Starting phenix.real_space_refine on Mon Mar 18 06:10:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euw_28619/03_2024/8euw_28619.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euw_28619/03_2024/8euw_28619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euw_28619/03_2024/8euw_28619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euw_28619/03_2024/8euw_28619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euw_28619/03_2024/8euw_28619.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euw_28619/03_2024/8euw_28619.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 12444 2.51 5 N 3336 2.21 5 O 4131 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 659": "OD1" <-> "OD2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C ASP 107": "OD1" <-> "OD2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C ASP 412": "OD1" <-> "OD2" Residue "D ASP 624": "OD1" <-> "OD2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D GLU 657": "OE1" <-> "OE2" Residue "E GLU 87": "OE1" <-> "OE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 325": "OD1" <-> "OD2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "F ASP 624": "OD1" <-> "OD2" Residue "F ASP 632": "OD1" <-> "OD2" Residue "F GLU 648": "OE1" <-> "OE2" Residue "F GLU 654": "OE1" <-> "OE2" Residue "F ASP 659": "OD1" <-> "OD2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "I TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 100": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "K TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 56": "OD1" <-> "OD2" 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: 20040 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "C" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "E" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "G" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.43, per 1000 atoms: 0.52 Number of scatterers: 20040 At special positions: 0 Unit cell: (153.55, 143.59, 121.18, 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 129 16.00 O 4131 8.00 N 3336 7.00 C 12444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN W 4 " - " MAN W 5 " " MAN g 4 " - " MAN g 5 " ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA W 3 " - " MAN W 4 " " BMA g 3 " - " MAN g 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 295 " " NAG A 604 " - " ASN A 301 " " NAG A 605 " - " ASN A 197 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 133 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 295 " " NAG C 604 " - " ASN C 301 " " NAG C 605 " - " ASN C 197 " " NAG C 606 " - " ASN C 276 " " NAG C 607 " - " ASN C 133 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 392 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 301 " " NAG E 605 " - " ASN E 197 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 133 " " NAG M 1 " - " ASN A 160 " " NAG N 1 " - " ASN A 88 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 156 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN A 363 " " NAG T 1 " - " ASN C 160 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN C 386 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 332 " " NAG Z 1 " - " ASN C 363 " " NAG a 1 " - " ASN A 448 " " NAG b 1 " - " ASN E 160 " " NAG c 1 " - " ASN C 448 " " NAG d 1 " - " ASN E 88 " " NAG e 1 " - " ASN E 448 " " NAG f 1 " - " ASN E 386 " " NAG g 1 " - " ASN E 262 " " NAG h 1 " - " ASN E 156 " " NAG i 1 " - " ASN E 332 " " NAG j 1 " - " ASN E 363 " Time building additional restraints: 8.46 Conformation dependent library (CDL) restraints added in 3.4 seconds 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 44 sheets defined 21.5% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.878A pdb=" N ALA A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.053A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 removed outlier: 4.010A pdb=" N ARG A 151 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.943A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.986A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.309A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.151A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 574 Processing helix chain 'B' and resid 575 through 595 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.800A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.810A pdb=" N ALA C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.047A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 removed outlier: 4.035A pdb=" N ARG C 151 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.978A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.969A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.209A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.647A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 removed outlier: 3.849A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.787A pdb=" N ALA E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.031A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.299A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.965A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.186A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.677A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 595 removed outlier: 4.182A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN F 577 " --> pdb=" O ILE F 573 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.949A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 removed outlier: 3.810A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.923A pdb=" N ASN G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.826A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 100A removed outlier: 3.609A pdb=" N ASN G 100 " --> pdb=" O TYR G 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.934A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.985A pdb=" N ASN I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.782A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.016A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.873A pdb=" N ASN K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.790A pdb=" N THR K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 100A removed outlier: 3.649A pdb=" N ASN K 100 " --> pdb=" O TYR K 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.904A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.646A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.778A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.410A 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 removed outlier: 6.933A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) 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 120 through 121 removed outlier: 3.835A pdb=" N VAL A 120 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 6.320A 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 Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.444A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.401A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.411A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.863A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.411A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.401A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.511A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.886A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.775A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.954A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.409A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.446A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.342A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.915A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.342A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.511A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.787A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.746A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.938A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.389A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.446A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.969A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.379A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.020A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.379A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.969A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.440A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.377A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.807A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 7 removed outlier: 11.870A pdb=" N CYS H 23 " --> pdb=" O THR H 74 " (cutoff:3.500A) removed outlier: 10.953A pdb=" N THR H 74 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 11.911A pdb=" N ALA H 25 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 11.627A pdb=" N THR H 72 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N GLN H 27 " --> pdb=" O HIS H 70 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N HIS H 70 " --> pdb=" O GLN H 27 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 13 removed outlier: 7.107A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.474A pdb=" N LEU I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.805A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 4 through 7 removed outlier: 11.953A pdb=" N CYS J 23 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N THR J 74 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N ALA J 25 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 11.603A pdb=" N THR J 72 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 11.264A pdb=" N GLN J 27 " --> pdb=" O HIS J 70 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N HIS J 70 " --> pdb=" O GLN J 27 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 10 through 13 removed outlier: 7.200A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.902A pdb=" N THR J 97 " --> pdb=" O HIS J 90 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.378A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.805A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 4 through 7 removed outlier: 11.951A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.855A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.523A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.169A pdb=" N GLN L 27 " --> pdb=" O HIS L 70 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N HIS L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.112A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.933A pdb=" N THR L 97 " --> pdb=" O HIS L 90 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 1962 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: 8.02 Time building geometry restraints manager: 9.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.28: 3154 1.28 - 1.58: 16932 1.58 - 1.89: 175 1.89 - 2.19: 0 2.19 - 2.49: 1 Bond restraints: 20262 Sorted by residual: bond pdb=" CB PRO J 95 " pdb=" CG PRO J 95 " ideal model delta sigma weight residual 1.506 2.490 -0.984 3.90e-02 6.57e+02 6.37e+02 bond pdb=" CG PRO J 95 " pdb=" CD PRO J 95 " ideal model delta sigma weight residual 1.512 0.982 0.530 2.70e-02 1.37e+03 3.86e+02 bond pdb=" N PRO J 95 " pdb=" CA PRO J 95 " ideal model delta sigma weight residual 1.468 1.305 0.163 1.70e-02 3.46e+03 9.25e+01 bond pdb=" N PRO J 95 " pdb=" CD PRO J 95 " ideal model delta sigma weight residual 1.474 1.597 -0.123 1.40e-02 5.10e+03 7.69e+01 bond pdb=" CA PRO J 95 " pdb=" CB PRO J 95 " ideal model delta sigma weight residual 1.533 1.428 0.105 1.80e-02 3.09e+03 3.40e+01 ... (remaining 20257 not shown) Histogram of bond angle deviations from ideal: 14.91 - 38.74: 1 38.74 - 62.57: 0 62.57 - 86.40: 0 86.40 - 110.23: 4909 110.23 - 134.06: 22594 Bond angle restraints: 27504 Sorted by residual: angle pdb=" CB PRO J 95 " pdb=" CG PRO J 95 " pdb=" CD PRO J 95 " ideal model delta sigma weight residual 105.40 14.91 90.49 2.30e+00 1.89e-01 1.55e+03 angle pdb=" N PRO J 95 " pdb=" CA PRO J 95 " pdb=" CB PRO J 95 " ideal model delta sigma weight residual 102.60 87.77 14.83 1.10e+00 8.26e-01 1.82e+02 angle pdb=" CA PRO J 95 " pdb=" N PRO J 95 " pdb=" CD PRO J 95 " ideal model delta sigma weight residual 111.50 95.16 16.34 1.40e+00 5.10e-01 1.36e+02 angle pdb=" N PRO J 95 " pdb=" CD PRO J 95 " pdb=" CG PRO J 95 " ideal model delta sigma weight residual 103.80 91.22 12.58 1.20e+00 6.94e-01 1.10e+02 angle pdb=" CA PRO J 95 " pdb=" CB PRO J 95 " pdb=" CG PRO J 95 " ideal model delta sigma weight residual 104.00 89.67 14.33 1.90e+00 2.77e-01 5.69e+01 ... (remaining 27499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 11947 21.71 - 43.42: 915 43.42 - 65.13: 216 65.13 - 86.84: 56 86.84 - 108.55: 27 Dihedral angle restraints: 13161 sinusoidal: 6276 harmonic: 6885 Sorted by residual: dihedral pdb=" CB CYS C 201 " pdb=" SG CYS C 201 " pdb=" SG CYS C 433 " pdb=" CB CYS C 433 " ideal model delta sinusoidal sigma weight residual -86.00 -147.90 61.90 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CB CYS A 201 " pdb=" SG CYS A 201 " pdb=" SG CYS A 433 " pdb=" CB CYS A 433 " ideal model delta sinusoidal sigma weight residual -86.00 -145.66 59.66 1 1.00e+01 1.00e-02 4.75e+01 dihedral pdb=" CB CYS E 201 " pdb=" SG CYS E 201 " pdb=" SG CYS E 433 " pdb=" CB CYS E 433 " ideal model delta sinusoidal sigma weight residual -86.00 -145.08 59.08 1 1.00e+01 1.00e-02 4.67e+01 ... (remaining 13158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 3257 0.129 - 0.257: 54 0.257 - 0.386: 9 0.386 - 0.515: 0 0.515 - 0.643: 1 Chirality restraints: 3321 Sorted by residual: chirality pdb=" CA PRO J 95 " pdb=" N PRO J 95 " pdb=" C PRO J 95 " pdb=" CB PRO J 95 " both_signs ideal model delta sigma weight residual False 2.72 2.07 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3318 not shown) Planarity restraints: 3444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR J 94 " -0.103 5.00e-02 4.00e+02 1.45e-01 3.36e+01 pdb=" N PRO J 95 " 0.250 5.00e-02 4.00e+02 pdb=" CA PRO J 95 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO J 95 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 136 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C ASN E 136 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN E 136 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN E 137 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN J 79 " 0.038 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO J 80 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO J 80 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 80 " 0.033 5.00e-02 4.00e+02 ... (remaining 3441 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 232 2.64 - 3.20: 16996 3.20 - 3.77: 30714 3.77 - 4.33: 45236 4.33 - 4.90: 73383 Nonbonded interactions: 166561 Sorted by model distance: nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.072 2.440 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.085 2.440 nonbonded pdb=" OG SER C 56 " pdb=" OG1 THR C 71 " model vdw 2.121 2.440 nonbonded pdb=" OG SER E 56 " pdb=" OG1 THR E 71 " model vdw 2.125 2.440 nonbonded pdb=" OG SER A 56 " pdb=" OG1 THR A 71 " model vdw 2.140 2.440 ... (remaining 166556 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'N' selection = chain 'U' selection = chain 'd' } ncs_group { reference = chain 'P' selection = chain 'W' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 19.920 Check model and map are aligned: 0.350 Set scattering table: 0.180 Process input model: 54.570 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.320 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:14.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.009 0.984 20262 Z= 0.537 Angle : 0.892 90.495 27504 Z= 0.424 Chirality : 0.051 0.643 3321 Planarity : 0.005 0.145 3399 Dihedral : 16.628 108.549 8601 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.48 % Allowed : 12.64 % Favored : 86.88 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.06 % 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: 0.65 (0.18), residues: 2352 helix: 1.14 (0.29), residues: 411 sheet: 0.33 (0.18), residues: 780 loop : 0.40 (0.20), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 47 HIS 0.005 0.001 HIS I 35 PHE 0.009 0.001 PHE C 382 TYR 0.028 0.001 TYR A 173 ARG 0.007 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 224 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 637 ASN cc_start: 0.7362 (m110) cc_final: 0.6809 (m110) REVERT: L 79 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.5775 (tm-30) outliers start: 10 outliers final: 7 residues processed: 234 average time/residue: 1.3235 time to fit residues: 349.8963 Evaluate side-chains 225 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 280 ASN B 591 GLN C 130 GLN E 130 GLN E 136 ASN E 422 GLN F 591 GLN G 32 ASN G 76 ASN I 32 ASN I 76 ASN J 90 HIS K 32 ASN K 76 ASN L 37 GLN L 90 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 20262 Z= 0.217 Angle : 0.549 7.601 27504 Z= 0.284 Chirality : 0.045 0.285 3321 Planarity : 0.004 0.061 3399 Dihedral : 9.862 73.277 4241 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.44 % Allowed : 12.36 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.82 (0.18), residues: 2352 helix: 1.06 (0.28), residues: 423 sheet: 0.44 (0.18), residues: 801 loop : 0.62 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 96 HIS 0.005 0.001 HIS K 35 PHE 0.016 0.002 PHE E 383 TYR 0.015 0.001 TYR C 173 ARG 0.004 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 236 time to evaluate : 2.155 Fit side-chains revert: symmetry clash REVERT: A 325 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7223 (t0) REVERT: B 637 ASN cc_start: 0.7472 (m110) cc_final: 0.6865 (m-40) REVERT: C 325 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7121 (t0) REVERT: J 91 MET cc_start: 0.5847 (OUTLIER) cc_final: 0.5594 (ptp) REVERT: L 79 GLN cc_start: 0.6753 (OUTLIER) cc_final: 0.6131 (tm-30) REVERT: L 91 MET cc_start: 0.5797 (ptt) cc_final: 0.5281 (ptp) outliers start: 51 outliers final: 21 residues processed: 267 average time/residue: 1.2900 time to fit residues: 389.4502 Evaluate side-chains 250 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 225 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 91 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 232 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 213 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 130 GLN C 130 GLN C 440 GLN E 130 GLN E 440 GLN G 32 ASN G 76 ASN I 32 ASN I 76 ASN K 32 ASN K 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20262 Z= 0.296 Angle : 0.599 10.878 27504 Z= 0.307 Chirality : 0.047 0.302 3321 Planarity : 0.004 0.062 3399 Dihedral : 8.611 60.515 4233 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.44 % Allowed : 13.75 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.68 (0.18), residues: 2352 helix: 0.94 (0.27), residues: 423 sheet: 0.36 (0.18), residues: 759 loop : 0.51 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 35 HIS 0.006 0.001 HIS E 352 PHE 0.020 0.002 PHE E 383 TYR 0.015 0.002 TYR E 384 ARG 0.004 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 228 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7302 (mppt) REVERT: A 92 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: A 325 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7242 (t0) REVERT: B 637 ASN cc_start: 0.7479 (m110) cc_final: 0.6869 (m-40) REVERT: C 130 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8189 (mp-120) REVERT: C 325 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7083 (t0) REVERT: C 440 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8072 (tp-100) REVERT: D 588 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7775 (tmm160) REVERT: H 79 GLN cc_start: 0.6634 (OUTLIER) cc_final: 0.5915 (tm-30) REVERT: L 79 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6210 (tm-30) REVERT: L 91 MET cc_start: 0.5863 (ptt) cc_final: 0.5434 (ptp) outliers start: 51 outliers final: 22 residues processed: 257 average time/residue: 1.3916 time to fit residues: 402.1575 Evaluate side-chains 251 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 220 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 103 GLN A 130 GLN E 130 GLN E 136 ASN E 440 GLN G 32 ASN I 32 ASN I 76 ASN K 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 20262 Z= 0.459 Angle : 0.701 9.467 27504 Z= 0.357 Chirality : 0.051 0.339 3321 Planarity : 0.005 0.070 3399 Dihedral : 8.548 59.824 4233 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.26 % Allowed : 14.42 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.27 (0.17), residues: 2352 helix: 0.09 (0.25), residues: 447 sheet: 0.32 (0.18), residues: 750 loop : 0.30 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 427 HIS 0.009 0.002 HIS A 352 PHE 0.023 0.002 PHE E 383 TYR 0.022 0.002 TYR E 384 ARG 0.004 0.001 ARG E 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 217 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7327 (mppt) REVERT: A 92 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7262 (tp30) REVERT: B 637 ASN cc_start: 0.7502 (m110) cc_final: 0.6879 (m-40) REVERT: C 325 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7080 (t0) REVERT: D 588 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7780 (tmm160) REVERT: H 79 GLN cc_start: 0.6601 (OUTLIER) cc_final: 0.5921 (tm-30) REVERT: J 42 LYS cc_start: 0.6348 (OUTLIER) cc_final: 0.5931 (ptpp) REVERT: L 79 GLN cc_start: 0.6868 (OUTLIER) cc_final: 0.6406 (tm-30) REVERT: L 91 MET cc_start: 0.6024 (ptt) cc_final: 0.5623 (ptp) outliers start: 68 outliers final: 37 residues processed: 262 average time/residue: 1.3541 time to fit residues: 399.4535 Evaluate side-chains 258 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 214 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 91 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 195 optimal weight: 0.2980 chunk 158 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN C 130 GLN C 440 GLN E 130 GLN E 137 ASN G 32 ASN K 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20262 Z= 0.226 Angle : 0.562 10.229 27504 Z= 0.289 Chirality : 0.045 0.319 3321 Planarity : 0.004 0.067 3399 Dihedral : 7.608 59.787 4233 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.63 % Allowed : 15.90 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.63 (0.18), residues: 2352 helix: 0.89 (0.27), residues: 423 sheet: 0.34 (0.18), residues: 768 loop : 0.47 (0.20), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 427 HIS 0.003 0.001 HIS K 35 PHE 0.018 0.001 PHE E 383 TYR 0.012 0.001 TYR C 318 ARG 0.002 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 227 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7216 (tp30) REVERT: B 637 ASN cc_start: 0.7418 (m110) cc_final: 0.6837 (m-40) REVERT: C 246 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.6245 (tm-30) REVERT: C 325 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.7031 (t0) REVERT: D 588 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7773 (tmm160) REVERT: E 91 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: H 79 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.5981 (tm-30) REVERT: J 42 LYS cc_start: 0.6367 (OUTLIER) cc_final: 0.5955 (ptpp) REVERT: L 79 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6465 (tm-30) REVERT: L 91 MET cc_start: 0.6090 (ptt) cc_final: 0.5685 (ptp) outliers start: 55 outliers final: 32 residues processed: 263 average time/residue: 1.3671 time to fit residues: 405.8075 Evaluate side-chains 255 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 215 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 91 MET Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 chunk 190 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 130 GLN C 130 GLN C 355 ASN C 422 GLN C 440 GLN E 130 GLN E 440 GLN G 32 ASN K 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20262 Z= 0.353 Angle : 0.635 12.031 27504 Z= 0.324 Chirality : 0.048 0.332 3321 Planarity : 0.005 0.066 3399 Dihedral : 7.450 59.792 4233 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.11 % Allowed : 16.28 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.49 (0.18), residues: 2352 helix: 0.55 (0.26), residues: 429 sheet: 0.30 (0.18), residues: 762 loop : 0.45 (0.20), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 427 HIS 0.005 0.001 HIS C 352 PHE 0.022 0.002 PHE E 383 TYR 0.017 0.002 TYR E 384 ARG 0.003 0.000 ARG E 444 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 217 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7318 (mppt) REVERT: A 92 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7227 (tp30) REVERT: B 637 ASN cc_start: 0.7463 (m110) cc_final: 0.6873 (m-40) REVERT: C 137 ASN cc_start: 0.7685 (m-40) cc_final: 0.7424 (m-40) REVERT: C 246 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.6362 (tm-30) REVERT: C 325 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7054 (t0) REVERT: D 588 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7765 (tmm160) REVERT: E 87 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7307 (mm-30) REVERT: E 178 ARG cc_start: 0.8256 (tpt90) cc_final: 0.8048 (tpt90) REVERT: E 289 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8729 (p0) REVERT: H 79 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.6012 (tm-30) REVERT: J 42 LYS cc_start: 0.6442 (OUTLIER) cc_final: 0.6043 (ptpp) REVERT: K 69 MET cc_start: 0.7614 (mtt) cc_final: 0.7318 (mtp) REVERT: L 79 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6566 (tm-30) REVERT: L 91 MET cc_start: 0.6120 (ptt) cc_final: 0.5746 (ptp) outliers start: 65 outliers final: 38 residues processed: 260 average time/residue: 1.4017 time to fit residues: 409.6005 Evaluate side-chains 259 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 212 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 91 MET Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 129 optimal weight: 0.0770 chunk 193 optimal weight: 0.6980 chunk 128 optimal weight: 0.0970 chunk 228 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 130 GLN C 130 GLN C 355 ASN C 440 GLN D 630 GLN E 130 GLN E 136 ASN E 440 GLN F 543 ASN G 32 ASN K 32 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20262 Z= 0.155 Angle : 0.513 12.385 27504 Z= 0.264 Chirality : 0.043 0.311 3321 Planarity : 0.004 0.063 3399 Dihedral : 6.553 59.905 4233 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.01 % Allowed : 17.39 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.76 (0.18), residues: 2352 helix: 1.08 (0.27), residues: 429 sheet: 0.41 (0.18), residues: 768 loop : 0.53 (0.20), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 427 HIS 0.003 0.001 HIS K 35 PHE 0.014 0.001 PHE E 383 TYR 0.013 0.001 TYR C 173 ARG 0.001 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 234 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.7800 (ptpt) cc_final: 0.7537 (pttm) REVERT: B 589 ASP cc_start: 0.8245 (m-30) cc_final: 0.8027 (m-30) REVERT: B 637 ASN cc_start: 0.7359 (m110) cc_final: 0.6839 (m-40) REVERT: C 137 ASN cc_start: 0.7605 (m-40) cc_final: 0.7344 (m-40) REVERT: C 246 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.6179 (tm-30) REVERT: C 325 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7015 (t0) REVERT: D 588 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7734 (tmm160) REVERT: E 440 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7965 (tp-100) REVERT: H 32 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6794 (mm-30) REVERT: H 79 GLN cc_start: 0.6640 (OUTLIER) cc_final: 0.6018 (tm-30) REVERT: J 42 LYS cc_start: 0.6413 (OUTLIER) cc_final: 0.6019 (ptpp) REVERT: L 79 GLN cc_start: 0.6785 (OUTLIER) cc_final: 0.6521 (tm-30) REVERT: L 91 MET cc_start: 0.6080 (ptt) cc_final: 0.5635 (ptp) outliers start: 42 outliers final: 20 residues processed: 261 average time/residue: 1.3725 time to fit residues: 401.8112 Evaluate side-chains 257 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 229 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 91 MET Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 155 optimal weight: 0.3980 chunk 112 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 207 optimal weight: 30.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 280 ASN C 130 GLN C 355 ASN C 440 GLN E 130 GLN F 543 ASN G 32 ASN K 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 20262 Z= 0.373 Angle : 0.650 14.599 27504 Z= 0.329 Chirality : 0.048 0.328 3321 Planarity : 0.005 0.064 3399 Dihedral : 6.821 59.700 4233 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.30 % Allowed : 17.34 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.58 (0.18), residues: 2352 helix: 0.76 (0.27), residues: 423 sheet: 0.40 (0.18), residues: 756 loop : 0.41 (0.20), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 427 HIS 0.006 0.001 HIS K 35 PHE 0.022 0.002 PHE C 383 TYR 0.019 0.002 TYR E 384 ARG 0.003 0.000 ARG E 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 216 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7221 (tp30) REVERT: B 637 ASN cc_start: 0.7347 (m110) cc_final: 0.6831 (m-40) REVERT: C 137 ASN cc_start: 0.7691 (m-40) cc_final: 0.7429 (m-40) REVERT: C 325 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7054 (t0) REVERT: D 588 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7750 (tmm160) REVERT: E 87 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7303 (mm-30) REVERT: E 269 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6675 (mm-30) REVERT: H 79 GLN cc_start: 0.6667 (OUTLIER) cc_final: 0.6035 (tm-30) REVERT: J 42 LYS cc_start: 0.6489 (OUTLIER) cc_final: 0.6104 (ptpp) REVERT: L 91 MET cc_start: 0.6175 (ptt) cc_final: 0.5830 (ptp) outliers start: 48 outliers final: 30 residues processed: 247 average time/residue: 1.4510 time to fit residues: 401.3930 Evaluate side-chains 249 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 213 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 91 MET Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 212 optimal weight: 20.0000 chunk 128 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 192 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 225 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 280 ASN B 591 GLN C 130 GLN C 355 ASN C 440 GLN E 130 GLN E 440 GLN F 543 ASN G 32 ASN K 32 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20262 Z= 0.296 Angle : 0.606 14.023 27504 Z= 0.308 Chirality : 0.046 0.321 3321 Planarity : 0.004 0.065 3399 Dihedral : 6.667 59.913 4233 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.68 % Allowed : 16.95 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.55 (0.18), residues: 2352 helix: 0.71 (0.27), residues: 429 sheet: 0.40 (0.18), residues: 756 loop : 0.38 (0.20), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 427 HIS 0.006 0.001 HIS K 35 PHE 0.019 0.002 PHE E 383 TYR 0.015 0.002 TYR E 384 ARG 0.003 0.000 ARG E 444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 215 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7207 (tp30) REVERT: A 430 ILE cc_start: 0.8852 (mm) cc_final: 0.8642 (mp) REVERT: B 637 ASN cc_start: 0.7234 (m110) cc_final: 0.6782 (m110) REVERT: C 137 ASN cc_start: 0.7632 (m-40) cc_final: 0.7361 (m-40) REVERT: C 325 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7002 (t0) REVERT: D 588 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7748 (tmm160) REVERT: E 87 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7183 (mm-30) REVERT: E 91 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6963 (tm-30) REVERT: E 269 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6670 (mm-30) REVERT: F 641 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8053 (pp) REVERT: H 79 GLN cc_start: 0.6688 (OUTLIER) cc_final: 0.6040 (tm-30) REVERT: J 42 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.6034 (ptpp) REVERT: L 91 MET cc_start: 0.6174 (ptt) cc_final: 0.5833 (ptp) outliers start: 56 outliers final: 37 residues processed: 249 average time/residue: 1.3810 time to fit residues: 385.4665 Evaluate side-chains 256 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 211 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 91 MET Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 236 optimal weight: 8.9990 chunk 217 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 280 ASN C 130 GLN C 355 ASN C 440 GLN E 130 GLN E 440 GLN F 543 ASN G 32 ASN K 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20262 Z= 0.212 Angle : 0.564 13.679 27504 Z= 0.288 Chirality : 0.044 0.316 3321 Planarity : 0.004 0.063 3399 Dihedral : 6.417 59.869 4233 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.39 % Allowed : 17.34 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.69 (0.18), residues: 2352 helix: 0.96 (0.27), residues: 426 sheet: 0.43 (0.18), residues: 756 loop : 0.46 (0.20), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 427 HIS 0.005 0.001 HIS G 35 PHE 0.016 0.001 PHE E 383 TYR 0.011 0.001 TYR C 173 ARG 0.003 0.000 ARG E 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 217 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7181 (tp30) REVERT: B 637 ASN cc_start: 0.7245 (m110) cc_final: 0.6821 (m110) REVERT: C 137 ASN cc_start: 0.7607 (m-40) cc_final: 0.7340 (m-40) REVERT: C 325 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7014 (t0) REVERT: C 440 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8118 (tp-100) REVERT: D 588 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7730 (tmm160) REVERT: E 91 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6977 (tm-30) REVERT: E 269 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6651 (mm-30) REVERT: F 641 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8030 (pp) REVERT: F 655 LYS cc_start: 0.7244 (pttt) cc_final: 0.6378 (tmtm) REVERT: H 32 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6811 (mm-30) REVERT: H 79 GLN cc_start: 0.6673 (OUTLIER) cc_final: 0.6025 (tm-30) REVERT: J 42 LYS cc_start: 0.6488 (OUTLIER) cc_final: 0.6044 (ptpp) REVERT: K 69 MET cc_start: 0.7648 (mtt) cc_final: 0.7369 (mtp) REVERT: L 91 MET cc_start: 0.6157 (ptt) cc_final: 0.5844 (ptp) outliers start: 50 outliers final: 33 residues processed: 249 average time/residue: 1.4668 time to fit residues: 411.4692 Evaluate side-chains 260 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 217 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 91 MET Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 0.0010 chunk 173 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 188 optimal weight: 0.0050 chunk 78 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 165 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 280 ASN C 130 GLN C 355 ASN E 130 GLN E 440 GLN G 32 ASN K 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.194945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.141127 restraints weight = 20014.550| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.75 r_work: 0.3292 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20262 Z= 0.145 Angle : 0.516 13.200 27504 Z= 0.265 Chirality : 0.043 0.305 3321 Planarity : 0.004 0.063 3399 Dihedral : 5.904 59.726 4233 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.11 % Allowed : 17.91 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.87 (0.18), residues: 2352 helix: 1.23 (0.27), residues: 426 sheet: 0.49 (0.18), residues: 762 loop : 0.56 (0.20), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 427 HIS 0.004 0.001 HIS K 35 PHE 0.013 0.001 PHE A 382 TYR 0.013 0.001 TYR C 173 ARG 0.003 0.000 ARG C 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7341.71 seconds wall clock time: 131 minutes 4.35 seconds (7864.35 seconds total)