Starting phenix.real_space_refine on Sat Feb 17 19:55:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u02_20594/02_2024/6u02_20594.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u02_20594/02_2024/6u02_20594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u02_20594/02_2024/6u02_20594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u02_20594/02_2024/6u02_20594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u02_20594/02_2024/6u02_20594.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u02_20594/02_2024/6u02_20594.pdb" } resolution = 3.05 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= 0.160 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 120 5.16 5 C 12284 2.51 5 N 3336 2.21 5 O 3932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 283": "OE1" <-> "OE2" Residue "J TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19672 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3054 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 366} Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "B" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3054 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 366} Chain: "C" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "E" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3054 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 366} Chain: "F" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "J" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3054 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 366} Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "K" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "M" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "N" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "O" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "P" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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 Time building chain proxies: 10.38, per 1000 atoms: 0.53 Number of scatterers: 19672 At special positions: 0 Unit cell: (198.79, 198.79, 84.46, 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 120 16.00 O 3932 8.00 N 3336 7.00 C 12284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.04 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.04 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.02 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.02 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.02 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.09 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.04 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.02 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.02 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.09 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 417 " distance=2.04 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.04 Simple disulfide: pdb=" SG CYS E 175 " - pdb=" SG CYS E 193 " distance=2.03 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 230 " distance=2.02 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 237 " distance=2.02 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 291 " distance=2.02 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 289 " distance=2.02 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.02 Simple disulfide: pdb=" SG CYS E 421 " - pdb=" SG CYS E 447 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.09 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.04 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.04 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.03 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 230 " distance=2.02 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.02 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.02 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.02 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.02 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.09 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " 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 M 4 " - " MAN M 5 " " MAN M 5 " - " MAN M 6 " " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN P 4 " - " MAN P 5 " " MAN P 5 " - " MAN P 6 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " MAN M 7 " - " MAN M 8 " " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " BMA O 3 " - " MAN O 4 " " MAN O 7 " - " MAN O 8 " " BMA P 3 " - " MAN P 4 " " MAN P 7 " - " MAN P 8 " ALPHA1-6 " BMA M 3 " - " MAN M 7 " " MAN M 7 " - " MAN M 9 " " BMA N 3 " - " MAN N 7 " " MAN N 7 " - " MAN N 9 " " BMA O 3 " - " MAN O 7 " " MAN O 7 " - " MAN O 9 " " BMA P 3 " - " MAN P 7 " " MAN P 7 " - " MAN P 9 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG A 510 " - " ASN A 86 " " NAG A 511 " - " ASN A 146 " " NAG B 510 " - " ASN B 86 " " NAG B 511 " - " ASN B 146 " " NAG E 510 " - " ASN E 86 " " NAG E 511 " - " ASN E 146 " " NAG J 510 " - " ASN J 86 " " NAG J 511 " - " ASN J 146 " " NAG M 1 " - " ASN A 200 " " NAG N 1 " - " ASN B 200 " " NAG O 1 " - " ASN E 200 " " NAG P 1 " - " ASN J 200 " Time building additional restraints: 8.56 Conformation dependent library (CDL) restraints added in 3.5 seconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 48 sheets defined 7.0% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 356 through 359 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.131A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 356 through 359 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.131A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 356 through 359 Processing helix chain 'E' and resid 463 through 468 Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.131A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 104 through 109 Processing helix chain 'J' and resid 142 through 146 Processing helix chain 'J' and resid 356 through 359 Processing helix chain 'J' and resid 463 through 468 Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.131A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.725A pdb=" N SER A 445 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA A 420 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 125 removed outlier: 4.716A pdb=" N LEU A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR A 138 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 158 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.633A pdb=" N ALA A 203 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU A 214 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 205 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 236 through 244 removed outlier: 7.433A pdb=" N THR A 252 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER A 267 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A 254 " --> pdb=" O TRP A 265 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TRP A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR A 256 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 283 removed outlier: 4.626A pdb=" N CYS A 278 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR A 290 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS A 280 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR A 288 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY A 282 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.870A pdb=" N SER A 372 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.643A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.251A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.251A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.606A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AB4, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.726A pdb=" N SER B 445 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA B 420 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 115 through 125 removed outlier: 4.715A pdb=" N LEU B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR B 138 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU B 158 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.633A pdb=" N ALA B 203 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU B 214 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 205 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 236 through 244 removed outlier: 7.434A pdb=" N THR B 252 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER B 267 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE B 254 " --> pdb=" O TRP B 265 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRP B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR B 256 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 276 through 283 removed outlier: 4.627A pdb=" N CYS B 278 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N THR B 290 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS B 280 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR B 288 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY B 282 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.870A pdb=" N SER B 372 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU B 399 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 393 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.644A pdb=" N SER C 67 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.607A pdb=" N MET D 34 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA D 40 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLY D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AC7, first strand: chain 'E' and resid 96 through 102 removed outlier: 6.726A pdb=" N SER E 445 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALA E 420 " --> pdb=" O SER E 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 115 through 125 removed outlier: 4.715A pdb=" N LEU E 115 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR E 138 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU E 158 " --> pdb=" O GLU E 174 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 179 through 184 removed outlier: 6.634A pdb=" N ALA E 203 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU E 214 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL E 205 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 236 through 244 removed outlier: 7.434A pdb=" N THR E 252 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER E 267 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE E 254 " --> pdb=" O TRP E 265 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TRP E 265 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR E 256 " --> pdb=" O LEU E 263 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 276 through 283 removed outlier: 4.626A pdb=" N CYS E 278 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR E 290 " --> pdb=" O CYS E 278 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS E 280 " --> pdb=" O THR E 288 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR E 288 " --> pdb=" O CYS E 280 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY E 282 " --> pdb=" O GLY E 286 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 353 through 354 removed outlier: 6.870A pdb=" N SER E 372 " --> pdb=" O LEU E 399 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU E 399 " --> pdb=" O SER E 372 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR E 374 " --> pdb=" O ILE E 397 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN E 393 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.644A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.607A pdb=" N MET G 34 " --> pdb=" O ASN G 50 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA G 40 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLY G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 11 Processing sheet with id=AE1, first strand: chain 'J' and resid 96 through 102 removed outlier: 6.726A pdb=" N SER J 445 " --> pdb=" O TYR J 100 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALA J 420 " --> pdb=" O SER J 448 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 115 through 125 removed outlier: 4.716A pdb=" N LEU J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR J 138 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU J 158 " --> pdb=" O GLU J 174 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 179 through 184 removed outlier: 6.633A pdb=" N ALA J 203 " --> pdb=" O GLU J 214 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU J 214 " --> pdb=" O ALA J 203 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL J 205 " --> pdb=" O VAL J 212 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 236 through 244 removed outlier: 7.434A pdb=" N THR J 252 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER J 267 " --> pdb=" O THR J 252 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE J 254 " --> pdb=" O TRP J 265 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TRP J 265 " --> pdb=" O ILE J 254 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR J 256 " --> pdb=" O LEU J 263 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 276 through 283 removed outlier: 4.626A pdb=" N CYS J 278 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR J 290 " --> pdb=" O CYS J 278 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS J 280 " --> pdb=" O THR J 288 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR J 288 " --> pdb=" O CYS J 280 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY J 282 " --> pdb=" O GLY J 286 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY J 286 " --> pdb=" O GLY J 282 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 353 through 354 removed outlier: 6.870A pdb=" N SER J 372 " --> pdb=" O LEU J 399 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU J 399 " --> pdb=" O SER J 372 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR J 374 " --> pdb=" O ILE J 397 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN J 393 " --> pdb=" O LYS J 378 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.644A pdb=" N SER I 67 " --> pdb=" O ASP I 70 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.251A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.251A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.606A pdb=" N MET K 34 " --> pdb=" O ASN K 50 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA K 40 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLY K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 11 684 hydrogen bonds defined for protein. 1536 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: 7.61 Time building geometry restraints manager: 9.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3633 1.31 - 1.45: 6238 1.45 - 1.58: 10129 1.58 - 1.71: 16 1.71 - 1.85: 144 Bond restraints: 20160 Sorted by residual: bond pdb=" C1 NAG A 510 " pdb=" O5 NAG A 510 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C1 NAG J 510 " pdb=" O5 NAG J 510 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C1 NAG B 510 " pdb=" O5 NAG B 510 " ideal model delta sigma weight residual 1.406 1.543 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C1 NAG E 510 " pdb=" O5 NAG E 510 " ideal model delta sigma weight residual 1.406 1.543 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.542 -0.136 2.00e-02 2.50e+03 4.63e+01 ... (remaining 20155 not shown) Histogram of bond angle deviations from ideal: 93.81 - 101.93: 76 101.93 - 110.06: 5285 110.06 - 118.18: 10187 118.18 - 126.30: 11489 126.30 - 134.43: 375 Bond angle restraints: 27412 Sorted by residual: angle pdb=" C TYR A 341 " pdb=" N PRO A 342 " pdb=" CA PRO A 342 " ideal model delta sigma weight residual 120.03 129.26 -9.23 9.90e-01 1.02e+00 8.68e+01 angle pdb=" C TYR J 341 " pdb=" N PRO J 342 " pdb=" CA PRO J 342 " ideal model delta sigma weight residual 120.03 129.25 -9.22 9.90e-01 1.02e+00 8.67e+01 angle pdb=" C TYR B 341 " pdb=" N PRO B 342 " pdb=" CA PRO B 342 " ideal model delta sigma weight residual 120.03 129.24 -9.21 9.90e-01 1.02e+00 8.66e+01 angle pdb=" C TYR E 341 " pdb=" N PRO E 342 " pdb=" CA PRO E 342 " ideal model delta sigma weight residual 120.03 129.22 -9.19 9.90e-01 1.02e+00 8.62e+01 angle pdb=" C ASP A 330 " pdb=" N PRO A 331 " pdb=" CA PRO A 331 " ideal model delta sigma weight residual 120.98 130.76 -9.78 1.07e+00 8.73e-01 8.35e+01 ... (remaining 27407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 12088 21.67 - 43.35: 292 43.35 - 65.02: 80 65.02 - 86.70: 40 86.70 - 108.37: 20 Dihedral angle restraints: 12520 sinusoidal: 5464 harmonic: 7056 Sorted by residual: dihedral pdb=" CB CYS J 318 " pdb=" SG CYS J 318 " pdb=" SG CYS J 337 " pdb=" CB CYS J 337 " ideal model delta sinusoidal sigma weight residual 93.00 130.69 -37.69 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CB CYS B 318 " pdb=" SG CYS B 318 " pdb=" SG CYS B 337 " pdb=" CB CYS B 337 " ideal model delta sinusoidal sigma weight residual 93.00 130.68 -37.68 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 130.65 -37.65 1 1.00e+01 1.00e-02 2.00e+01 ... (remaining 12517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2212 0.102 - 0.204: 716 0.204 - 0.306: 111 0.306 - 0.408: 21 0.408 - 0.510: 4 Chirality restraints: 3064 Sorted by residual: chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.32e+01 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.30e+01 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.19e+01 ... (remaining 3061 not shown) Planarity restraints: 3476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 155 " -0.056 2.00e-02 2.50e+03 2.85e-02 1.63e+01 pdb=" CG TYR B 155 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 155 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 155 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 155 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 155 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 155 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 155 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 155 " -0.056 2.00e-02 2.50e+03 2.84e-02 1.61e+01 pdb=" CG TYR E 155 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR E 155 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR E 155 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR E 155 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 155 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR E 155 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 155 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 155 " 0.056 2.00e-02 2.50e+03 2.83e-02 1.60e+01 pdb=" CG TYR J 155 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR J 155 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR J 155 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR J 155 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR J 155 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR J 155 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR J 155 " 0.033 2.00e-02 2.50e+03 ... (remaining 3473 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 9692 2.94 - 3.43: 16837 3.43 - 3.92: 34456 3.92 - 4.41: 41521 4.41 - 4.90: 67558 Nonbonded interactions: 170064 Sorted by model distance: nonbonded pdb=" N ASP B 434 " pdb=" OD1 ASP B 434 " model vdw 2.449 2.520 nonbonded pdb=" N ASP J 416 " pdb=" OD1 ASP J 416 " model vdw 2.450 2.520 nonbonded pdb=" N ASP J 434 " pdb=" OD1 ASP J 434 " model vdw 2.450 2.520 nonbonded pdb=" N ASP E 416 " pdb=" OD1 ASP E 416 " model vdw 2.450 2.520 nonbonded pdb=" N ASP A 434 " pdb=" OD1 ASP A 434 " model vdw 2.451 2.520 ... (remaining 170059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 1.570 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: 8.150 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 55.280 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 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 : 0.022 0.138 20160 Z= 1.475 Angle : 1.791 10.926 27412 Z= 1.184 Chirality : 0.101 0.510 3064 Planarity : 0.009 0.044 3464 Dihedral : 12.227 108.370 7900 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.49 % Allowed : 2.31 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.75 (0.17), residues: 2428 helix: -2.15 (0.51), residues: 48 sheet: 1.08 (0.17), residues: 892 loop : 0.31 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.008 TRP A 456 HIS 0.006 0.002 HIS E 274 PHE 0.032 0.008 PHE B 241 TYR 0.056 0.008 TYR B 155 ARG 0.010 0.001 ARG B 292 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 614 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 SER cc_start: 0.7720 (p) cc_final: 0.7408 (m) REVERT: L 54 LEU cc_start: 0.7564 (mt) cc_final: 0.7143 (mt) REVERT: B 372 SER cc_start: 0.6967 (p) cc_final: 0.6711 (m) REVERT: E 372 SER cc_start: 0.7259 (p) cc_final: 0.6968 (m) REVERT: J 372 SER cc_start: 0.7742 (p) cc_final: 0.7410 (m) REVERT: I 54 LEU cc_start: 0.7628 (mt) cc_final: 0.7230 (mt) outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.3105 time to fit residues: 290.5929 Evaluate side-chains 366 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.5980 chunk 178 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 214 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN H 72 HIS B 329 ASN D 50 ASN D 81 GLN E 329 ASN F 37 GLN G 50 ASN G 72 HIS I 37 GLN K 72 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20160 Z= 0.281 Angle : 0.710 8.584 27412 Z= 0.377 Chirality : 0.047 0.181 3064 Planarity : 0.005 0.033 3464 Dihedral : 8.834 74.480 3568 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.92 % Favored : 96.91 % Rotamer: Outliers : 2.56 % Allowed : 9.96 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2428 helix: -2.02 (0.68), residues: 48 sheet: 0.50 (0.16), residues: 960 loop : 0.10 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP J 206 HIS 0.004 0.002 HIS E 312 PHE 0.036 0.002 PHE H 67 TYR 0.018 0.002 TYR G 79 ARG 0.005 0.001 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 445 time to evaluate : 2.306 Fit side-chains revert: symmetry clash REVERT: A 372 SER cc_start: 0.8045 (p) cc_final: 0.7767 (m) REVERT: B 372 SER cc_start: 0.7748 (p) cc_final: 0.7498 (m) REVERT: C 24 ARG cc_start: 0.7455 (tpp80) cc_final: 0.7191 (tpp80) REVERT: C 97 THR cc_start: 0.6831 (p) cc_final: 0.6455 (p) REVERT: E 118 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.6994 (ttp-170) REVERT: E 372 SER cc_start: 0.7787 (p) cc_final: 0.7537 (m) REVERT: F 24 ARG cc_start: 0.7562 (tpp80) cc_final: 0.7234 (tpp80) REVERT: J 372 SER cc_start: 0.7983 (p) cc_final: 0.7687 (m) outliers start: 54 outliers final: 33 residues processed: 480 average time/residue: 0.3172 time to fit residues: 232.4610 Evaluate side-chains 391 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 357 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 216 ASN Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain I residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 0.0470 chunk 66 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 172 optimal weight: 0.0370 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN L 37 GLN H 50 ASN B 441 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 325 ASN I 37 GLN K 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 20160 Z= 0.327 Angle : 0.689 10.372 27412 Z= 0.367 Chirality : 0.047 0.306 3064 Planarity : 0.005 0.048 3464 Dihedral : 7.548 59.603 3568 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.97 % Favored : 96.87 % Rotamer: Outliers : 3.84 % Allowed : 11.86 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.35 (0.18), residues: 2428 helix: -2.30 (0.55), residues: 48 sheet: 0.50 (0.16), residues: 1008 loop : 0.23 (0.18), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 33 HIS 0.004 0.001 HIS B 150 PHE 0.047 0.002 PHE K 67 TYR 0.020 0.002 TYR B 121 ARG 0.016 0.001 ARG J 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 388 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 372 SER cc_start: 0.8314 (p) cc_final: 0.7976 (m) REVERT: E 118 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7666 (ttp-170) REVERT: F 24 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7490 (tpp80) outliers start: 81 outliers final: 49 residues processed: 433 average time/residue: 0.3158 time to fit residues: 207.8281 Evaluate side-chains 379 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 329 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 125 ASP Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 216 ASN Chi-restraints excluded: chain J residue 222 ILE Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 280 CYS Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 0.1980 chunk 161 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 0.0170 chunk 144 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 204 optimal weight: 0.0270 chunk 61 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN D 50 ASN D 72 HIS ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 20160 Z= 0.226 Angle : 0.598 14.648 27412 Z= 0.311 Chirality : 0.045 0.286 3064 Planarity : 0.004 0.052 3464 Dihedral : 6.801 49.929 3568 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 3.23 % Allowed : 14.99 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.39 (0.17), residues: 2428 helix: -2.32 (0.54), residues: 48 sheet: 0.66 (0.17), residues: 936 loop : 0.17 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 206 HIS 0.002 0.001 HIS E 150 PHE 0.033 0.002 PHE H 67 TYR 0.018 0.001 TYR L 36 ARG 0.008 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 366 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8616 (m-80) cc_final: 0.8262 (m-80) REVERT: B 170 TYR cc_start: 0.8623 (m-80) cc_final: 0.8295 (m-80) REVERT: C 24 ARG cc_start: 0.7748 (tpp80) cc_final: 0.7459 (tpp80) REVERT: E 118 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7651 (ttp-170) REVERT: E 170 TYR cc_start: 0.8664 (m-80) cc_final: 0.8328 (m-80) REVERT: F 24 ARG cc_start: 0.7896 (tpp80) cc_final: 0.7557 (tpp80) REVERT: J 170 TYR cc_start: 0.8700 (m-80) cc_final: 0.8379 (m-80) outliers start: 68 outliers final: 45 residues processed: 406 average time/residue: 0.3296 time to fit residues: 202.2084 Evaluate side-chains 385 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 339 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain J residue 125 ASP Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 280 CYS Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 81 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 157 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN H 50 ASN B 274 HIS ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN B 333 ASN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52AGLN E 274 HIS ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52AGLN J 274 HIS J 333 ASN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.9259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 20160 Z= 0.360 Angle : 0.731 18.611 27412 Z= 0.379 Chirality : 0.049 0.367 3064 Planarity : 0.005 0.076 3464 Dihedral : 7.486 52.567 3568 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.78 % Favored : 95.06 % Rotamer: Outliers : 4.03 % Allowed : 14.85 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2428 helix: -2.70 (0.47), residues: 48 sheet: 0.45 (0.17), residues: 992 loop : -0.00 (0.18), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 33 HIS 0.006 0.001 HIS J 98 PHE 0.033 0.003 PHE K 67 TYR 0.029 0.002 TYR A 418 ARG 0.007 0.001 ARG J 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 346 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 HIS cc_start: 0.7553 (m-70) cc_final: 0.7222 (m-70) REVERT: A 170 TYR cc_start: 0.9086 (m-80) cc_final: 0.8827 (m-80) REVERT: L 54 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8758 (mp) REVERT: B 170 TYR cc_start: 0.9071 (m-80) cc_final: 0.8792 (m-80) REVERT: C 24 ARG cc_start: 0.8116 (tpp80) cc_final: 0.7825 (ttm110) REVERT: D 70 SER cc_start: 0.7747 (OUTLIER) cc_final: 0.7404 (p) REVERT: E 118 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7767 (ttp-170) REVERT: E 170 TYR cc_start: 0.9072 (m-80) cc_final: 0.8791 (m-80) REVERT: F 24 ARG cc_start: 0.8210 (tpp80) cc_final: 0.7839 (ttm110) REVERT: J 170 TYR cc_start: 0.9086 (m-80) cc_final: 0.8810 (m-80) REVERT: I 24 ARG cc_start: 0.8182 (tpp80) cc_final: 0.7971 (ttm110) outliers start: 85 outliers final: 50 residues processed: 401 average time/residue: 0.3155 time to fit residues: 192.4462 Evaluate side-chains 353 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 300 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 125 ASP Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 280 CYS Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 35 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 189 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.9811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 20160 Z= 0.287 Angle : 0.635 16.075 27412 Z= 0.329 Chirality : 0.047 0.293 3064 Planarity : 0.004 0.053 3464 Dihedral : 6.912 48.788 3568 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.55 % Favored : 97.28 % Rotamer: Outliers : 3.04 % Allowed : 15.89 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2428 helix: -2.80 (0.44), residues: 48 sheet: 0.54 (0.17), residues: 992 loop : 0.07 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 33 HIS 0.009 0.001 HIS A 312 PHE 0.033 0.002 PHE H 67 TYR 0.016 0.001 TYR B 121 ARG 0.007 0.001 ARG E 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 308 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 HIS cc_start: 0.7661 (m-70) cc_final: 0.7362 (m-70) REVERT: B 190 MET cc_start: 0.8177 (ttm) cc_final: 0.7935 (ttp) REVERT: C 24 ARG cc_start: 0.8228 (tpp80) cc_final: 0.8024 (ttm110) REVERT: E 118 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7668 (ttp-170) REVERT: E 170 ASN cc_start: 0.8185 (t0) cc_final: 0.7836 (t0) REVERT: G 70 SER cc_start: 0.7939 (OUTLIER) cc_final: 0.7618 (p) REVERT: K 67 PHE cc_start: 0.7869 (m-80) cc_final: 0.7658 (m-80) outliers start: 64 outliers final: 52 residues processed: 351 average time/residue: 0.3152 time to fit residues: 169.4256 Evaluate side-chains 347 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 293 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain J residue 125 ASP Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 280 CYS Chi-restraints excluded: chain J residue 325 ASN Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 166 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 441 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 441 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 1.0197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20160 Z= 0.235 Angle : 0.596 14.746 27412 Z= 0.308 Chirality : 0.045 0.305 3064 Planarity : 0.004 0.052 3464 Dihedral : 6.628 46.449 3568 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.54 % Favored : 96.29 % Rotamer: Outliers : 3.32 % Allowed : 16.18 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2428 helix: -2.67 (0.44), residues: 48 sheet: 0.53 (0.17), residues: 1012 loop : 0.08 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 33 HIS 0.007 0.001 HIS A 312 PHE 0.033 0.002 PHE G 67 TYR 0.016 0.001 TYR E 121 ARG 0.005 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 301 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 HIS cc_start: 0.7724 (m-70) cc_final: 0.7426 (m-70) REVERT: A 209 ARG cc_start: 0.8492 (mtp85) cc_final: 0.8239 (mtp85) REVERT: L 5 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8109 (p) REVERT: L 24 ARG cc_start: 0.8188 (tpp80) cc_final: 0.7920 (ttm110) REVERT: H 66 ARG cc_start: 0.7527 (mtm110) cc_final: 0.7204 (mtm110) REVERT: H 82 MET cc_start: 0.7967 (mtp) cc_final: 0.7728 (mtp) REVERT: B 190 MET cc_start: 0.8181 (ttm) cc_final: 0.7960 (ttp) REVERT: B 209 ARG cc_start: 0.8509 (mtp85) cc_final: 0.8253 (mtp85) REVERT: C 24 ARG cc_start: 0.8270 (tpp80) cc_final: 0.8010 (ttm110) REVERT: D 70 SER cc_start: 0.8122 (OUTLIER) cc_final: 0.7906 (p) REVERT: D 81 GLN cc_start: 0.7400 (tt0) cc_final: 0.7142 (tt0) REVERT: E 209 ARG cc_start: 0.8530 (mtp85) cc_final: 0.8257 (mtp85) REVERT: G 38 ARG cc_start: 0.8589 (ptt180) cc_final: 0.8372 (ptt180) REVERT: G 66 ARG cc_start: 0.7359 (mtm110) cc_final: 0.7120 (mtm110) REVERT: G 70 SER cc_start: 0.8098 (OUTLIER) cc_final: 0.7845 (p) REVERT: K 66 ARG cc_start: 0.7559 (mtm110) cc_final: 0.7263 (mtm110) outliers start: 70 outliers final: 50 residues processed: 346 average time/residue: 0.3534 time to fit residues: 187.4046 Evaluate side-chains 333 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 280 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 325 ASN Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain J residue 125 ASP Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 280 CYS Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 206 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170AASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170AASN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52AGLN E 170AASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 170AASN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 1.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 20160 Z= 0.354 Angle : 0.661 14.480 27412 Z= 0.344 Chirality : 0.047 0.288 3064 Planarity : 0.004 0.052 3464 Dihedral : 7.170 52.410 3568 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.67 % Favored : 96.17 % Rotamer: Outliers : 3.42 % Allowed : 16.46 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2428 helix: -2.94 (0.41), residues: 48 sheet: 0.48 (0.17), residues: 1008 loop : -0.14 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 33 HIS 0.010 0.001 HIS A 312 PHE 0.035 0.002 PHE H 67 TYR 0.016 0.002 TYR E 121 ARG 0.011 0.001 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 270 time to evaluate : 2.454 Fit side-chains revert: symmetry clash REVERT: H 32 TYR cc_start: 0.9059 (m-80) cc_final: 0.8735 (m-80) REVERT: B 190 MET cc_start: 0.8299 (ttm) cc_final: 0.8094 (ttp) REVERT: B 209 ARG cc_start: 0.8549 (mtp85) cc_final: 0.8295 (mtp85) REVERT: C 24 ARG cc_start: 0.8291 (tpp80) cc_final: 0.8074 (ttm110) REVERT: E 209 ARG cc_start: 0.8518 (mtp85) cc_final: 0.8271 (mtp85) REVERT: G 70 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8152 (p) outliers start: 72 outliers final: 55 residues processed: 326 average time/residue: 0.3267 time to fit residues: 162.7603 Evaluate side-chains 311 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 255 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 325 ASN Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 125 ASP Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 280 CYS Chi-restraints excluded: chain J residue 325 ASN Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 101 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 65 optimal weight: 0.0980 chunk 191 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 1.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 20160 Z= 0.211 Angle : 0.597 13.908 27412 Z= 0.309 Chirality : 0.045 0.280 3064 Planarity : 0.004 0.054 3464 Dihedral : 6.626 46.722 3568 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.80 % Favored : 97.03 % Rotamer: Outliers : 2.56 % Allowed : 17.79 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2428 helix: -2.73 (0.44), residues: 48 sheet: 0.57 (0.17), residues: 1012 loop : -0.05 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.006 0.001 HIS A 312 PHE 0.037 0.002 PHE D 67 TYR 0.012 0.001 TYR K 79 ARG 0.007 0.000 ARG I 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 265 time to evaluate : 2.375 Fit side-chains revert: symmetry clash REVERT: L 5 THR cc_start: 0.8470 (p) cc_final: 0.8187 (p) REVERT: H 32 TYR cc_start: 0.9000 (m-80) cc_final: 0.8774 (m-80) REVERT: B 209 ARG cc_start: 0.8555 (mtp85) cc_final: 0.8349 (mtp85) REVERT: D 32 TYR cc_start: 0.9011 (m-80) cc_final: 0.8733 (m-80) REVERT: D 66 ARG cc_start: 0.7620 (mtm110) cc_final: 0.7397 (mtm110) REVERT: E 209 ARG cc_start: 0.8501 (mtp85) cc_final: 0.8287 (mtp85) REVERT: G 32 TYR cc_start: 0.9038 (m-80) cc_final: 0.8730 (m-80) REVERT: G 67 PHE cc_start: 0.7761 (m-80) cc_final: 0.7538 (m-80) REVERT: G 70 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.8176 (p) outliers start: 54 outliers final: 43 residues processed: 300 average time/residue: 0.3367 time to fit residues: 153.8963 Evaluate side-chains 296 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 252 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 325 ASN Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 417 CYS Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 125 ASP Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 280 CYS Chi-restraints excluded: chain J residue 325 ASN Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 216 optimal weight: 0.0980 chunk 187 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 148 optimal weight: 0.0670 chunk 199 optimal weight: 1.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 1.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 20160 Z= 0.274 Angle : 0.618 13.820 27412 Z= 0.320 Chirality : 0.046 0.280 3064 Planarity : 0.004 0.053 3464 Dihedral : 6.675 47.740 3568 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.09 % Favored : 96.75 % Rotamer: Outliers : 2.42 % Allowed : 17.46 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2428 helix: -2.73 (0.42), residues: 48 sheet: 0.57 (0.17), residues: 1012 loop : -0.10 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 33 HIS 0.007 0.001 HIS A 312 PHE 0.038 0.002 PHE D 67 TYR 0.014 0.001 TYR E 121 ARG 0.008 0.001 ARG G 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 243 time to evaluate : 2.326 Fit side-chains revert: symmetry clash REVERT: B 209 ARG cc_start: 0.8603 (mtp85) cc_final: 0.8387 (mtp85) REVERT: D 32 TYR cc_start: 0.9025 (m-80) cc_final: 0.8788 (m-80) REVERT: E 209 ARG cc_start: 0.8619 (mtp85) cc_final: 0.8401 (mtp85) REVERT: G 32 TYR cc_start: 0.9036 (m-80) cc_final: 0.8753 (m-80) REVERT: G 70 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8244 (p) outliers start: 51 outliers final: 46 residues processed: 284 average time/residue: 0.3343 time to fit residues: 144.3295 Evaluate side-chains 284 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 237 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 325 ASN Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 125 ASP Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 280 CYS Chi-restraints excluded: chain J residue 325 ASN Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 101 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 192 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 ASN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.109267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.081974 restraints weight = 25468.725| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.19 r_work: 0.2824 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 1.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20160 Z= 0.220 Angle : 0.595 13.984 27412 Z= 0.307 Chirality : 0.045 0.270 3064 Planarity : 0.004 0.053 3464 Dihedral : 6.399 44.187 3568 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.51 % Favored : 97.32 % Rotamer: Outliers : 2.42 % Allowed : 17.65 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.19 (0.17), residues: 2428 helix: -2.57 (0.45), residues: 48 sheet: 0.67 (0.17), residues: 1004 loop : -0.12 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 178 HIS 0.006 0.001 HIS A 312 PHE 0.033 0.002 PHE D 67 TYR 0.013 0.001 TYR E 418 ARG 0.010 0.001 ARG G 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4842.83 seconds wall clock time: 88 minutes 47.28 seconds (5327.28 seconds total)