Starting phenix.real_space_refine on Sun Mar 17 23:04:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p62_20259/03_2024/6p62_20259.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p62_20259/03_2024/6p62_20259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p62_20259/03_2024/6p62_20259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p62_20259/03_2024/6p62_20259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p62_20259/03_2024/6p62_20259.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p62_20259/03_2024/6p62_20259.pdb" } resolution = 3.57 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= 0.010 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 132 5.16 5 C 12021 2.51 5 N 3171 2.21 5 O 3879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 78": "OD1" <-> "OD2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 78": "OD1" <-> "OD2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19203 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 4343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4343 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 23, 'TRANS': 527} Chain breaks: 5 Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 4343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4343 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 23, 'TRANS': 527} Chain breaks: 5 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "D" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "E" Number of atoms: 4343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4343 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 23, 'TRANS': 527} Chain breaks: 5 Chain: "F" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "G" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 10.85, per 1000 atoms: 0.57 Number of scatterers: 19203 At special positions: 0 Unit cell: (149.35, 149.35, 115.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 3879 8.00 N 3171 7.00 C 12021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.11 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.10 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 35A" - pdb=" SG CYS H 50 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.06 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.11 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.01 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.10 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35A" - pdb=" SG CYS C 50 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.06 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.11 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.01 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.10 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.04 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 35A" - pdb=" SG CYS F 50 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN Q 4 " - " MAN Q 5 " " MAN Q 5 " - " MAN Q 6 " " MAN W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " BMA Q 3 " - " MAN Q 7 " " BMA W 3 " - " MAN W 7 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 703 " - " ASN A 160 " " NAG A 704 " - " ASN A 197 " " NAG A 718 " - " ASN A 295 " " NAG A 719 " - " ASN A 301 " " NAG A 720 " - " ASN A 332 " " NAG A 721 " - " ASN A 133 " " NAG A 722 " - " ASN A 339 " " NAG A 727 " - " ASN A 392 " " NAG A 728 " - " ASN A 448 " " NAG B 703 " - " ASN B 160 " " NAG B 704 " - " ASN B 197 " " NAG B 718 " - " ASN B 295 " " NAG B 719 " - " ASN B 301 " " NAG B 720 " - " ASN B 332 " " NAG B 721 " - " ASN B 133 " " NAG B 722 " - " ASN B 339 " " NAG B 727 " - " ASN B 392 " " NAG B 728 " - " ASN B 448 " " NAG E 703 " - " ASN E 160 " " NAG E 704 " - " ASN E 197 " " NAG E 718 " - " ASN E 295 " " NAG E 719 " - " ASN E 301 " " NAG E 720 " - " ASN E 332 " " NAG E 721 " - " ASN E 133 " " NAG E 722 " - " ASN E 339 " " NAG E 727 " - " ASN E 392 " " NAG E 728 " - " ASN E 448 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 363 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN B 156 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 262 " " NAG S 1 " - " ASN B 276 " " NAG T 1 " - " ASN B 363 " " NAG U 1 " - " ASN B 386 " " NAG V 1 " - " ASN E 156 " " NAG W 1 " - " ASN E 234 " " NAG X 1 " - " ASN E 262 " " NAG Y 1 " - " ASN E 276 " " NAG Z 1 " - " ASN E 363 " " NAG a 1 " - " ASN E 386 " Time building additional restraints: 8.69 Conformation dependent library (CDL) restraints added in 3.7 seconds 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4284 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 45 sheets defined 20.7% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.169A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.865A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.790A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.344A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.591A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 546 removed outlier: 3.893A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 546 " --> pdb=" O ARG A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 596 Processing helix chain 'A' and resid 611 through 615 Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.907A pdb=" N ASP A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 649 removed outlier: 3.500A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.168A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 334 through 354 removed outlier: 3.864A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 Processing helix chain 'B' and resid 476 through 484 removed outlier: 3.790A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.344A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.593A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.893A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.908A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 removed outlier: 3.898A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 657 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.168A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 334 through 354 removed outlier: 3.865A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 476 through 484 removed outlier: 3.790A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.344A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.592A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 546 removed outlier: 3.893A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 544 " --> pdb=" O GLN E 540 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU E 545 " --> pdb=" O ALA E 541 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER E 546 " --> pdb=" O ARG E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 596 Processing helix chain 'E' and resid 611 through 615 Processing helix chain 'E' and resid 618 through 624 removed outlier: 3.908A pdb=" N ASP E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 649 removed outlier: 3.500A pdb=" N GLU E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU E 648 " --> pdb=" O GLY E 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 652 through 657 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 497 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.781A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 122 removed outlier: 4.320A pdb=" N CYS A 201 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.621A pdb=" N THR A 132 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.527A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.829A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.943A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.580A pdb=" N LEU H 18 " --> pdb=" O MET H 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.701A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N CYS H 50 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET H 35 " --> pdb=" O CYS H 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR H 52 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR H 33 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.701A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N CYS H 50 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET H 35 " --> pdb=" O CYS H 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR H 52 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR H 33 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB6, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AB7, first strand: chain 'B' and resid 495 through 497 Processing sheet with id=AB8, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.781A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'B' and resid 121 through 122 removed outlier: 4.320A pdb=" N CYS B 201 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 169 through 177 removed outlier: 3.621A pdb=" N THR B 132 " --> pdb=" O ASN B 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 393 through 395 removed outlier: 6.527A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL B 442 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS B 296 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 450 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.828A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL B 442 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS B 296 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 450 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 315 through 323A removed outlier: 6.943A pdb=" N ALA B 316 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE B 309 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TYR B 318 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE B 307 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N THR B 320 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS B 305 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN B 301 " --> pdb=" O ILE B 323A" (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.581A pdb=" N LEU C 18 " --> pdb=" O MET C 81 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.702A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N CYS C 50 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET C 35 " --> pdb=" O CYS C 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR C 52 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR C 33 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.702A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N CYS C 50 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET C 35 " --> pdb=" O CYS C 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR C 52 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR C 33 " --> pdb=" O TYR C 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AD2, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AD3, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AD4, first strand: chain 'E' and resid 495 through 497 Processing sheet with id=AD5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.781A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'E' and resid 121 through 122 removed outlier: 4.320A pdb=" N CYS E 201 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.621A pdb=" N THR E 132 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 393 through 395 removed outlier: 6.527A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.657A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.829A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.657A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 315 through 323A removed outlier: 6.943A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.581A pdb=" N LEU F 18 " --> pdb=" O MET F 81 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.702A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N CYS F 50 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET F 35 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR F 52 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR F 33 " --> pdb=" O TYR F 52 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.702A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N CYS F 50 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET F 35 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR F 52 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR F 33 " --> pdb=" O TYR F 52 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AE8, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AE9, first strand: chain 'G' and resid 48 through 49 745 hydrogen bonds defined for protein. 1866 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: 6.97 Time building geometry restraints manager: 9.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 5903 1.34 - 1.48: 5988 1.48 - 1.63: 7519 1.63 - 1.78: 83 1.78 - 1.93: 94 Bond restraints: 19587 Sorted by residual: bond pdb=" CB TYR L 36 " pdb=" CG TYR L 36 " ideal model delta sigma weight residual 1.512 1.351 0.161 2.20e-02 2.07e+03 5.34e+01 bond pdb=" CB TYR D 36 " pdb=" CG TYR D 36 " ideal model delta sigma weight residual 1.512 1.352 0.160 2.20e-02 2.07e+03 5.31e+01 bond pdb=" CB TYR G 36 " pdb=" CG TYR G 36 " ideal model delta sigma weight residual 1.512 1.352 0.160 2.20e-02 2.07e+03 5.29e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.09e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.08e+01 ... (remaining 19582 not shown) Histogram of bond angle deviations from ideal: 95.78 - 103.50: 261 103.50 - 111.23: 8148 111.23 - 118.95: 8314 118.95 - 126.68: 9605 126.68 - 134.40: 294 Bond angle restraints: 26622 Sorted by residual: angle pdb=" N ASP D 95B" pdb=" CA ASP D 95B" pdb=" C ASP D 95B" ideal model delta sigma weight residual 109.79 123.89 -14.10 1.56e+00 4.11e-01 8.17e+01 angle pdb=" N ASP G 95B" pdb=" CA ASP G 95B" pdb=" C ASP G 95B" ideal model delta sigma weight residual 109.79 123.88 -14.09 1.56e+00 4.11e-01 8.16e+01 angle pdb=" N ASP L 95B" pdb=" CA ASP L 95B" pdb=" C ASP L 95B" ideal model delta sigma weight residual 109.79 123.88 -14.09 1.56e+00 4.11e-01 8.15e+01 angle pdb=" N ARG G 61 " pdb=" CA ARG G 61 " pdb=" C ARG G 61 " ideal model delta sigma weight residual 114.04 103.31 10.73 1.24e+00 6.50e-01 7.49e+01 angle pdb=" N ARG D 61 " pdb=" CA ARG D 61 " pdb=" C ARG D 61 " ideal model delta sigma weight residual 114.04 103.31 10.73 1.24e+00 6.50e-01 7.48e+01 ... (remaining 26617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 12245 21.72 - 43.45: 316 43.45 - 65.17: 108 65.17 - 86.90: 45 86.90 - 108.62: 24 Dihedral angle restraints: 12738 sinusoidal: 6063 harmonic: 6675 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 157 " pdb=" CB CYS B 157 " ideal model delta sinusoidal sigma weight residual 93.00 45.36 47.64 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS E 131 " pdb=" SG CYS E 131 " pdb=" SG CYS E 157 " pdb=" CB CYS E 157 " ideal model delta sinusoidal sigma weight residual 93.00 45.39 47.61 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 157 " pdb=" CB CYS A 157 " ideal model delta sinusoidal sigma weight residual 93.00 45.40 47.60 1 1.00e+01 1.00e-02 3.13e+01 ... (remaining 12735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2398 0.109 - 0.218: 751 0.218 - 0.326: 88 0.326 - 0.435: 6 0.435 - 0.544: 12 Chirality restraints: 3255 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.57e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.57e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.51e+01 ... (remaining 3252 not shown) Planarity restraints: 3318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 197 " 0.052 2.00e-02 2.50e+03 5.54e-02 3.84e+01 pdb=" CG ASN B 197 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 197 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 197 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG B 704 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 197 " 0.052 2.00e-02 2.50e+03 5.54e-02 3.84e+01 pdb=" CG ASN E 197 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN E 197 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN E 197 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG E 704 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 197 " 0.052 2.00e-02 2.50e+03 5.54e-02 3.84e+01 pdb=" CG ASN A 197 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 197 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 197 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.067 2.00e-02 2.50e+03 ... (remaining 3315 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5208 2.80 - 3.32: 17127 3.32 - 3.85: 31345 3.85 - 4.37: 37289 4.37 - 4.90: 61179 Nonbonded interactions: 152148 Sorted by model distance: nonbonded pdb=" O PRO H 100F" pdb=" OH TYR L 36 " model vdw 2.272 2.440 nonbonded pdb=" O PRO C 100F" pdb=" OH TYR D 36 " model vdw 2.272 2.440 nonbonded pdb=" O PRO F 100F" pdb=" OH TYR G 36 " model vdw 2.272 2.440 nonbonded pdb=" O3 NAG Z 2 " pdb=" O7 NAG Z 2 " model vdw 2.363 2.440 nonbonded pdb=" O3 NAG T 2 " pdb=" O7 NAG T 2 " model vdw 2.363 2.440 ... (remaining 152143 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'W' } ncs_group { reference = chain 'K' selection = chain 'R' selection = chain 'X' } 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: 1.580 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: 0.010 Extract box with map and model: 7.330 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 53.310 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.230 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: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 : 0.023 0.161 19587 Z= 1.461 Angle : 1.814 14.101 26622 Z= 1.165 Chirality : 0.103 0.544 3255 Planarity : 0.009 0.046 3273 Dihedral : 12.688 108.619 8337 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.15 % Allowed : 0.45 % Favored : 99.40 % 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: -0.40 (0.17), residues: 2286 helix: -0.34 (0.25), residues: 378 sheet: 0.04 (0.18), residues: 756 loop : -0.33 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.008 TRP E 479 HIS 0.013 0.003 HIS B 105 PHE 0.044 0.007 PHE F 95 TYR 0.055 0.008 TYR L 92 ARG 0.008 0.001 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 578 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7815 (p0) cc_final: 0.7535 (t0) REVERT: A 424 ILE cc_start: 0.9068 (pt) cc_final: 0.8787 (pt) REVERT: A 426 MET cc_start: 0.8732 (tpt) cc_final: 0.8520 (tpt) REVERT: A 577 GLN cc_start: 0.7460 (mt0) cc_final: 0.7252 (tp40) REVERT: H 2 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7436 (mp10) REVERT: H 75 THR cc_start: 0.7991 (p) cc_final: 0.7631 (t) REVERT: L 65 SER cc_start: 0.8755 (p) cc_final: 0.8476 (m) REVERT: B 130 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7195 (mm-40) REVERT: B 174 SER cc_start: 0.8911 (t) cc_final: 0.8642 (p) REVERT: B 302 TYR cc_start: 0.7788 (m-80) cc_final: 0.7577 (m-10) REVERT: C 77 VAL cc_start: 0.8581 (t) cc_final: 0.8322 (p) REVERT: D 8 PRO cc_start: 0.7436 (Cg_endo) cc_final: 0.7169 (Cg_exo) REVERT: D 65 SER cc_start: 0.8689 (p) cc_final: 0.8377 (m) REVERT: E 54 CYS cc_start: 0.8508 (p) cc_final: 0.8114 (m) REVERT: E 99 ASN cc_start: 0.7591 (p0) cc_final: 0.7319 (t0) REVERT: E 104 MET cc_start: 0.8587 (ttt) cc_final: 0.8372 (ttt) REVERT: E 174 SER cc_start: 0.8972 (t) cc_final: 0.8748 (p) REVERT: E 577 GLN cc_start: 0.7692 (mt0) cc_final: 0.7435 (tp40) REVERT: F 2 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7295 (mp10) REVERT: F 86 ASP cc_start: 0.8065 (m-30) cc_final: 0.7712 (m-30) REVERT: G 52 SER cc_start: 0.9125 (p) cc_final: 0.8921 (t) REVERT: G 65 SER cc_start: 0.8669 (p) cc_final: 0.8356 (m) REVERT: G 74 THR cc_start: 0.8637 (m) cc_final: 0.8430 (p) outliers start: 3 outliers final: 3 residues processed: 581 average time/residue: 0.3206 time to fit residues: 275.9811 Evaluate side-chains 326 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 323 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain E residue 448 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS A 478 ASN A 651 ASN H 80 GLN ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 105 HIS ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN B 425 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN C 80 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS E 352 HIS E 425 ASN E 428 GLN E 651 ASN E 653 GLN F 80 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19587 Z= 0.246 Angle : 0.770 13.106 26622 Z= 0.410 Chirality : 0.048 0.185 3255 Planarity : 0.004 0.042 3273 Dihedral : 9.856 66.246 4209 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.95 % Allowed : 8.20 % Favored : 88.86 % 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: -0.46 (0.17), residues: 2286 helix: 0.69 (0.28), residues: 384 sheet: -0.21 (0.18), residues: 717 loop : -0.63 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 62 HIS 0.003 0.001 HIS A 216 PHE 0.024 0.003 PHE H 95 TYR 0.016 0.002 TYR A 217 ARG 0.008 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 376 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.7475 (mm-40) cc_final: 0.7127 (mm-40) REVERT: A 161 MET cc_start: 0.8280 (tpt) cc_final: 0.8060 (tpt) REVERT: A 530 MET cc_start: 0.7652 (mtp) cc_final: 0.7324 (mtp) REVERT: H 2 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7158 (mp10) REVERT: H 62 TRP cc_start: 0.7432 (p-90) cc_final: 0.6908 (p-90) REVERT: L 65 SER cc_start: 0.8980 (p) cc_final: 0.8646 (m) REVERT: B 174 SER cc_start: 0.9048 (t) cc_final: 0.8631 (p) REVERT: C 23 LYS cc_start: 0.8550 (tttt) cc_final: 0.8261 (tptt) REVERT: C 75 THR cc_start: 0.7861 (p) cc_final: 0.7638 (p) REVERT: D 8 PRO cc_start: 0.7121 (Cg_endo) cc_final: 0.6875 (Cg_exo) REVERT: D 65 SER cc_start: 0.8902 (p) cc_final: 0.8632 (m) REVERT: E 54 CYS cc_start: 0.8464 (p) cc_final: 0.8175 (m) REVERT: E 130 GLN cc_start: 0.7652 (mm-40) cc_final: 0.6819 (mm-40) REVERT: E 174 SER cc_start: 0.9155 (t) cc_final: 0.8705 (p) REVERT: E 530 MET cc_start: 0.7593 (mtp) cc_final: 0.7306 (mtp) REVERT: E 577 GLN cc_start: 0.7651 (mt0) cc_final: 0.7399 (tp40) REVERT: F 80 GLN cc_start: 0.7316 (mp-120) cc_final: 0.7057 (mp10) REVERT: F 102 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8055 (mp) REVERT: G 65 SER cc_start: 0.8830 (p) cc_final: 0.8580 (m) REVERT: G 74 THR cc_start: 0.8769 (m) cc_final: 0.8543 (p) outliers start: 59 outliers final: 36 residues processed: 410 average time/residue: 0.2778 time to fit residues: 178.1090 Evaluate side-chains 324 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 287 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 95 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 205 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 GLN L 24 GLN L 37 GLN L 38 HIS B 540 GLN B 575 GLN D 24 GLN D 38 HIS E 540 GLN E 575 GLN G 24 GLN G 37 GLN G 38 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 19587 Z= 0.448 Angle : 0.801 10.773 26622 Z= 0.416 Chirality : 0.049 0.212 3255 Planarity : 0.005 0.048 3273 Dihedral : 8.589 54.176 4209 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.10 % Allowed : 10.04 % Favored : 85.86 % 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: -0.94 (0.17), residues: 2286 helix: 0.33 (0.27), residues: 387 sheet: -0.46 (0.18), residues: 813 loop : -1.02 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 35 HIS 0.006 0.001 HIS A 352 PHE 0.029 0.003 PHE C 95 TYR 0.018 0.002 TYR D 92 ARG 0.011 0.001 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 298 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 THR cc_start: 0.9295 (t) cc_final: 0.9090 (m) REVERT: H 2 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7703 (mp10) REVERT: H 62 TRP cc_start: 0.7839 (p-90) cc_final: 0.7203 (p-90) REVERT: L 65 SER cc_start: 0.8900 (p) cc_final: 0.8629 (m) REVERT: B 104 MET cc_start: 0.8836 (ttm) cc_final: 0.8530 (ttt) REVERT: C 2 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7580 (mp10) REVERT: C 18 LEU cc_start: 0.7244 (mt) cc_final: 0.7043 (tp) REVERT: C 75 THR cc_start: 0.7907 (p) cc_final: 0.7702 (t) REVERT: D 8 PRO cc_start: 0.7439 (Cg_endo) cc_final: 0.7195 (Cg_exo) REVERT: D 65 SER cc_start: 0.8861 (p) cc_final: 0.8618 (m) REVERT: D 74 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8669 (p) REVERT: E 54 CYS cc_start: 0.8503 (p) cc_final: 0.8245 (m) REVERT: E 202 THR cc_start: 0.9314 (p) cc_final: 0.9041 (p) REVERT: E 530 MET cc_start: 0.7902 (mtp) cc_final: 0.7595 (mtp) REVERT: F 2 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7248 (mp10) outliers start: 82 outliers final: 57 residues processed: 350 average time/residue: 0.2718 time to fit residues: 150.6746 Evaluate side-chains 314 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 256 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 34 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 95 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 208 optimal weight: 8.9990 chunk 220 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 197 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 GLN D 37 GLN E 425 ASN E 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19587 Z= 0.236 Angle : 0.646 10.908 26622 Z= 0.333 Chirality : 0.045 0.212 3255 Planarity : 0.004 0.041 3273 Dihedral : 7.419 59.074 4209 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.00 % Allowed : 11.24 % Favored : 84.76 % 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: -0.96 (0.17), residues: 2286 helix: 0.82 (0.28), residues: 369 sheet: -0.43 (0.18), residues: 804 loop : -1.25 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 62 HIS 0.004 0.001 HIS A 352 PHE 0.018 0.002 PHE F 95 TYR 0.019 0.002 TYR G 67 ARG 0.007 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 276 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7305 (mp10) REVERT: H 62 TRP cc_start: 0.7875 (p-90) cc_final: 0.7562 (p-90) REVERT: L 65 SER cc_start: 0.8818 (p) cc_final: 0.8561 (m) REVERT: L 103 GLU cc_start: 0.7951 (tp30) cc_final: 0.7402 (tt0) REVERT: B 104 MET cc_start: 0.8748 (ttm) cc_final: 0.8441 (ttt) REVERT: B 482 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7507 (mm-30) REVERT: B 652 GLN cc_start: 0.7597 (tp40) cc_final: 0.7099 (tp40) REVERT: C 2 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7340 (mp10) REVERT: C 75 THR cc_start: 0.7900 (p) cc_final: 0.7683 (t) REVERT: E 54 CYS cc_start: 0.8614 (p) cc_final: 0.8245 (m) REVERT: E 202 THR cc_start: 0.9281 (p) cc_final: 0.9039 (p) REVERT: E 461 THR cc_start: 0.8554 (m) cc_final: 0.8322 (m) REVERT: G 33 VAL cc_start: 0.8925 (t) cc_final: 0.8696 (t) outliers start: 80 outliers final: 60 residues processed: 330 average time/residue: 0.2600 time to fit residues: 138.3684 Evaluate side-chains 301 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 241 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 95 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 90 optimal weight: 0.2980 chunk 188 optimal weight: 0.3980 chunk 152 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN E 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19587 Z= 0.316 Angle : 0.676 13.499 26622 Z= 0.347 Chirality : 0.046 0.268 3255 Planarity : 0.004 0.047 3273 Dihedral : 7.264 57.814 4209 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.95 % Allowed : 11.84 % Favored : 84.21 % 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 (0.17), residues: 2286 helix: 0.79 (0.28), residues: 369 sheet: -0.44 (0.19), residues: 777 loop : -1.36 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 62 HIS 0.004 0.001 HIS A 352 PHE 0.022 0.002 PHE A 53 TYR 0.021 0.002 TYR G 67 ARG 0.004 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 247 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 2 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7463 (mp10) REVERT: H 62 TRP cc_start: 0.7920 (p-90) cc_final: 0.7529 (p-90) REVERT: L 65 SER cc_start: 0.8763 (p) cc_final: 0.8518 (m) REVERT: L 105 VAL cc_start: 0.6491 (t) cc_final: 0.5909 (m) REVERT: B 104 MET cc_start: 0.8783 (ttm) cc_final: 0.8467 (ttt) REVERT: B 482 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7562 (mm-30) REVERT: B 652 GLN cc_start: 0.7605 (tp40) cc_final: 0.7036 (tp40) REVERT: C 2 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7361 (mp10) REVERT: D 47 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8421 (mt) REVERT: E 54 CYS cc_start: 0.8493 (p) cc_final: 0.8223 (m) REVERT: E 202 THR cc_start: 0.9251 (p) cc_final: 0.8991 (p) REVERT: E 482 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7722 (mm-30) REVERT: F 81 MET cc_start: 0.6709 (mtm) cc_final: 0.6506 (mtm) outliers start: 79 outliers final: 63 residues processed: 304 average time/residue: 0.2453 time to fit residues: 123.0728 Evaluate side-chains 305 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 241 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 95 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.9980 chunk 198 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN F 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 19587 Z= 0.470 Angle : 0.784 10.752 26622 Z= 0.399 Chirality : 0.048 0.210 3255 Planarity : 0.005 0.043 3273 Dihedral : 7.892 59.663 4207 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.40 % Allowed : 12.99 % Favored : 82.61 % 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: -1.37 (0.17), residues: 2286 helix: 0.56 (0.28), residues: 363 sheet: -0.64 (0.19), residues: 810 loop : -1.59 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 571 HIS 0.007 0.002 HIS B 66 PHE 0.029 0.003 PHE F 95 TYR 0.030 0.002 TYR G 67 ARG 0.006 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 262 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8611 (mmt) cc_final: 0.8391 (mmt) REVERT: H 2 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7443 (mp10) REVERT: H 62 TRP cc_start: 0.7977 (p-90) cc_final: 0.7505 (p-90) REVERT: L 65 SER cc_start: 0.8751 (p) cc_final: 0.8521 (m) REVERT: L 105 VAL cc_start: 0.6524 (t) cc_final: 0.5979 (m) REVERT: B 482 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7554 (mm-30) REVERT: C 2 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7362 (mp10) REVERT: C 33 TYR cc_start: 0.8462 (m-80) cc_final: 0.8114 (m-10) REVERT: C 81 MET cc_start: 0.6909 (mtm) cc_final: 0.6522 (mtm) REVERT: F 2 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7623 (mp10) REVERT: G 105 VAL cc_start: 0.6615 (t) cc_final: 0.5951 (m) outliers start: 88 outliers final: 71 residues processed: 324 average time/residue: 0.2587 time to fit residues: 136.8908 Evaluate side-chains 315 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 244 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 95 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 219 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19587 Z= 0.211 Angle : 0.634 14.158 26622 Z= 0.326 Chirality : 0.045 0.357 3255 Planarity : 0.004 0.043 3273 Dihedral : 7.038 59.688 4207 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.75 % Allowed : 14.19 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.17), residues: 2286 helix: 0.82 (0.28), residues: 363 sheet: -0.37 (0.19), residues: 759 loop : -1.61 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 62 HIS 0.002 0.001 HIS A 352 PHE 0.016 0.002 PHE A 53 TYR 0.022 0.002 TYR G 67 ARG 0.004 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 269 time to evaluate : 2.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8580 (mmt) cc_final: 0.8360 (mmt) REVERT: A 651 ASN cc_start: 0.7771 (t0) cc_final: 0.7230 (t0) REVERT: H 2 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7419 (mp10) REVERT: H 23 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8147 (tttp) REVERT: H 62 TRP cc_start: 0.8046 (p-90) cc_final: 0.7594 (p-90) REVERT: L 65 SER cc_start: 0.8683 (p) cc_final: 0.8435 (m) REVERT: B 482 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7455 (mm-30) REVERT: B 651 ASN cc_start: 0.7591 (t0) cc_final: 0.7367 (t0) REVERT: C 2 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7344 (mp10) REVERT: E 54 CYS cc_start: 0.8557 (p) cc_final: 0.8269 (m) REVERT: F 2 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7638 (mp10) REVERT: F 23 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7928 (tttm) REVERT: G 33 VAL cc_start: 0.8940 (t) cc_final: 0.8724 (t) outliers start: 75 outliers final: 61 residues processed: 318 average time/residue: 0.2496 time to fit residues: 130.2637 Evaluate side-chains 305 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 242 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 95 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 9.9990 chunk 87 optimal weight: 0.0270 chunk 131 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19587 Z= 0.220 Angle : 0.628 14.551 26622 Z= 0.322 Chirality : 0.045 0.309 3255 Planarity : 0.004 0.041 3273 Dihedral : 6.649 59.151 4207 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.80 % Allowed : 14.59 % Favored : 81.61 % 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: -1.19 (0.17), residues: 2286 helix: 0.84 (0.28), residues: 366 sheet: -0.33 (0.19), residues: 774 loop : -1.68 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 571 HIS 0.003 0.001 HIS G 38 PHE 0.021 0.002 PHE A 53 TYR 0.022 0.001 TYR G 67 ARG 0.005 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 258 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7436 (mp10) REVERT: H 23 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8033 (tttm) REVERT: H 62 TRP cc_start: 0.8110 (p-90) cc_final: 0.7647 (p-90) REVERT: B 482 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7438 (mm-30) REVERT: B 651 ASN cc_start: 0.7671 (t0) cc_final: 0.7437 (t0) REVERT: C 2 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7239 (mp10) REVERT: C 81 MET cc_start: 0.6712 (mtm) cc_final: 0.6384 (mtm) REVERT: F 2 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7650 (mp10) REVERT: G 33 VAL cc_start: 0.8965 (t) cc_final: 0.8734 (t) REVERT: G 105 VAL cc_start: 0.6769 (t) cc_final: 0.5827 (m) outliers start: 76 outliers final: 63 residues processed: 308 average time/residue: 0.2457 time to fit residues: 125.2882 Evaluate side-chains 307 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 243 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 95 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 9.9990 chunk 210 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 185 optimal weight: 0.9980 chunk 193 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN B 66 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN D 24 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN G 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19587 Z= 0.199 Angle : 0.633 17.624 26622 Z= 0.319 Chirality : 0.045 0.547 3255 Planarity : 0.004 0.040 3273 Dihedral : 6.405 58.263 4207 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.50 % Allowed : 14.89 % Favored : 81.61 % 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: -1.09 (0.18), residues: 2286 helix: 0.98 (0.29), residues: 363 sheet: -0.30 (0.19), residues: 774 loop : -1.61 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 571 HIS 0.002 0.001 HIS G 38 PHE 0.016 0.002 PHE A 53 TYR 0.021 0.001 TYR G 67 ARG 0.005 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 258 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7442 (mp10) REVERT: H 23 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8073 (tttp) REVERT: H 62 TRP cc_start: 0.8123 (p-90) cc_final: 0.7684 (p-90) REVERT: B 482 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7437 (mm-30) REVERT: C 2 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7247 (mp10) REVERT: C 81 MET cc_start: 0.6792 (mtm) cc_final: 0.6488 (mtm) REVERT: E 482 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7659 (mm-30) REVERT: E 577 GLN cc_start: 0.7463 (mt0) cc_final: 0.7182 (tp40) REVERT: E 651 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7470 (t0) REVERT: E 652 GLN cc_start: 0.7844 (tp40) cc_final: 0.7449 (tp40) REVERT: F 2 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7693 (mp10) REVERT: G 33 VAL cc_start: 0.8919 (t) cc_final: 0.8718 (t) outliers start: 70 outliers final: 57 residues processed: 306 average time/residue: 0.2450 time to fit residues: 123.1012 Evaluate side-chains 303 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 244 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 651 ASN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 95 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 143 optimal weight: 8.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19587 Z= 0.190 Angle : 0.621 15.146 26622 Z= 0.317 Chirality : 0.044 0.463 3255 Planarity : 0.004 0.043 3273 Dihedral : 6.166 57.424 4207 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.10 % Allowed : 15.09 % Favored : 81.81 % 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: -1.07 (0.18), residues: 2286 helix: 0.97 (0.29), residues: 363 sheet: -0.24 (0.19), residues: 774 loop : -1.63 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 571 HIS 0.002 0.001 HIS G 38 PHE 0.016 0.001 PHE H 67 TYR 0.022 0.001 TYR D 67 ARG 0.004 0.000 ARG E 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 249 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7459 (mp10) REVERT: H 23 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8113 (tttp) REVERT: H 62 TRP cc_start: 0.8097 (p-90) cc_final: 0.7669 (p-90) REVERT: H 81 MET cc_start: 0.7071 (mtm) cc_final: 0.6554 (mtm) REVERT: L 103 GLU cc_start: 0.7966 (tp30) cc_final: 0.7447 (tt0) REVERT: B 482 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7441 (mm-30) REVERT: C 2 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7241 (mp10) REVERT: C 81 MET cc_start: 0.6775 (mtm) cc_final: 0.6389 (mtm) REVERT: E 540 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7380 (mp-120) REVERT: E 577 GLN cc_start: 0.7445 (mt0) cc_final: 0.7153 (tp40) REVERT: E 651 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7674 (t0) REVERT: F 2 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7658 (mp10) outliers start: 62 outliers final: 56 residues processed: 293 average time/residue: 0.2524 time to fit residues: 121.0254 Evaluate side-chains 292 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 233 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 651 ASN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 95 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.092049 restraints weight = 37346.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.094713 restraints weight = 22981.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096463 restraints weight = 16720.865| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19587 Z= 0.198 Angle : 0.626 14.810 26622 Z= 0.316 Chirality : 0.044 0.397 3255 Planarity : 0.004 0.040 3273 Dihedral : 6.037 56.881 4207 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.05 % Allowed : 15.24 % Favored : 81.71 % 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: -1.02 (0.18), residues: 2286 helix: 1.11 (0.29), residues: 360 sheet: -0.21 (0.19), residues: 774 loop : -1.62 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 571 HIS 0.002 0.001 HIS A 85 PHE 0.015 0.001 PHE H 67 TYR 0.021 0.001 TYR G 67 ARG 0.005 0.000 ARG D 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3605.18 seconds wall clock time: 66 minutes 31.97 seconds (3991.97 seconds total)