Starting phenix.real_space_refine on Wed Feb 21 08:00:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej4_30669/02_2024/7ej4_30669.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej4_30669/02_2024/7ej4_30669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej4_30669/02_2024/7ej4_30669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej4_30669/02_2024/7ej4_30669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej4_30669/02_2024/7ej4_30669.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej4_30669/02_2024/7ej4_30669.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 19057 2.51 5 N 4886 2.21 5 O 5962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 73": "OD1" <-> "OD2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30040 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 7872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7872 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 50, 'TRANS': 957} Chain breaks: 8 Chain: "B" Number of atoms: 7986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7986 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 51, 'TRANS': 970} Chain breaks: 7 Chain: "C" Number of atoms: 7906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7906 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 50, 'TRANS': 960} Chain breaks: 8 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "I" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "M" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "J" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.15, per 1000 atoms: 0.47 Number of scatterers: 30040 At special positions: 0 Unit cell: (139.7, 170.5, 225.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 5962 8.00 N 4886 7.00 C 19057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " 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=2.04 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 B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 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=2.04 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 C 131 " - pdb=" SG CYS C 166 " 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=2.05 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 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=2.02 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 H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 89 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 89 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 234 " " NAG A2005 " - " ASN A 343 " " NAG A2006 " - " ASN A 603 " " NAG A2007 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 165 " " NAG B2004 " - " ASN B 331 " " NAG B2005 " - " ASN B 343 " " NAG B2006 " - " ASN B 603 " " NAG B2007 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 165 " " NAG C2004 " - " ASN C 234 " " NAG C2005 " - " ASN C 343 " " NAG C2006 " - " ASN C 603 " " NAG C2007 " - " ASN C 657 " " NAG D 1 " - " ASN A 282 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 709 " " NAG K 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A1074 " " NAG Q 1 " - " ASN A1098 " " NAG R 1 " - " ASN A1134 " " NAG S 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 282 " " NAG U 1 " - " ASN B 616 " " NAG V 1 " - " ASN B 709 " " NAG W 1 " - " ASN B 717 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B1074 " " NAG Z 1 " - " ASN B1098 " " NAG a 1 " - " ASN B1134 " " NAG b 1 " - " ASN C 282 " " NAG c 1 " - " ASN C 331 " " NAG d 1 " - " ASN C 616 " " NAG e 1 " - " ASN C 709 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 12.15 Conformation dependent library (CDL) restraints added in 5.3 seconds 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6946 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 57 sheets defined 21.6% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.039A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.937A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.843A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.556A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.706A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.524A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.734A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.557A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.968A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.594A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.984A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.579A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) 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: 3.549A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.239A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.870A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.163A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.960A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.247A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 5.697A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 624 removed outlier: 4.430A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 638 removed outlier: 3.890A pdb=" N VAL B 635 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.822A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 4.667A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.602A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.638A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.584A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.602A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 910 " --> pdb=" O PHE B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.427A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 912 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.509A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.907A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.569A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.664A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.224A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 4.074A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.360A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.716A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 removed outlier: 3.820A pdb=" N THR C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 634 through 638' Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.981A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.781A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.861A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (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 982 removed outlier: 3.556A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.207A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.924A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.094A pdb=" N ALA H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.173A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.953A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.163A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 84 removed outlier: 3.540A pdb=" N ASP M 83 " --> pdb=" O GLU M 80 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA M 84 " --> pdb=" O ALA M 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 80 through 84' Processing helix chain 'N' and resid 80 through 84 removed outlier: 4.108A pdb=" N ALA N 84 " --> pdb=" O ALA N 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.778A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.496A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.726A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.649A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.183A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.857A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.561A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL A 395 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER A 514 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 397 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 512 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER A 399 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A 510 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL A 401 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR A 508 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.565A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.791A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.647A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.700A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.781A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.599A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.575A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.507A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.803A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.583A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.246A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 715 through 719 removed outlier: 5.959A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 715 through 719 removed outlier: 5.959A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.615A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.842A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.769A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.921A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.943A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.699A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.663A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.153A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.711A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.677A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AE7, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AE8, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.966A pdb=" N ASN H 59 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.146A pdb=" N SER L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER L 68 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.088A pdb=" N GLU L 106 " --> pdb=" O VAL L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'L' and resid 49 through 50 Processing sheet with id=AF3, first strand: chain 'L' and resid 86 through 87 removed outlier: 3.674A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 19 through 21 Processing sheet with id=AF5, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.545A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AF7, first strand: chain 'M' and resid 12 through 14 removed outlier: 6.684A pdb=" N VAL M 13 " --> pdb=" O LYS M 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'M' and resid 54 through 55 removed outlier: 4.303A pdb=" N ILE M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 19 through 21 Processing sheet with id=AG1, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.822A pdb=" N ASN J 59 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU J 50 " --> pdb=" O ASN J 59 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA J 92 " --> pdb=" O VAL J 114 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL J 114 " --> pdb=" O ALA J 92 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.898A pdb=" N SER N 71 " --> pdb=" O SER N 68 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER N 68 " --> pdb=" O SER N 71 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 10 through 14 removed outlier: 6.073A pdb=" N MET N 11 " --> pdb=" O GLU N 106 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS N 108 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL N 13 " --> pdb=" O LYS N 108 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLN N 38 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU N 47 " --> pdb=" O GLN N 38 " (cutoff:3.500A) 1037 hydrogen bonds defined for protein. 2766 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.73 Time building geometry restraints manager: 12.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9479 1.34 - 1.46: 7680 1.46 - 1.58: 13368 1.58 - 1.70: 0 1.70 - 1.82: 177 Bond restraints: 30704 Sorted by residual: bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C1 NAG h 1 " pdb=" O5 NAG h 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.12e+00 ... (remaining 30699 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.02: 531 105.02 - 112.26: 15692 112.26 - 119.51: 9550 119.51 - 126.76: 15650 126.76 - 134.00: 339 Bond angle restraints: 41762 Sorted by residual: angle pdb=" C PHE C 486 " pdb=" N ASN C 487 " pdb=" CA ASN C 487 " ideal model delta sigma weight residual 122.61 128.22 -5.61 1.56e+00 4.11e-01 1.29e+01 angle pdb=" C PHE B 486 " pdb=" N ASN B 487 " pdb=" CA ASN B 487 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C ASN C 234 " pdb=" N ILE C 235 " pdb=" CA ILE C 235 " ideal model delta sigma weight residual 121.97 128.18 -6.21 1.80e+00 3.09e-01 1.19e+01 angle pdb=" N GLY A 593 " pdb=" CA GLY A 593 " pdb=" C GLY A 593 " ideal model delta sigma weight residual 110.63 115.32 -4.69 1.45e+00 4.76e-01 1.05e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.64 -3.94 1.22e+00 6.72e-01 1.05e+01 ... (remaining 41757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.01: 17639 20.01 - 40.02: 1261 40.02 - 60.03: 243 60.03 - 80.05: 38 80.05 - 100.06: 15 Dihedral angle restraints: 19196 sinusoidal: 8374 harmonic: 10822 Sorted by residual: 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 14.84 78.16 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -164.06 78.06 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 17.74 75.26 1 1.00e+01 1.00e-02 7.16e+01 ... (remaining 19193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 4900 0.140 - 0.280: 33 0.280 - 0.419: 0 0.419 - 0.559: 2 0.559 - 0.699: 1 Chirality restraints: 4936 Sorted by residual: chirality pdb=" C1 NAG j 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG j 1 " pdb=" O5 NAG j 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" C1 NAG A2007 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A2007 " pdb=" O5 NAG A2007 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 4933 not shown) Planarity restraints: 5326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.024 2.00e-02 2.50e+03 2.24e-02 6.30e+00 pdb=" CG ASN B 234 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.022 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO A 521 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.59e+00 pdb=" N PRO C 986 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.026 5.00e-02 4.00e+02 ... (remaining 5323 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 773 2.69 - 3.24: 29027 3.24 - 3.79: 45150 3.79 - 4.35: 56687 4.35 - 4.90: 94410 Nonbonded interactions: 226047 Sorted by model distance: nonbonded pdb=" OG1 THR H 33 " pdb=" O PHE H 99 " model vdw 2.132 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.150 2.440 nonbonded pdb=" OH TYR C 453 " pdb=" OG SER N 31 " model vdw 2.171 2.440 nonbonded pdb=" OG1 THR B 716 " pdb=" O GLN B1071 " model vdw 2.171 2.440 nonbonded pdb=" O PHE I 29 " pdb=" OG SER I 53 " model vdw 2.174 2.440 ... (remaining 226042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 622 or resid 636 through 827 or resid 855 throu \ gh 1146 or resid 2001 through 2007)) selection = (chain 'C' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 1146 or resid 2001 through 2007)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.650 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 78.270 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.550 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30704 Z= 0.227 Angle : 0.617 7.690 41762 Z= 0.313 Chirality : 0.048 0.699 4936 Planarity : 0.004 0.048 5279 Dihedral : 13.823 100.058 12121 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3661 helix: 1.71 (0.22), residues: 649 sheet: -0.51 (0.17), residues: 914 loop : -1.75 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 48 HIS 0.002 0.000 HIS C 655 PHE 0.019 0.001 PHE B 906 TYR 0.018 0.001 TYR I 95 ARG 0.004 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 3.263 Fit side-chains revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8717 (t80) cc_final: 0.7999 (t80) REVERT: A 902 MET cc_start: 0.8566 (mmm) cc_final: 0.8307 (mmt) REVERT: B 759 PHE cc_start: 0.7058 (p90) cc_final: 0.6807 (p90) REVERT: B 869 MET cc_start: 0.8448 (mpp) cc_final: 0.8024 (mpp) REVERT: B 1031 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8234 (tm-30) REVERT: C 740 MET cc_start: 0.8097 (tpt) cc_final: 0.7858 (mmm) REVERT: H 80 TYR cc_start: 0.9103 (m-80) cc_final: 0.8668 (m-80) REVERT: N 21 MET cc_start: 0.7488 (tmm) cc_final: 0.7255 (tmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.3924 time to fit residues: 107.7741 Evaluate side-chains 120 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 3.691 ------------------------------------------------------------------------------- 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: 20.0000 chunk 277 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 94 optimal weight: 0.0010 chunk 187 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 286 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 chunk 332 optimal weight: 50.0000 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30704 Z= 0.272 Angle : 0.598 8.982 41762 Z= 0.305 Chirality : 0.046 0.477 4936 Planarity : 0.004 0.048 5279 Dihedral : 8.215 74.187 5576 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.75 % Favored : 93.17 % Rotamer: Outliers : 0.40 % Allowed : 7.49 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3661 helix: 1.51 (0.21), residues: 677 sheet: -0.44 (0.17), residues: 917 loop : -1.79 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 48 HIS 0.005 0.001 HIS B 655 PHE 0.015 0.001 PHE C 559 TYR 0.018 0.001 TYR C 91 ARG 0.004 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 4.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8764 (t80) cc_final: 0.8299 (t80) REVERT: B 869 MET cc_start: 0.8549 (mpp) cc_final: 0.8103 (mpp) REVERT: C 452 LEU cc_start: 0.8477 (mm) cc_final: 0.7954 (tt) REVERT: C 740 MET cc_start: 0.8205 (tpt) cc_final: 0.7970 (mmm) REVERT: H 80 TYR cc_start: 0.9111 (m-80) cc_final: 0.8749 (m-80) REVERT: M 50 TYR cc_start: 0.6720 (t80) cc_final: 0.6132 (t80) REVERT: J 34 MET cc_start: 0.6786 (tpt) cc_final: 0.6375 (tpt) REVERT: N 21 MET cc_start: 0.7642 (tmm) cc_final: 0.7431 (tmm) outliers start: 13 outliers final: 11 residues processed: 141 average time/residue: 0.4075 time to fit residues: 97.5667 Evaluate side-chains 129 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain J residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 7.9990 chunk 103 optimal weight: 0.0870 chunk 276 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 332 optimal weight: 50.0000 chunk 359 optimal weight: 40.0000 chunk 296 optimal weight: 0.8980 chunk 330 optimal weight: 7.9990 chunk 113 optimal weight: 0.0980 chunk 267 optimal weight: 4.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30704 Z= 0.169 Angle : 0.541 9.254 41762 Z= 0.273 Chirality : 0.045 0.476 4936 Planarity : 0.004 0.047 5279 Dihedral : 7.513 67.837 5576 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.76 % Favored : 94.15 % Rotamer: Outliers : 0.71 % Allowed : 10.89 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3661 helix: 1.68 (0.22), residues: 665 sheet: -0.39 (0.17), residues: 934 loop : -1.73 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 48 HIS 0.005 0.001 HIS N 35 PHE 0.015 0.001 PHE B 759 TYR 0.017 0.001 TYR N 37 ARG 0.002 0.000 ARG N 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: A 490 PHE cc_start: 0.8825 (t80) cc_final: 0.8492 (t80) REVERT: B 869 MET cc_start: 0.8507 (mpp) cc_final: 0.8070 (mpp) REVERT: C 452 LEU cc_start: 0.8467 (mm) cc_final: 0.7937 (tt) REVERT: C 740 MET cc_start: 0.8108 (tpt) cc_final: 0.7889 (mmm) REVERT: H 80 TYR cc_start: 0.9146 (m-80) cc_final: 0.8714 (m-80) REVERT: I 102 TYR cc_start: 0.9332 (t80) cc_final: 0.8879 (t80) REVERT: M 29 VAL cc_start: 0.5432 (OUTLIER) cc_final: 0.5057 (m) outliers start: 23 outliers final: 17 residues processed: 147 average time/residue: 0.3804 time to fit residues: 95.4246 Evaluate side-chains 139 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 7.9990 chunk 250 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 158 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 334 optimal weight: 9.9990 chunk 353 optimal weight: 40.0000 chunk 174 optimal weight: 5.9990 chunk 316 optimal weight: 30.0000 chunk 95 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** M 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30704 Z= 0.215 Angle : 0.553 9.302 41762 Z= 0.279 Chirality : 0.045 0.490 4936 Planarity : 0.004 0.047 5279 Dihedral : 7.081 62.548 5576 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.45 % Favored : 93.47 % Rotamer: Outliers : 1.08 % Allowed : 12.91 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3661 helix: 1.59 (0.22), residues: 671 sheet: -0.36 (0.17), residues: 925 loop : -1.73 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 36 HIS 0.006 0.001 HIS N 35 PHE 0.013 0.001 PHE A 92 TYR 0.024 0.001 TYR A 91 ARG 0.002 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 3.315 Fit side-chains revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8812 (t80) cc_final: 0.8434 (t80) REVERT: B 869 MET cc_start: 0.8564 (mpp) cc_final: 0.8106 (mpp) REVERT: C 452 LEU cc_start: 0.8485 (mm) cc_final: 0.7966 (tt) REVERT: C 740 MET cc_start: 0.8162 (tpt) cc_final: 0.7914 (mmm) REVERT: H 80 TYR cc_start: 0.9163 (m-80) cc_final: 0.8932 (m-80) REVERT: L 33 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.6577 (m-80) REVERT: I 50 GLU cc_start: 0.8550 (pp20) cc_final: 0.8274 (tm-30) REVERT: I 102 TYR cc_start: 0.9308 (t80) cc_final: 0.8812 (t80) outliers start: 35 outliers final: 20 residues processed: 154 average time/residue: 0.3686 time to fit residues: 97.0888 Evaluate side-chains 139 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 35 HIS 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: 2.9990 chunk 5 optimal weight: 0.9990 chunk 263 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 301 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 317 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** M 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30704 Z= 0.245 Angle : 0.568 9.282 41762 Z= 0.286 Chirality : 0.045 0.495 4936 Planarity : 0.004 0.048 5279 Dihedral : 6.870 59.343 5576 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.34 % Favored : 93.58 % Rotamer: Outliers : 1.42 % Allowed : 14.64 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3661 helix: 1.66 (0.21), residues: 670 sheet: -0.36 (0.17), residues: 919 loop : -1.72 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 48 HIS 0.004 0.001 HIS A 49 PHE 0.013 0.001 PHE J 99 TYR 0.019 0.001 TYR C 91 ARG 0.003 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 125 time to evaluate : 3.423 Fit side-chains revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8801 (t80) cc_final: 0.8394 (t80) REVERT: B 869 MET cc_start: 0.8589 (mpp) cc_final: 0.8111 (mpp) REVERT: B 1031 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8368 (tm-30) REVERT: C 452 LEU cc_start: 0.8463 (mm) cc_final: 0.8193 (tp) REVERT: C 740 MET cc_start: 0.8182 (tpt) cc_final: 0.7916 (mmm) REVERT: L 33 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6504 (m-80) REVERT: I 102 TYR cc_start: 0.9302 (t80) cc_final: 0.8804 (t80) REVERT: M 29 VAL cc_start: 0.5530 (OUTLIER) cc_final: 0.5179 (m) REVERT: J 34 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6788 (tpp) REVERT: N 35 HIS cc_start: 0.6491 (OUTLIER) cc_final: 0.6266 (p90) REVERT: N 52 THR cc_start: 0.6274 (OUTLIER) cc_final: 0.6039 (p) REVERT: N 63 PHE cc_start: 0.4805 (t80) cc_final: 0.3961 (m-80) outliers start: 46 outliers final: 27 residues processed: 163 average time/residue: 0.3835 time to fit residues: 107.1774 Evaluate side-chains 148 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain N residue 35 HIS Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 52 THR 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: 9.9990 chunk 69 optimal weight: 0.4980 chunk 207 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 354 optimal weight: 30.0000 chunk 293 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 185 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 HIS N 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30704 Z= 0.152 Angle : 0.535 9.357 41762 Z= 0.268 Chirality : 0.044 0.491 4936 Planarity : 0.004 0.048 5279 Dihedral : 6.620 59.649 5576 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.26 % Rotamer: Outliers : 1.67 % Allowed : 15.04 % Favored : 83.29 % 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: -0.90 (0.14), residues: 3661 helix: 1.91 (0.22), residues: 648 sheet: -0.30 (0.17), residues: 930 loop : -1.63 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.021 0.001 HIS N 35 PHE 0.012 0.001 PHE J 99 TYR 0.016 0.001 TYR H 80 ARG 0.003 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 125 time to evaluate : 3.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8796 (t80) cc_final: 0.8376 (t80) REVERT: B 869 MET cc_start: 0.8531 (mpp) cc_final: 0.8056 (mpp) REVERT: C 452 LEU cc_start: 0.8447 (mm) cc_final: 0.8117 (tp) REVERT: C 740 MET cc_start: 0.8038 (tpt) cc_final: 0.7798 (mmm) REVERT: L 11 MET cc_start: 0.7279 (mpp) cc_final: 0.6629 (pmm) REVERT: L 33 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.6571 (m-10) REVERT: L 48 TRP cc_start: 0.4896 (OUTLIER) cc_final: 0.4482 (m-10) REVERT: I 50 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7866 (tp30) REVERT: I 102 TYR cc_start: 0.9331 (t80) cc_final: 0.8824 (t80) REVERT: J 1 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6964 (pp20) REVERT: J 29 PHE cc_start: 0.6877 (m-10) cc_final: 0.6089 (m-10) REVERT: J 34 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6889 (tpp) REVERT: N 52 THR cc_start: 0.6270 (OUTLIER) cc_final: 0.6019 (p) REVERT: N 63 PHE cc_start: 0.4722 (OUTLIER) cc_final: 0.3901 (m-80) outliers start: 54 outliers final: 27 residues processed: 169 average time/residue: 0.4028 time to fit residues: 118.1348 Evaluate side-chains 154 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 63 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 352 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 777 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 30704 Z= 0.366 Angle : 0.637 9.293 41762 Z= 0.322 Chirality : 0.046 0.498 4936 Planarity : 0.004 0.049 5279 Dihedral : 6.852 59.132 5576 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.43 % Favored : 92.49 % Rotamer: Outliers : 1.76 % Allowed : 16.16 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3661 helix: 1.42 (0.21), residues: 671 sheet: -0.43 (0.17), residues: 925 loop : -1.81 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 36 HIS 0.006 0.001 HIS A 49 PHE 0.017 0.002 PHE A 275 TYR 0.026 0.001 TYR C 91 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 122 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8850 (t80) cc_final: 0.8323 (t80) REVERT: A 985 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8206 (t0) REVERT: B 869 MET cc_start: 0.8613 (mpp) cc_final: 0.8150 (mpp) REVERT: C 452 LEU cc_start: 0.8439 (mm) cc_final: 0.8119 (tp) REVERT: C 740 MET cc_start: 0.8182 (tpt) cc_final: 0.7978 (mmm) REVERT: L 11 MET cc_start: 0.7349 (mpp) cc_final: 0.6718 (pmm) REVERT: L 33 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: L 48 TRP cc_start: 0.5039 (OUTLIER) cc_final: 0.4507 (m-10) REVERT: L 79 MET cc_start: 0.4516 (mtt) cc_final: 0.4292 (mpp) REVERT: I 50 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7943 (tp30) REVERT: J 1 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6887 (pp20) REVERT: J 29 PHE cc_start: 0.7134 (m-10) cc_final: 0.6335 (m-10) REVERT: J 34 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6863 (tpp) REVERT: N 63 PHE cc_start: 0.4702 (OUTLIER) cc_final: 0.4045 (m-80) outliers start: 57 outliers final: 39 residues processed: 169 average time/residue: 0.3867 time to fit residues: 112.3993 Evaluate side-chains 159 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 114 time to evaluate : 3.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 63 PHE 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: 4.9990 chunk 210 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 224 optimal weight: 4.9990 chunk 240 optimal weight: 0.0470 chunk 174 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30704 Z= 0.157 Angle : 0.546 9.361 41762 Z= 0.274 Chirality : 0.045 0.499 4936 Planarity : 0.004 0.048 5279 Dihedral : 6.532 59.546 5576 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.57 % Favored : 94.35 % Rotamer: Outliers : 1.55 % Allowed : 16.84 % Favored : 81.62 % 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: -0.99 (0.14), residues: 3661 helix: 1.83 (0.22), residues: 660 sheet: -0.37 (0.17), residues: 950 loop : -1.71 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.004 0.001 HIS N 93 PHE 0.017 0.001 PHE I 99 TYR 0.016 0.001 TYR C 91 ARG 0.002 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 125 time to evaluate : 3.459 Fit side-chains revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8899 (t80) cc_final: 0.8453 (t80) REVERT: A 985 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8205 (t0) REVERT: B 449 TYR cc_start: 0.7807 (m-80) cc_final: 0.7251 (m-80) REVERT: B 869 MET cc_start: 0.8526 (mpp) cc_final: 0.8043 (mpp) REVERT: C 740 MET cc_start: 0.8040 (tpt) cc_final: 0.7807 (mmm) REVERT: L 11 MET cc_start: 0.7346 (mpp) cc_final: 0.6782 (pmm) REVERT: L 33 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6886 (m-10) REVERT: L 48 TRP cc_start: 0.5206 (OUTLIER) cc_final: 0.4549 (m-10) REVERT: I 1 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6015 (pp20) REVERT: I 50 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8020 (tp30) REVERT: M 11 MET cc_start: 0.6874 (mmp) cc_final: 0.6466 (mpp) REVERT: J 1 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6925 (pp20) REVERT: J 29 PHE cc_start: 0.7080 (m-10) cc_final: 0.6281 (m-10) REVERT: J 34 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6880 (tpp) REVERT: N 63 PHE cc_start: 0.4412 (OUTLIER) cc_final: 0.3716 (m-80) outliers start: 50 outliers final: 34 residues processed: 166 average time/residue: 0.3835 time to fit residues: 110.2648 Evaluate side-chains 159 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 118 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain N residue 35 HIS Chi-restraints excluded: chain N residue 63 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 20.0000 chunk 337 optimal weight: 40.0000 chunk 308 optimal weight: 8.9990 chunk 328 optimal weight: 8.9990 chunk 197 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 258 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 297 optimal weight: 6.9990 chunk 310 optimal weight: 5.9990 chunk 327 optimal weight: 10.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 655 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 30704 Z= 0.442 Angle : 0.702 9.250 41762 Z= 0.355 Chirality : 0.048 0.514 4936 Planarity : 0.004 0.049 5279 Dihedral : 6.975 59.690 5576 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.19 % Favored : 91.70 % Rotamer: Outliers : 1.83 % Allowed : 17.33 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.13), residues: 3661 helix: 1.19 (0.20), residues: 673 sheet: -0.58 (0.17), residues: 945 loop : -1.90 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1102 HIS 0.008 0.001 HIS A 49 PHE 0.020 0.002 PHE A 275 TYR 0.029 0.002 TYR C 91 ARG 0.004 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 119 time to evaluate : 3.445 Fit side-chains revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8936 (t80) cc_final: 0.8447 (t80) REVERT: A 985 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8268 (t0) REVERT: B 449 TYR cc_start: 0.7948 (m-80) cc_final: 0.7418 (m-80) REVERT: B 869 MET cc_start: 0.8648 (mpp) cc_final: 0.8155 (mpp) REVERT: C 452 LEU cc_start: 0.8403 (mm) cc_final: 0.8172 (tp) REVERT: C 740 MET cc_start: 0.8195 (tpt) cc_final: 0.7995 (mmm) REVERT: L 11 MET cc_start: 0.7409 (mpp) cc_final: 0.6837 (pmm) REVERT: L 33 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: I 1 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.5962 (pp20) REVERT: I 50 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8051 (tp30) REVERT: M 11 MET cc_start: 0.6906 (mmp) cc_final: 0.6576 (mtm) REVERT: M 50 TYR cc_start: 0.6701 (t80) cc_final: 0.6236 (t80) REVERT: J 1 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7029 (pp20) REVERT: J 29 PHE cc_start: 0.7342 (m-10) cc_final: 0.6574 (m-10) REVERT: J 34 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6832 (tpp) REVERT: N 63 PHE cc_start: 0.4221 (OUTLIER) cc_final: 0.3518 (m-80) outliers start: 59 outliers final: 43 residues processed: 170 average time/residue: 0.3788 time to fit residues: 112.4710 Evaluate side-chains 164 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 115 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain N residue 35 HIS Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 63 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 2.9990 chunk 347 optimal weight: 0.5980 chunk 212 optimal weight: 0.4980 chunk 164 optimal weight: 0.0570 chunk 241 optimal weight: 0.4980 chunk 364 optimal weight: 30.0000 chunk 335 optimal weight: 20.0000 chunk 290 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 178 optimal weight: 0.6980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30704 Z= 0.146 Angle : 0.566 9.380 41762 Z= 0.282 Chirality : 0.045 0.504 4936 Planarity : 0.004 0.049 5279 Dihedral : 6.524 59.774 5576 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 1.15 % Allowed : 18.11 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3661 helix: 1.79 (0.21), residues: 656 sheet: -0.37 (0.17), residues: 945 loop : -1.77 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.003 0.001 HIS N 93 PHE 0.012 0.001 PHE C1095 TYR 0.015 0.001 TYR J 102 ARG 0.004 0.000 ARG H 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 126 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8211 (t0) REVERT: B 869 MET cc_start: 0.8549 (mpp) cc_final: 0.8022 (mpp) REVERT: C 740 MET cc_start: 0.8010 (tpt) cc_final: 0.7774 (mmm) REVERT: L 11 MET cc_start: 0.7434 (mpp) cc_final: 0.6833 (pmm) REVERT: L 48 TRP cc_start: 0.5483 (OUTLIER) cc_final: 0.4680 (m-10) REVERT: I 1 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5816 (pp20) REVERT: I 50 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8096 (tp30) REVERT: M 11 MET cc_start: 0.7021 (mmp) cc_final: 0.6704 (mtm) REVERT: J 1 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7123 (pp20) REVERT: J 29 PHE cc_start: 0.7236 (m-10) cc_final: 0.6439 (m-10) REVERT: J 34 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6899 (tpp) REVERT: N 63 PHE cc_start: 0.4206 (OUTLIER) cc_final: 0.3512 (m-80) outliers start: 37 outliers final: 28 residues processed: 156 average time/residue: 0.4162 time to fit residues: 108.6563 Evaluate side-chains 152 residues out of total 3231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 118 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain N residue 35 HIS Chi-restraints excluded: chain N residue 63 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 6.9990 chunk 309 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 290 optimal weight: 0.5980 chunk 121 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 HIS N 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.098379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.063477 restraints weight = 132945.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.065433 restraints weight = 74389.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.065766 restraints weight = 54284.214| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30704 Z= 0.161 Angle : 0.559 9.683 41762 Z= 0.278 Chirality : 0.044 0.501 4936 Planarity : 0.004 0.049 5279 Dihedral : 6.432 59.757 5576 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.26 % Rotamer: Outliers : 1.27 % Allowed : 18.14 % Favored : 80.59 % 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: -0.95 (0.14), residues: 3661 helix: 1.84 (0.21), residues: 668 sheet: -0.33 (0.17), residues: 953 loop : -1.71 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.013 0.001 HIS N 35 PHE 0.009 0.001 PHE C 201 TYR 0.016 0.001 TYR M 33 ARG 0.004 0.000 ARG H 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4734.54 seconds wall clock time: 89 minutes 4.87 seconds (5344.87 seconds total)