side-chains 38 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 2.723 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2711 time to fit residues: 4.3863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 185 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 272 optimal weight: 3.9990 chunk 294 optimal weight: 0.0070 chunk 243 optimal weight: 9.9990 chunk 270 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 25341 Z= 0.200 Angle : 0.523 10.248 34479 Z= 0.291 Chirality : 0.049 0.884 4338 Planarity : 0.004 0.064 4257 Dihedral : 9.566 104.579 4098 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.54 % 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: 1.59 (0.20), residues: 693 sheet: -0.66 (0.20), residues: 591 loop : -0.48 (0.15), residues: 1668 *********************** 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 54 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 51 average time/residue: 0.3103 time to fit residues: 31.1201 Evaluate side-chains 44 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 3.032 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.2190 time to fit residues: 6.9029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 289 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 259 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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** C 205 GLN C1057 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.054 25341 Z= 0.493 Angle : 0.660 9.776 34479 Z= 0.355 Chirality : 0.051 0.892 4338 Planarity : 0.004 0.066 4257 Dihedral : 9.836 104.742 4098 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 1.04 % 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: -0.24 (0.16), residues: 2952 helix: 1.47 (0.20), residues: 684 sheet: -0.80 (0.20), residues: 612 loop : -0.56 (0.16), residues: 1656 *********************** 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 63 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 36 time to evaluate : 3.156 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 63 average time/residue: 0.3079 time to fit residues: 37.0235 Evaluate side-chains 48 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 34 time to evaluate : 3.079 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2210 time to fit residues: 10.0138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 C1057 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 25341 Z= 0.223 Angle : 0.535 8.406 34479 Z= 0.297 Chirality : 0.049 0.884 4338 Planarity : 0.003 0.063 4257 Dihedral : 9.687 105.186 4098 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.02 (0.16), residues: 2952 helix: 1.76 (0.20), residues: 684 sheet: -0.64 (0.21), residues: 588 loop : -0.49 (0.15), residues: 1680 *********************** 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 50 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 35 time to evaluate : 2.937 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 49 average time/residue: 0.3191 time to fit residues: 29.8329 Evaluate side-chains 42 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 2.790 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2098 time to fit residues: 6.4925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 290 optimal weight: 0.1980 chunk 240 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 152 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 497 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.058 25341 Z= 0.158 Angle : 0.510 8.804 34479 Z= 0.284 Chirality : 0.048 0.840 4338 Planarity : 0.003 0.059 4257 Dihedral : 9.511 104.838 4098 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2952 helix: 1.91 (0.20), residues: 693 sheet: -0.51 (0.21), residues: 588 loop : -0.44 (0.16), residues: 1671 *********************** 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 51 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 50 average time/residue: 0.3285 time to fit residues: 31.1828 Evaluate side-chains 42 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 2.837 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2045 time to fit residues: 5.9670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 165 optimal weight: 0.7980 chunk 211 optimal weight: 0.0070 chunk 164 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 162 optimal weight: 0.6980 chunk 289 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 overall best weight: 2.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 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 : 0.004 0.049 25341 Z= 0.294 Angle : 0.543 8.681 34479 Z= 0.298 Chirality : 0.048 0.822 4338 Planarity : 0.003 0.058 4257 Dihedral : 9.563 104.466 4098 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.77 % 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: 1.98 (0.20), residues: 684 sheet: -0.51 (0.21), residues: 582 loop : -0.46 (0.16), residues: 1686 *********************** 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 55 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 35 time to evaluate : 3.139 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 54 average time/residue: 0.3519 time to fit residues: 34.7990 Evaluate side-chains 45 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 34 time to evaluate : 2.838 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2732 time to fit residues: 8.9348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 0.9990 chunk 115 optimal weight: 0.0370 chunk 172 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 196 optimal weight: 0.0170 chunk 142 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 263 optimal weight: 7.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 25341 Z= 0.188 Angle : 0.519 8.671 34479 Z= 0.286 Chirality : 0.048 0.813 4338 Planarity : 0.003 0.058 4257 Dihedral : 9.502 104.264 4098 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2952 helix: 2.03 (0.20), residues: 684 sheet: -0.48 (0.21), residues: 588 loop : -0.43 (0.16), residues: 1680 *********************** 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 43 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 3.153 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 42 average time/residue: 0.3375 time to fit residues: 27.8802 Evaluate side-chains 40 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 3.115 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2367 time to fit residues: 5.9129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.9990 chunk 252 optimal weight: 0.8980 chunk 269 optimal weight: 0.1980 chunk 276 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 117 optimal weight: 0.0020 chunk 211 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 243 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 chunk 268 optimal weight: 4.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 ASN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.121 25341 Z= 0.174 Angle : 0.516 13.735 34479 Z= 0.286 Chirality : 0.048 0.795 4338 Planarity : 0.003 0.056 4257 Dihedral : 9.629 104.066 4098 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.22 (0.16), residues: 2952 helix: 1.99 (0.20), residues: 693 sheet: -0.41 (0.21), residues: 588 loop : -0.40 (0.16), residues: 1671 *********************** 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 44 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 44 average time/residue: 0.3538 time to fit residues: 29.4529 Evaluate side-chains 39 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 2.924 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2274 time to fit residues: 4.7919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.0570 chunk 284 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 chunk 298 optimal weight: 0.9990 chunk 275 optimal weight: 0.6980 chunk 237 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1128 GLN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.076 25341 Z= 0.163 Angle : 0.508 11.656 34479 Z= 0.281 Chirality : 0.047 0.760 4338 Planarity : 0.003 0.056 4257 Dihedral : 9.621 103.634 4098 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.15 % 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: 0.28 (0.16), residues: 2952 helix: 2.00 (0.20), residues: 693 sheet: -0.25 (0.21), residues: 612 loop : -0.40 (0.16), residues: 1647 ********************** 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 44 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 43 average time/residue: 0.3811 time to fit residues: 30.3862 Evaluate side-chains 39 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 3.081 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2649 time to fit residues: 5.0919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 72 optimal weight: 6.9990 chunk 219 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 238 optimal weight: 0.9980 chunk 99 optimal weight: 0.2980 chunk 244 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 988 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.046988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.036298 restraints weight = 152501.482| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 4.79 r_work: 0.2906 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work: 0.2892 rms_B_bonded: 4.49 restraints_weight: 0.1250 r_work: 0.2884 rms_B_bonded: 4.50 restraints_weight: 0.0625 r_work: 0.2877 rms_B_bonded: 4.53 restraints_weight: 0.0312 r_work: 0.2869 rms_B_bonded: 4.58 restraints_weight: 0.0156 r_work: 0.2862 rms_B_bonded: 4.63 restraints_weight: 0.0078 r_work: 0.2854 rms_B_bonded: 4.70 restraints_weight: 0.0039 r_work: 0.2846 rms_B_bonded: 4.78 restraints_weight: 0.0020 r_work: 0.2839 rms_B_bonded: 4.87 restraints_weight: 0.0010 r_work: 0.2831 rms_B_bonded: 4.97 restraints_weight: 0.0005 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 25341 Z= 0.279 Angle : 0.537 9.270 34479 Z= 0.295 Chirality : 0.047 0.751 4338 Planarity : 0.003 0.054 4257 Dihedral : 9.730 107.020 4098 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.23 (0.16), residues: 2952 helix: 2.07 (0.20), residues: 684 sheet: -0.42 (0.21), residues: 588 loop : -0.41 (0.16), residues: 1680 =============================================================================== Job complete usr+sys time: 3176.65 seconds wall clock time: 61 minutes 15.61 seconds (3675.61 seconds total)