Starting phenix.real_space_refine (version: dev) on Thu Aug 4 03:57:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cya_27072/08_2022/8cya_27072_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cya_27072/08_2022/8cya_27072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cya_27072/08_2022/8cya_27072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cya_27072/08_2022/8cya_27072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cya_27072/08_2022/8cya_27072_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cya_27072/08_2022/8cya_27072_trim.pdb" } resolution = 2.7 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= 0.028 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 "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4680/modules/chem_data/mon_lib" Total number of atoms: 57833 Number of models: 1 Model: "" Number of chains: 29 Chain: "B" Number of atoms: 16951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 16951 Classifications: {'peptide': 1100} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 16955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 16955 Classifications: {'peptide': 1100} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 16954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 16954 Classifications: {'peptide': 1100} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1932 Classifications: {'peptide': 127} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "E" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1932 Classifications: {'peptide': 127} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "F" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1927 Classifications: {'peptide': 127} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 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: "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: 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: "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: 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: "P" 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: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 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: 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: "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: 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: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 19.63, per 1000 atoms: 0.34 Number of scatterers: 57833 At special positions: 0 Unit cell: (157.176, 162.504, 221.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 129 16.00 O 5928 8.00 N 4884 7.00 C 18957 6.00 H 27935 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 99 " 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " 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 Z 2 " - " BMA Z 3 " BETA1-6 " NAG P 1 " - " FUC P 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG X 1 " - " FUC X 3 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 165 " " NAG A1306 " - " ASN A 282 " " NAG B1303 " - " ASN B 616 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 234 " " NAG B1308 " - " ASN B 165 " " NAG B1310 " - " ASN B 122 " " NAG B1312 " - " ASN B 17 " " NAG C1301 " - " ASN C 17 " " NAG C1305 " - " ASN C 234 " " NAG G 1 " - " ASN B1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 709 " " NAG L 1 " - " ASN B 331 " " NAG O 1 " - " ASN A 717 " " NAG R 1 " - " ASN A1134 " " NAG S 1 " - " ASN C 282 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 36.85 Conformation dependent library (CDL) restraints added in 4.0 seconds 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6852 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 55 sheets defined 22.9% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 336 through 342 removed outlier: 3.787A pdb=" N GLU B 340 " --> pdb=" O CYS B 336 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.558A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.717A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.881A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 853 removed outlier: 3.589A pdb=" N GLN B 853 " --> pdb=" O ILE B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.950A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.578A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.515A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.404A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.556A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.101A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.625A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.543A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 638 removed outlier: 3.546A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.747A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 854 removed outlier: 4.154A pdb=" N LYS A 854 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.986A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.583A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.525A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.377A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 336 through 343 removed outlier: 4.250A pdb=" N GLU C 340 " --> pdb=" O CYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 removed outlier: 4.343A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.905A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.563A pdb=" N ILE C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 638 removed outlier: 3.718A pdb=" N THR C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.717A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 853 removed outlier: 3.543A pdb=" N GLN C 853 " --> pdb=" O ILE C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.969A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.587A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.399A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.745A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 68 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'E' and resid 65 through 68 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'F' and resid 65 through 68 Processing helix chain 'F' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.837A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.025A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.884A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.525A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 157 removed outlier: 6.567A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.966A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.055A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE B 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.996A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 376 through 378 removed outlier: 3.858A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.723A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.002A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.602A pdb=" N LYS A 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.860A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1047 through 1050 removed outlier: 5.356A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AB8, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.999A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.781A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.560A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.621A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.543A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 141 through 146 removed outlier: 6.778A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AC6, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.353A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.058A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 378 through 379 removed outlier: 3.904A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 402 through 403 Processing sheet with id=AD1, first strand: chain 'A' and resid 553 through 554 removed outlier: 4.216A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.029A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.638A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.111A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1047 through 1050 removed outlier: 5.388A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AD7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.510A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 28 removed outlier: 3.823A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.974A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.964A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 151 through 157 removed outlier: 6.761A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N TYR C 145 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 259 " --> pdb=" O HIS C 245 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.491A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.938A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.938A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.034A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.509A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.767A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.074A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.074A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.028A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N SER E 126 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.028A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N SER E 126 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.095A pdb=" N GLY F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N SER F 126 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL F 12 " --> pdb=" O SER F 126 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.095A pdb=" N GLY F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N SER F 126 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL F 12 " --> pdb=" O SER F 126 " (cutoff:3.500A) 1064 hydrogen bonds defined for protein. 2826 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: 23.85 Time building geometry restraints manager: 38.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 27920 1.03 - 1.23: 16 1.23 - 1.42: 13046 1.42 - 1.62: 17361 1.62 - 1.82: 165 Bond restraints: 58508 Sorted by residual: bond pdb=" CB ASN A1134 " pdb=" CG ASN A1134 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.64e+00 bond pdb=" CB ASN B1134 " pdb=" CG ASN B1134 " ideal model delta sigma weight residual 1.516 1.561 -0.045 2.50e-02 1.60e+03 3.30e+00 bond pdb=" ND2 ASN A1134 " pdb="HD22 ASN A1134 " ideal model delta sigma weight residual 0.860 0.829 0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C1 BMA T 3 " pdb=" C2 BMA T 3 " ideal model delta sigma weight residual 1.538 1.590 -0.052 3.60e-02 7.72e+02 2.08e+00 bond pdb=" ND2 ASN B1134 " pdb="HD22 ASN B1134 " ideal model delta sigma weight residual 0.860 0.832 0.028 2.00e-02 2.50e+03 1.94e+00 ... (remaining 58503 not shown) Histogram of bond angle deviations from ideal: 73.17 - 88.62: 44 88.62 - 104.07: 385 104.07 - 119.52: 79354 119.52 - 134.97: 24984 134.97 - 150.42: 18 Bond angle restraints: 104785 Sorted by residual: angle pdb="HD21 ASN A 122 " pdb=" ND2 ASN A 122 " pdb="HD22 ASN A 122 " ideal model delta sigma weight residual 120.00 73.17 46.83 3.00e+00 1.11e-01 2.44e+02 angle pdb=" CG ASN A 122 " pdb=" ND2 ASN A 122 " pdb="HD22 ASN A 122 " ideal model delta sigma weight residual 120.00 73.39 46.61 3.00e+00 1.11e-01 2.41e+02 angle pdb="HD21 ASN A 61 " pdb=" ND2 ASN A 61 " pdb="HD22 ASN A 61 " ideal model delta sigma weight residual 120.00 73.43 46.57 3.00e+00 1.11e-01 2.41e+02 angle pdb="HD21 ASN B1134 " pdb=" ND2 ASN B1134 " pdb="HD22 ASN B1134 " ideal model delta sigma weight residual 120.00 73.46 46.54 3.00e+00 1.11e-01 2.41e+02 angle pdb="HD21 ASN A1134 " pdb=" ND2 ASN A1134 " pdb="HD22 ASN A1134 " ideal model delta sigma weight residual 120.00 73.52 46.48 3.00e+00 1.11e-01 2.40e+02 ... (remaining 104780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.39: 23109 22.39 - 44.78: 730 44.78 - 67.17: 79 67.17 - 89.56: 35 89.56 - 111.95: 11 Dihedral angle restraints: 23964 sinusoidal: 11112 harmonic: 12852 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -173.88 87.88 1 1.00e+01 1.00e-02 9.25e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 173.79 -80.79 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" C2 NAG A1307 " pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " pdb=" C5 NAG A1307 " ideal model delta sinusoidal sigma weight residual -50.00 61.95 -111.95 1 2.00e+01 2.50e-03 3.30e+01 ... (remaining 23961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 4895 0.126 - 0.252: 21 0.252 - 0.378: 0 0.378 - 0.505: 0 0.505 - 0.631: 1 Chirality restraints: 4917 Sorted by residual: chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.94e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 4914 not shown) Planarity restraints: 8789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 81 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO B 82 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 156 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C GLU A 156 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU A 156 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A 157 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 156 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C GLU B 156 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU B 156 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE B 157 " 0.009 2.00e-02 2.50e+03 ... (remaining 8786 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 3038 2.19 - 2.79: 117304 2.79 - 3.40: 159054 3.40 - 4.00: 211377 4.00 - 4.60: 323508 Nonbonded interactions: 814281 Sorted by model distance: nonbonded pdb=" HE ARG B 905 " pdb=" O LEU B1049 " model vdw 1.588 1.850 nonbonded pdb=" HG1 THR B 716 " pdb=" OD1 ASN B 717 " model vdw 1.613 1.850 nonbonded pdb=" OG1 THR C1105 " pdb=" H GLU C1111 " model vdw 1.628 1.850 nonbonded pdb=" OG1 THR A1105 " pdb=" H GLU A1111 " model vdw 1.629 1.850 nonbonded pdb=" O ILE C 100 " pdb=" H ALA C 243 " model vdw 1.631 1.850 ... (remaining 814276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 123 through 233 or (resid 234 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 235 \ through 281 or (resid 282 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 \ or name HD21)) or resid 283 through 330 or (resid 331 and (name N or name CA or \ name C or name O or name CB or name CG or name OD1 or name ND2 or name H or nam \ e HA or name HB2 or name HB3 or name HD21)) or resid 332 through 475 or (resid 4 \ 76 and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid \ 477 through 615 or (resid 616 and (name N or name CA or name C or name O or nam \ e CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name \ HB3 or name HD21)) or resid 617 through 716 or (resid 717 and (name N or name C \ A or name C or name O or name CB or name CG or name OD1 or name ND2 or name H or \ name HA or name HB2 or name HB3 or name HD21)) or resid 718 through 1073 or (re \ sid 1074 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or \ resid 1075 through 1147 or resid 1301 through 1309)) selection = (chain 'B' and (resid 15 through 281 or (resid 282 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 283 through 486 or (resid 487 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame ND2 or name H or name HA or name HB2 or name HB3)) or resid 488 through 1073 \ or (resid 1074 and (name N or name CA or name C or name O or name CB or name CG \ or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD \ 21)) or resid 1075 through 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 15 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 123 through 330 or (resid 331 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 332 \ through 475 or (resid 476 and (name N or name CA or name C or name O or name HA \ 2 or name HA3)) or resid 477 through 486 or (resid 487 and (name N or name CA or \ name C or name O or name CB or name CG or name OD1 or name ND2 or name H or nam \ e HA or name HB2 or name HB3)) or resid 488 through 615 or (resid 616 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 o \ r name H or name HA or name HB2 or name HB3 or name HD21)) or resid 617 through \ 716 or (resid 717 and (name N or name CA or name C or name O or name CB or name \ CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name \ HD21)) or resid 718 through 1147 or resid 1301 through 1309)) } ncs_group { reference = (chain 'D' and (resid 1 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 53 or (re \ sid 54 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or r \ esid 55 through 105 or (resid 106 and (name N or name CA or name C or name O or \ name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 o \ r name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or \ name HD13)) or resid 107 or (resid 108 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 109 through 127)) selection = (chain 'E' and (resid 1 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 53 or (re \ sid 54 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or r \ esid 55 through 105 or (resid 106 and (name N or name CA or name C or name O or \ name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 o \ r name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or \ name HD13)) or resid 107 or (resid 108 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 109 through 127)) selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 5 Type Number sf(0) Gaussians S 129 5.16 5 C 18957 2.51 5 N 4884 2.21 5 O 5928 1.98 5 H 27935 0.53 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=0.00 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.640 Extract box with map and model: 10.230 Check model and map are aligned: 0.620 Convert atoms to be neutral: 0.370 Process input model: 139.180 Find NCS groups from input model: 2.630 Set up NCS constraints: 0.270 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:9.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 : 0.002 0.052 30573 Z= 0.137 Angle : 0.438 5.500 41614 Z= 0.246 Chirality : 0.041 0.631 4917 Planarity : 0.003 0.072 5271 Dihedral : 11.931 111.949 11072 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.79 % Favored : 95.02 % Rotamer Outliers : 0.06 % 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: 0.52 (0.15), residues: 3657 helix: 3.26 (0.21), residues: 630 sheet: 0.02 (0.19), residues: 879 loop : -0.38 (0.14), residues: 2148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 3.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 151 average time/residue: 1.5532 time to fit residues: 302.0979 Evaluate side-chains 116 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 3.391 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 4.2999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 3.9990 chunk 277 optimal weight: 0.4980 chunk 153 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 286 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 332 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 30573 Z= 0.320 Angle : 0.496 4.941 41614 Z= 0.265 Chirality : 0.042 0.464 4917 Planarity : 0.003 0.065 5271 Dihedral : 6.732 109.941 4562 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.39 % Favored : 94.42 % Rotamer Outliers : 0.38 % 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: 0.20 (0.15), residues: 3657 helix: 2.79 (0.20), residues: 654 sheet: -0.14 (0.19), residues: 870 loop : -0.59 (0.14), residues: 2133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 129 average time/residue: 1.5490 time to fit residues: 258.4390 Evaluate side-chains 112 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 3.360 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.9031 time to fit residues: 10.8405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 276 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 332 optimal weight: 20.0000 chunk 359 optimal weight: 0.0770 chunk 296 optimal weight: 0.7980 chunk 330 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 267 optimal weight: 50.0000 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 30573 Z= 0.194 Angle : 0.436 5.449 41614 Z= 0.229 Chirality : 0.041 0.508 4917 Planarity : 0.003 0.075 5271 Dihedral : 6.669 111.000 4562 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.48 % Favored : 95.32 % Rotamer Outliers : 0.35 % 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: 0.25 (0.15), residues: 3657 helix: 2.95 (0.20), residues: 636 sheet: 0.00 (0.19), residues: 837 loop : -0.62 (0.14), residues: 2184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 3.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 119 average time/residue: 1.5341 time to fit residues: 240.2725 Evaluate side-chains 112 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 3.377 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.8902 time to fit residues: 9.5952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 0.9980 chunk 250 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 chunk 334 optimal weight: 40.0000 chunk 353 optimal weight: 50.0000 chunk 174 optimal weight: 0.4980 chunk 316 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 30573 Z= 0.293 Angle : 0.473 5.270 41614 Z= 0.251 Chirality : 0.042 0.474 4917 Planarity : 0.003 0.046 5271 Dihedral : 6.790 110.285 4562 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.63 % Favored : 94.18 % Rotamer Outliers : 0.47 % 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 (0.14), residues: 3657 helix: 2.62 (0.20), residues: 651 sheet: -0.25 (0.19), residues: 834 loop : -0.73 (0.13), residues: 2172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 3.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 113 average time/residue: 1.4648 time to fit residues: 219.0074 Evaluate side-chains 106 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 3.369 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.7820 time to fit residues: 9.1083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 263 optimal weight: 20.0000 chunk 145 optimal weight: 30.0000 chunk 301 optimal weight: 1.9990 chunk 244 optimal weight: 30.0000 chunk 0 optimal weight: 9.9990 chunk 180 optimal weight: 0.9980 chunk 317 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 30573 Z= 0.199 Angle : 0.443 4.953 41614 Z= 0.233 Chirality : 0.041 0.486 4917 Planarity : 0.003 0.042 5271 Dihedral : 6.763 110.708 4562 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.57 % Favored : 95.24 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3657 helix: 2.69 (0.20), residues: 651 sheet: -0.17 (0.19), residues: 858 loop : -0.69 (0.14), residues: 2148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 114 average time/residue: 1.5061 time to fit residues: 227.5136 Evaluate side-chains 109 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 3.379 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 1.3962 time to fit residues: 9.8220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 4.9990 chunk 318 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 354 optimal weight: 40.0000 chunk 293 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 ASN B1005 GLN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 30573 Z= 0.240 Angle : 0.454 6.505 41614 Z= 0.240 Chirality : 0.041 0.472 4917 Planarity : 0.003 0.042 5271 Dihedral : 6.791 110.586 4562 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.20 % Favored : 94.61 % Rotamer Outliers : 0.50 % 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 (0.15), residues: 3657 helix: 2.66 (0.20), residues: 651 sheet: -0.19 (0.19), residues: 912 loop : -0.68 (0.14), residues: 2094 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 3.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 112 average time/residue: 1.4985 time to fit residues: 222.1833 Evaluate side-chains 112 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 3.404 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.8001 time to fit residues: 9.2863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 50.0000 chunk 39 optimal weight: 30.0000 chunk 201 optimal weight: 0.7980 chunk 258 optimal weight: 20.0000 chunk 200 optimal weight: 0.5980 chunk 298 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 352 optimal weight: 50.0000 chunk 220 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 30573 Z= 0.194 Angle : 0.442 5.902 41614 Z= 0.233 Chirality : 0.041 0.474 4917 Planarity : 0.003 0.077 5271 Dihedral : 6.782 110.722 4562 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.76 % Favored : 95.05 % Rotamer Outliers : 0.57 % 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: 0.10 (0.15), residues: 3657 helix: 2.77 (0.20), residues: 645 sheet: -0.20 (0.19), residues: 912 loop : -0.67 (0.14), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 115 average time/residue: 1.4324 time to fit residues: 216.9625 Evaluate side-chains 116 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 3.326 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 5 average time/residue: 0.7596 time to fit residues: 10.0434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 277 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 30573 Z= 0.236 Angle : 0.457 7.351 41614 Z= 0.240 Chirality : 0.041 0.468 4917 Planarity : 0.003 0.067 5271 Dihedral : 6.808 110.655 4562 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.36 % Favored : 94.45 % Rotamer Outliers : 0.44 % 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: 0.04 (0.15), residues: 3657 helix: 2.72 (0.20), residues: 645 sheet: -0.25 (0.19), residues: 912 loop : -0.70 (0.14), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 4.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 111 average time/residue: 1.5293 time to fit residues: 227.0981 Evaluate side-chains 113 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 3.406 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.9321 time to fit residues: 8.5098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 0.9980 chunk 337 optimal weight: 40.0000 chunk 308 optimal weight: 0.9980 chunk 328 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 143 optimal weight: 20.0000 chunk 258 optimal weight: 20.0000 chunk 100 optimal weight: 0.7980 chunk 297 optimal weight: 0.9980 chunk 310 optimal weight: 1.9990 chunk 327 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 30573 Z= 0.175 Angle : 0.443 7.240 41614 Z= 0.232 Chirality : 0.041 0.470 4917 Planarity : 0.003 0.061 5271 Dihedral : 6.787 110.791 4562 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.79 % Favored : 95.02 % Rotamer Outliers : 0.47 % 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: 0.11 (0.15), residues: 3657 helix: 2.79 (0.20), residues: 645 sheet: -0.22 (0.19), residues: 912 loop : -0.65 (0.14), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 3.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 112 average time/residue: 1.6158 time to fit residues: 242.0958 Evaluate side-chains 112 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 3.530 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 1.0919 time to fit residues: 9.1296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 1.9990 chunk 347 optimal weight: 30.0000 chunk 212 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 241 optimal weight: 0.3980 chunk 364 optimal weight: 40.0000 chunk 335 optimal weight: 4.9990 chunk 290 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 30573 Z= 0.187 Angle : 0.445 6.964 41614 Z= 0.233 Chirality : 0.041 0.470 4917 Planarity : 0.003 0.059 5271 Dihedral : 6.781 110.805 4562 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.00 % Favored : 94.80 % Rotamer Outliers : 0.44 % 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: 0.11 (0.15), residues: 3657 helix: 2.80 (0.20), residues: 645 sheet: -0.25 (0.18), residues: 921 loop : -0.64 (0.14), residues: 2091 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue TYR 489 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 3.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 112 average time/residue: 1.4451 time to fit residues: 213.9192 Evaluate side-chains 111 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 3.412 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 1.0354 time to fit residues: 7.1976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 5.9990 chunk 309 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 267 optimal weight: 40.0000 chunk 42 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 290 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 298 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 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 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.134047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.086539 restraints weight = 235296.782| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.02 r_work: 0.3432 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work: 0.3405 rms_B_bonded: 2.80 restraints_weight: 0.1250 r_work: 0.3390 rms_B_bonded: 2.88 restraints_weight: 0.0625 r_work: 0.3374 rms_B_bonded: 3.00 restraints_weight: 0.0312 r_work: 0.3357 rms_B_bonded: 3.18 restraints_weight: 0.0156 r_work: 0.3338 rms_B_bonded: 3.41 restraints_weight: 0.0078 r_work: 0.3317 rms_B_bonded: 3.70 restraints_weight: 0.0039 r_work: 0.3294 rms_B_bonded: 4.07 restraints_weight: 0.0020 r_work: 0.3269 rms_B_bonded: 4.53 restraints_weight: 0.0010 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4382 r_free = 0.4382 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4382 r_free = 0.4382 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 30573 Z= 0.290 Angle : 0.475 7.369 41614 Z= 0.252 Chirality : 0.042 0.463 4917 Planarity : 0.003 0.058 5271 Dihedral : 6.850 110.576 4562 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.44 % Favored : 94.39 % Rotamer Outliers : 0.53 % 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: -0.02 (0.14), residues: 3657 helix: 2.65 (0.20), residues: 645 sheet: -0.34 (0.18), residues: 921 loop : -0.71 (0.14), residues: 2091 =============================================================================== Job complete usr+sys time: 7567.94 seconds wall clock time: 134 minutes 1.65 seconds (8041.65 seconds total)