Starting phenix.real_space_refine on Sat Feb 17 00:52:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk5_29248/02_2024/8fk5_29248_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk5_29248/02_2024/8fk5_29248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk5_29248/02_2024/8fk5_29248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk5_29248/02_2024/8fk5_29248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk5_29248/02_2024/8fk5_29248_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk5_29248/02_2024/8fk5_29248_updated.pdb" } resolution = 3.4 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= 0.003 sd= 0.062 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 117 5.16 5 C 10559 2.51 5 N 2802 2.21 5 O 3502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 584": "OE1" <-> "OE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G GLU 211": "OE1" <-> "OE2" Residue "G TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 482": "OE1" <-> "OE2" Residue "I TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 211": "OE1" <-> "OE2" Residue "I PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16980 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "G" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1102 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 801 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "I" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 9.06, per 1000 atoms: 0.53 Number of scatterers: 16980 At special positions: 0 Unit cell: (131.043, 125.628, 166.782, 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 117 16.00 O 3502 8.00 N 2802 7.00 C 10559 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN Q 4 " - " MAN Q 5 " " MAN X 4 " - " MAN X 5 " " MAN e 5 " - " MAN e 6 " " MAN e 8 " - " MAN e 9 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA Q 3 " - " MAN Q 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA a 3 " - " MAN a 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 8 " " MAN e 4 " - " MAN e 7 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA Q 3 " - " MAN Q 6 " " BMA V 3 " - " MAN V 5 " " BMA X 3 " - " MAN X 6 " " BMA a 3 " - " MAN a 5 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG A 703 " - " ASN A 618 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 332 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 355 " " NAG C 609 " - " ASN C 392 " " NAG C 610 " - " ASN C 448 " " NAG C 611 " - " ASN C 137 " " NAG D 1 " - " ASN C 160 " " NAG E 1 " - " ASN C 197 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 156 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 332 " " NAG G 607 " - " ASN G 339 " " NAG G 608 " - " ASN G 355 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 137 " " NAG G 611 " - " ASN G 276 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 234 " " NAG I 604 " - " ASN I 301 " " NAG I 605 " - " ASN I 332 " " NAG I 606 " - " ASN I 339 " " NAG I 607 " - " ASN I 355 " " NAG I 608 " - " ASN I 392 " " NAG I 609 " - " ASN I 137 " " NAG J 1 " - " ASN C 262 " " NAG K 1 " - " ASN C 276 " " NAG M 1 " - " ASN C 295 " " NAG N 1 " - " ASN C 363 " " NAG O 1 " - " ASN C 386 " " NAG P 1 " - " ASN G 197 " " NAG Q 1 " - " ASN G 262 " " NAG R 1 " - " ASN G 295 " " NAG S 1 " - " ASN G 363 " " NAG T 1 " - " ASN G 386 " " NAG U 1 " - " ASN G 448 " " NAG V 1 " - " ASN G 160 " " NAG W 1 " - " ASN I 197 " " NAG X 1 " - " ASN I 262 " " NAG Y 1 " - " ASN I 276 " " NAG Z 1 " - " ASN I 295 " " NAG a 1 " - " ASN I 363 " " NAG b 1 " - " ASN I 386 " " NAG c 1 " - " ASN I 448 " " NAG d 1 " - " ASN I 156 " " NAG e 1 " - " ASN I 160 " Time building additional restraints: 7.89 Conformation dependent library (CDL) restraints added in 3.0 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 34 sheets defined 21.8% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 524 through 527 removed outlier: 4.543A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 524 through 527' Processing helix chain 'A' and resid 530 through 543 removed outlier: 4.158A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 595 removed outlier: 3.552A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 628 through 661 removed outlier: 5.893A pdb=" N ASN A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TYR A 638 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLN A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE A 641 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 543 removed outlier: 3.779A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 537 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N THR B 538 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 539 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 removed outlier: 3.758A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 623 No H-bonds generated for 'chain 'B' and resid 620 through 623' Processing helix chain 'B' and resid 628 through 634 removed outlier: 3.930A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 663 removed outlier: 3.504A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 Processing helix chain 'C' and resid 100 through 114 Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 352 removed outlier: 3.587A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.746A pdb=" N ARG C 480 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER C 481 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 535 removed outlier: 4.021A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 544 removed outlier: 3.729A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 removed outlier: 3.547A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 621 No H-bonds generated for 'chain 'F' and resid 619 through 621' Processing helix chain 'F' and resid 628 through 635 removed outlier: 4.071A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 661 removed outlier: 3.570A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 62 Processing helix chain 'G' and resid 99 through 114 Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 140 through 150 No H-bonds generated for 'chain 'G' and resid 140 through 150' Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 194 through 197 removed outlier: 4.011A pdb=" N ASN G 197 " --> pdb=" O ILE G 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 194 through 197' Processing helix chain 'G' and resid 335 through 352 removed outlier: 3.821A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 372 No H-bonds generated for 'chain 'G' and resid 369 through 372' Processing helix chain 'G' and resid 387 through 389 No H-bonds generated for 'chain 'G' and resid 387 through 389' Processing helix chain 'G' and resid 475 through 485 removed outlier: 4.081A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS G 485 " --> pdb=" O SER G 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 62 Processing helix chain 'I' and resid 99 through 114 Processing helix chain 'I' and resid 178 through 180 No H-bonds generated for 'chain 'I' and resid 178 through 180' Processing helix chain 'I' and resid 194 through 197 removed outlier: 4.088A pdb=" N ASN I 197 " --> pdb=" O ILE I 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 194 through 197' Processing helix chain 'I' and resid 335 through 353 removed outlier: 3.614A pdb=" N LYS I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 372 No H-bonds generated for 'chain 'I' and resid 369 through 372' Processing helix chain 'I' and resid 476 through 480 Processing helix chain 'I' and resid 483 through 485 No H-bonds generated for 'chain 'I' and resid 483 through 485' Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 100J through 100L No H-bonds generated for 'chain 'H' and resid 100J through 100L' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.517A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 53 through 56 Processing sheet with id= D, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.820A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= F, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.335A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 443 through 449 removed outlier: 3.628A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 304 through 307 Processing sheet with id= J, first strand: chain 'G' and resid 35 through 40 Processing sheet with id= K, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.388A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 53 through 55 Processing sheet with id= M, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.779A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 130 through 133 Processing sheet with id= O, first strand: chain 'G' and resid 181 through 183 Processing sheet with id= P, first strand: chain 'G' and resid 271 through 273 removed outlier: 4.213A pdb=" N THR G 467 " --> pdb=" O ASP G 457 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N ALA G 362 " --> pdb=" O PRO G 470 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 374 through 378 removed outlier: 4.003A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 304 through 307 Processing sheet with id= S, first strand: chain 'I' and resid 35 through 40 removed outlier: 3.523A pdb=" N THR I 499 " --> pdb=" O TRP I 35 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.786A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 53 through 55 Processing sheet with id= V, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.741A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 130 through 133 Processing sheet with id= X, first strand: chain 'I' and resid 181 through 183 Processing sheet with id= Y, first strand: chain 'I' and resid 271 through 274 removed outlier: 3.522A pdb=" N ILE I 359 " --> pdb=" O TRP I 395 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER I 393 " --> pdb=" O PHE I 361 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 443 through 446 removed outlier: 3.861A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 259 through 261 removed outlier: 3.760A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.759A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.713A pdb=" N ARG H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER H 25 " --> pdb=" O ARG H 3 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.634A pdb=" N GLY H 10 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 95 through 98 removed outlier: 4.522A pdb=" N TYR H 100S" --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY H 98 " --> pdb=" O TYR H 100Q" (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR H 100Q" --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'L' and resid 9 through 14 removed outlier: 5.983A pdb=" N LYS L 103 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLY L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR L 105 " --> pdb=" O GLY L 13 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN L 37 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'L' and resid 19 through 24 Processing sheet with id= AH, first strand: chain 'L' and resid 89 through 91 511 hydrogen bonds defined for protein. 1395 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: 5.33 Time building geometry restraints manager: 8.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2659 1.32 - 1.45: 4959 1.45 - 1.57: 9526 1.57 - 1.70: 2 1.70 - 1.83: 154 Bond restraints: 17300 Sorted by residual: bond pdb=" C1 MAN e 9 " pdb=" O5 MAN e 9 " ideal model delta sigma weight residual 1.399 1.552 -0.153 2.00e-02 2.50e+03 5.82e+01 bond pdb=" C1 MAN e 9 " pdb=" C2 MAN e 9 " ideal model delta sigma weight residual 1.526 1.667 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" OH TYS H 100G" pdb=" S TYS H 100G" ideal model delta sigma weight residual 1.679 1.573 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" OH TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.679 1.587 0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" CZ TYS H 100G" pdb=" OH TYS H 100G" ideal model delta sigma weight residual 1.371 1.432 -0.061 2.00e-02 2.50e+03 9.33e+00 ... (remaining 17295 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.88: 548 106.88 - 113.69: 10280 113.69 - 120.50: 5880 120.50 - 127.31: 6555 127.31 - 134.12: 217 Bond angle restraints: 23480 Sorted by residual: angle pdb=" N THR I 467 " pdb=" CA THR I 467 " pdb=" C THR I 467 " ideal model delta sigma weight residual 108.23 120.77 -12.54 1.72e+00 3.38e-01 5.32e+01 angle pdb=" C THR I 467 " pdb=" CA THR I 467 " pdb=" CB THR I 467 " ideal model delta sigma weight residual 111.05 119.59 -8.54 1.69e+00 3.50e-01 2.55e+01 angle pdb=" N THR I 467 " pdb=" CA THR I 467 " pdb=" CB THR I 467 " ideal model delta sigma weight residual 110.24 116.75 -6.51 1.45e+00 4.76e-01 2.02e+01 angle pdb=" CA TYS H 100H" pdb=" C TYS H 100H" pdb=" O TYS H 100H" ideal model delta sigma weight residual 120.80 113.20 7.60 1.70e+00 3.46e-01 2.00e+01 angle pdb=" N ASP I 457 " pdb=" CA ASP I 457 " pdb=" C ASP I 457 " ideal model delta sigma weight residual 110.28 104.19 6.09 1.48e+00 4.57e-01 1.69e+01 ... (remaining 23475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.33: 11023 22.33 - 44.66: 598 44.66 - 66.98: 118 66.98 - 89.31: 64 89.31 - 111.64: 31 Dihedral angle restraints: 11834 sinusoidal: 6158 harmonic: 5676 Sorted by residual: dihedral pdb=" C THR I 467 " pdb=" N THR I 467 " pdb=" CA THR I 467 " pdb=" CB THR I 467 " ideal model delta harmonic sigma weight residual -122.00 -160.68 38.68 0 2.50e+00 1.60e-01 2.39e+02 dihedral pdb=" N THR I 467 " pdb=" C THR I 467 " pdb=" CA THR I 467 " pdb=" CB THR I 467 " ideal model delta harmonic sigma weight residual 123.40 160.13 -36.73 0 2.50e+00 1.60e-01 2.16e+02 dihedral pdb=" CB CYS I 378 " pdb=" SG CYS I 378 " pdb=" SG CYS I 445 " pdb=" CB CYS I 445 " ideal model delta sinusoidal sigma weight residual -86.00 -159.37 73.37 1 1.00e+01 1.00e-02 6.85e+01 ... (remaining 11831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 2956 0.331 - 0.661: 2 0.661 - 0.992: 0 0.992 - 1.323: 0 1.323 - 1.653: 1 Chirality restraints: 2959 Sorted by residual: chirality pdb=" CA THR I 467 " pdb=" N THR I 467 " pdb=" C THR I 467 " pdb=" CB THR I 467 " both_signs ideal model delta sigma weight residual False 2.53 0.87 1.65 2.00e-01 2.50e+01 6.83e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN G 448 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.41e+00 chirality pdb=" C1 MAN e 9 " pdb=" O2 MAN e 8 " pdb=" C2 MAN e 9 " pdb=" O5 MAN e 9 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 5.34e+00 ... (remaining 2956 not shown) Planarity restraints: 2901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG I 456 " 0.015 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ARG I 456 " -0.055 2.00e-02 2.50e+03 pdb=" O ARG I 456 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP I 457 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYS H 100H" 0.012 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C TYS H 100H" -0.045 2.00e-02 2.50e+03 pdb=" O TYS H 100H" 0.016 2.00e-02 2.50e+03 pdb=" N ASP H 100I" 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 3 " -0.165 9.50e-02 1.11e+02 7.42e-02 3.38e+00 pdb=" NE ARG H 3 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG H 3 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG H 3 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 3 " -0.006 2.00e-02 2.50e+03 ... (remaining 2898 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 202 2.62 - 3.19: 14986 3.19 - 3.76: 23673 3.76 - 4.33: 34587 4.33 - 4.90: 57211 Nonbonded interactions: 130659 Sorted by model distance: nonbonded pdb=" O ASP A 632 " pdb=" OG SER A 636 " model vdw 2.052 2.440 nonbonded pdb=" OD1 ASP C 457 " pdb=" OG1 THR C 467 " model vdw 2.090 2.440 nonbonded pdb=" NH2 ARG G 350 " pdb=" O ASN G 398 " model vdw 2.168 2.520 nonbonded pdb=" OG1 THR B 627 " pdb=" OE1 GLN B 630 " model vdw 2.168 2.440 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.198 2.440 ... (remaining 130654 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 519 through 664 or resid 701 through 702)) selection = chain 'B' selection = (chain 'F' and (resid 519 through 546 or resid 569 through 664 or resid 701 thro \ ugh 702)) } ncs_group { reference = (chain 'C' and (resid 33 through 505 or resid 601 through 609)) selection = (chain 'G' and (resid 33 through 505 or resid 601 through 609)) selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'X' } ncs_group { reference = chain 'V' selection = chain 'a' selection = chain 'd' } 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.220 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 47.270 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.260 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 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 : 0.005 0.153 17300 Z= 0.306 Angle : 0.723 12.540 23480 Z= 0.326 Chirality : 0.059 1.653 2959 Planarity : 0.003 0.074 2840 Dihedral : 15.600 111.638 8059 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.12 % Allowed : 0.23 % Favored : 99.65 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.20), residues: 1932 helix: 0.93 (0.29), residues: 369 sheet: 0.69 (0.24), residues: 505 loop : -0.15 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 479 HIS 0.003 0.001 HIS C 216 PHE 0.006 0.001 PHE C 53 TYR 0.008 0.001 TYR L 49 ARG 0.004 0.000 ARG F 585 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 330 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 THR cc_start: 0.8904 (t) cc_final: 0.8562 (p) REVERT: C 38 VAL cc_start: 0.8998 (p) cc_final: 0.8605 (m) REVERT: C 46 LYS cc_start: 0.8449 (pttp) cc_final: 0.8215 (pttp) REVERT: G 39 TYR cc_start: 0.8834 (m-80) cc_final: 0.8569 (m-80) REVERT: H 94 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.7246 (ttt180) REVERT: L 36 TYR cc_start: 0.7830 (m-80) cc_final: 0.7506 (m-80) outliers start: 2 outliers final: 0 residues processed: 331 average time/residue: 0.3213 time to fit residues: 153.0074 Evaluate side-chains 190 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN A 577 GLN A 651 ASN B 540 GLN B 543 ASN B 616 ASN C 82 GLN C 105 HIS C 249 HIS C 374 HIS C 478 ASN G 249 HIS G 374 HIS I 99 ASN I 374 HIS H 100CASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 17300 Z= 0.277 Angle : 0.693 10.215 23480 Z= 0.334 Chirality : 0.049 0.384 2959 Planarity : 0.004 0.050 2840 Dihedral : 12.040 112.405 4403 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.85 % Allowed : 7.05 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.19), residues: 1932 helix: 0.91 (0.28), residues: 359 sheet: 0.68 (0.23), residues: 504 loop : -0.18 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 35 HIS 0.004 0.001 HIS H 59 PHE 0.029 0.002 PHE C 53 TYR 0.016 0.002 TYR F 638 ARG 0.004 0.001 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 212 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 THR cc_start: 0.8278 (m) cc_final: 0.7920 (t) REVERT: A 584 GLU cc_start: 0.7872 (pt0) cc_final: 0.7641 (mt-10) REVERT: B 536 THR cc_start: 0.8790 (t) cc_final: 0.8412 (p) REVERT: C 46 LYS cc_start: 0.8569 (pttp) cc_final: 0.8351 (pttp) REVERT: C 326 ILE cc_start: 0.8189 (mm) cc_final: 0.7823 (mm) REVERT: C 491 ILE cc_start: 0.8303 (mm) cc_final: 0.7780 (mt) REVERT: G 100 MET cc_start: 0.8676 (mtp) cc_final: 0.8436 (mtp) REVERT: G 217 TYR cc_start: 0.8488 (m-80) cc_final: 0.8229 (m-80) REVERT: G 485 LYS cc_start: 0.7777 (ttmt) cc_final: 0.7216 (tttp) REVERT: I 246 GLN cc_start: 0.7005 (pm20) cc_final: 0.6726 (pm20) REVERT: H 38 ARG cc_start: 0.7237 (ptt180) cc_final: 0.6962 (ptt180) REVERT: H 94 ARG cc_start: 0.7792 (ttp-170) cc_final: 0.7450 (ttt-90) REVERT: L 36 TYR cc_start: 0.7892 (m-80) cc_final: 0.7322 (m-80) outliers start: 32 outliers final: 21 residues processed: 234 average time/residue: 0.3396 time to fit residues: 116.3115 Evaluate side-chains 194 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 173 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 0.0670 chunk 54 optimal weight: 0.9980 chunk 146 optimal weight: 0.1980 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 176 optimal weight: 0.4980 chunk 190 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 GLN B 540 GLN I 99 ASN H 81 GLN H 100CASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17300 Z= 0.193 Angle : 0.593 10.947 23480 Z= 0.285 Chirality : 0.046 0.320 2959 Planarity : 0.003 0.044 2840 Dihedral : 11.117 117.434 4403 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.77 % Allowed : 8.55 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.34 (0.19), residues: 1932 helix: 0.90 (0.27), residues: 377 sheet: 0.71 (0.23), residues: 504 loop : -0.20 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 35 HIS 0.007 0.001 HIS H 100R PHE 0.015 0.001 PHE C 391 TYR 0.017 0.001 TYR C 484 ARG 0.008 0.000 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 181 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 THR cc_start: 0.8102 (m) cc_final: 0.7762 (t) REVERT: B 536 THR cc_start: 0.8751 (t) cc_final: 0.8402 (p) REVERT: B 588 ARG cc_start: 0.8023 (tpp-160) cc_final: 0.7635 (tpp-160) REVERT: C 95 MET cc_start: 0.8586 (ptm) cc_final: 0.7525 (ttp) REVERT: C 326 ILE cc_start: 0.8185 (mm) cc_final: 0.7848 (mm) REVERT: C 491 ILE cc_start: 0.8247 (mm) cc_final: 0.7748 (mt) REVERT: G 100 MET cc_start: 0.8688 (mtp) cc_final: 0.8470 (mtp) REVERT: G 434 MET cc_start: 0.8201 (ttp) cc_final: 0.7956 (ttp) REVERT: H 38 ARG cc_start: 0.7244 (ptt180) cc_final: 0.6904 (ptt180) REVERT: H 81 GLN cc_start: 0.6096 (OUTLIER) cc_final: 0.4834 (mp-120) REVERT: H 94 ARG cc_start: 0.7803 (ttp-170) cc_final: 0.7205 (ttt180) REVERT: H 100 TYR cc_start: 0.8207 (m-80) cc_final: 0.7684 (m-80) REVERT: L 36 TYR cc_start: 0.7914 (m-80) cc_final: 0.7446 (m-80) outliers start: 48 outliers final: 29 residues processed: 216 average time/residue: 0.3182 time to fit residues: 101.1039 Evaluate side-chains 203 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 118 optimal weight: 0.0030 chunk 177 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 167 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 ASN G 428 GLN I 103 GLN I 114 GLN H 81 GLN H 100CASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17300 Z= 0.200 Angle : 0.591 9.944 23480 Z= 0.281 Chirality : 0.046 0.359 2959 Planarity : 0.003 0.042 2840 Dihedral : 10.403 115.337 4403 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.54 % Allowed : 10.40 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 1932 helix: 1.03 (0.28), residues: 376 sheet: 0.67 (0.23), residues: 504 loop : -0.21 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 35 HIS 0.005 0.001 HIS H 100R PHE 0.015 0.001 PHE C 391 TYR 0.015 0.001 TYR G 173 ARG 0.004 0.000 ARG G 500 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 175 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 THR cc_start: 0.8122 (m) cc_final: 0.7760 (t) REVERT: A 655 LYS cc_start: 0.7157 (tptp) cc_final: 0.6823 (tptt) REVERT: B 536 THR cc_start: 0.8743 (t) cc_final: 0.8394 (p) REVERT: C 46 LYS cc_start: 0.8289 (pttm) cc_final: 0.7995 (pttp) REVERT: C 95 MET cc_start: 0.8604 (ptm) cc_final: 0.7705 (ttp) REVERT: C 326 ILE cc_start: 0.8254 (mm) cc_final: 0.7917 (mm) REVERT: C 491 ILE cc_start: 0.8288 (mm) cc_final: 0.7770 (mt) REVERT: G 100 MET cc_start: 0.8731 (mtp) cc_final: 0.8480 (mtp) REVERT: I 246 GLN cc_start: 0.7110 (pm20) cc_final: 0.6739 (pm20) REVERT: H 38 ARG cc_start: 0.7392 (ptt180) cc_final: 0.7153 (ptt180) REVERT: H 81 GLN cc_start: 0.5986 (OUTLIER) cc_final: 0.4941 (mp-120) REVERT: H 94 ARG cc_start: 0.7835 (ttp-170) cc_final: 0.7264 (ttt180) REVERT: H 100 TYR cc_start: 0.8203 (m-80) cc_final: 0.7656 (m-80) REVERT: L 36 TYR cc_start: 0.7939 (m-80) cc_final: 0.7473 (m-80) outliers start: 44 outliers final: 31 residues processed: 204 average time/residue: 0.3219 time to fit residues: 97.1053 Evaluate side-chains 196 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 95 optimal weight: 0.0000 chunk 168 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN G 422 GLN G 428 GLN I 99 ASN I 103 GLN I 422 GLN H 81 GLN H 100CASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17300 Z= 0.316 Angle : 0.653 10.492 23480 Z= 0.310 Chirality : 0.049 0.386 2959 Planarity : 0.004 0.042 2840 Dihedral : 9.843 113.881 4403 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.18 % Allowed : 10.75 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 1932 helix: 0.90 (0.28), residues: 376 sheet: 0.54 (0.22), residues: 513 loop : -0.39 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 35 HIS 0.004 0.001 HIS H 100R PHE 0.025 0.002 PHE C 53 TYR 0.016 0.001 TYR L 49 ARG 0.006 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 200 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 THR cc_start: 0.8232 (m) cc_final: 0.7884 (t) REVERT: A 655 LYS cc_start: 0.7112 (tptp) cc_final: 0.6907 (tptt) REVERT: B 523 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8393 (tt) REVERT: B 536 THR cc_start: 0.8805 (t) cc_final: 0.8442 (p) REVERT: C 38 VAL cc_start: 0.8785 (p) cc_final: 0.8521 (m) REVERT: C 46 LYS cc_start: 0.8224 (pttm) cc_final: 0.7939 (pttp) REVERT: C 95 MET cc_start: 0.8818 (ptm) cc_final: 0.7828 (ttp) REVERT: C 326 ILE cc_start: 0.8400 (mm) cc_final: 0.8199 (mm) REVERT: G 423 ILE cc_start: 0.8410 (mm) cc_final: 0.8154 (mt) REVERT: I 161 MET cc_start: 0.7884 (mmm) cc_final: 0.7472 (tpp) REVERT: I 246 GLN cc_start: 0.7062 (pm20) cc_final: 0.6602 (pm20) REVERT: H 38 ARG cc_start: 0.7484 (ptt180) cc_final: 0.7195 (ptt180) REVERT: H 94 ARG cc_start: 0.7741 (ttp-170) cc_final: 0.7192 (ttt180) REVERT: H 100 TYR cc_start: 0.8216 (m-80) cc_final: 0.7759 (m-80) REVERT: L 36 TYR cc_start: 0.7954 (m-80) cc_final: 0.7547 (m-80) outliers start: 55 outliers final: 37 residues processed: 242 average time/residue: 0.3293 time to fit residues: 117.9122 Evaluate side-chains 218 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 155 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 0.0770 chunk 62 optimal weight: 0.0980 chunk 98 optimal weight: 0.8980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN G 103 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17300 Z= 0.165 Angle : 0.586 11.659 23480 Z= 0.277 Chirality : 0.046 0.393 2959 Planarity : 0.003 0.040 2840 Dihedral : 9.207 112.743 4403 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.06 % Allowed : 11.90 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 1932 helix: 1.20 (0.28), residues: 369 sheet: 0.81 (0.24), residues: 475 loop : -0.40 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 35 HIS 0.004 0.001 HIS H 100R PHE 0.018 0.001 PHE C 53 TYR 0.014 0.001 TYR G 173 ARG 0.006 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 190 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 ARG cc_start: 0.7127 (ttp-110) cc_final: 0.6782 (mtp180) REVERT: B 536 THR cc_start: 0.8720 (t) cc_final: 0.8377 (p) REVERT: C 38 VAL cc_start: 0.8747 (p) cc_final: 0.8480 (m) REVERT: C 46 LYS cc_start: 0.8223 (pttm) cc_final: 0.7955 (pttp) REVERT: C 95 MET cc_start: 0.8802 (ptm) cc_final: 0.7735 (ttp) REVERT: F 584 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7299 (mt-10) REVERT: I 161 MET cc_start: 0.7719 (mmm) cc_final: 0.7435 (tpp) REVERT: I 308 ARG cc_start: 0.7597 (mmm-85) cc_final: 0.7316 (ttp-110) REVERT: H 38 ARG cc_start: 0.7393 (ptt180) cc_final: 0.7087 (ptt180) REVERT: H 94 ARG cc_start: 0.7794 (ttp-170) cc_final: 0.7238 (ttt180) REVERT: H 100 TYR cc_start: 0.8200 (m-80) cc_final: 0.7689 (m-80) REVERT: L 36 TYR cc_start: 0.7925 (m-80) cc_final: 0.7533 (m-80) outliers start: 53 outliers final: 40 residues processed: 231 average time/residue: 0.3020 time to fit residues: 103.8404 Evaluate side-chains 217 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 177 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 428 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17300 Z= 0.297 Angle : 0.651 11.851 23480 Z= 0.306 Chirality : 0.048 0.404 2959 Planarity : 0.004 0.041 2840 Dihedral : 8.938 111.552 4403 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.35 % Allowed : 12.71 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 1932 helix: 1.19 (0.29), residues: 359 sheet: 0.61 (0.23), residues: 523 loop : -0.46 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 35 HIS 0.004 0.001 HIS H 100R PHE 0.018 0.002 PHE C 53 TYR 0.015 0.001 TYR L 49 ARG 0.007 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 189 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 523 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8328 (tt) REVERT: B 536 THR cc_start: 0.8801 (t) cc_final: 0.8439 (p) REVERT: C 38 VAL cc_start: 0.8771 (p) cc_final: 0.8497 (m) REVERT: G 423 ILE cc_start: 0.8399 (mm) cc_final: 0.8185 (mt) REVERT: H 38 ARG cc_start: 0.7384 (ptt180) cc_final: 0.7178 (ptt180) REVERT: L 36 TYR cc_start: 0.7928 (m-80) cc_final: 0.7560 (m-80) outliers start: 58 outliers final: 44 residues processed: 234 average time/residue: 0.3086 time to fit residues: 107.3698 Evaluate side-chains 221 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 176 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 56 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 chunk 118 optimal weight: 0.0070 chunk 127 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 99 ASN I 103 GLN I 114 GLN H 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17300 Z= 0.195 Angle : 0.602 12.169 23480 Z= 0.283 Chirality : 0.046 0.404 2959 Planarity : 0.003 0.040 2840 Dihedral : 8.434 110.510 4403 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.29 % Allowed : 13.00 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 1932 helix: 1.34 (0.29), residues: 359 sheet: 0.63 (0.23), residues: 512 loop : -0.45 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 35 HIS 0.003 0.001 HIS C 216 PHE 0.015 0.001 PHE C 53 TYR 0.012 0.001 TYR G 173 ARG 0.005 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 189 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 523 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8219 (tt) REVERT: B 536 THR cc_start: 0.8764 (t) cc_final: 0.8402 (p) REVERT: B 544 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8123 (mt) REVERT: C 38 VAL cc_start: 0.8746 (p) cc_final: 0.8486 (m) REVERT: C 46 LYS cc_start: 0.8039 (pttm) cc_final: 0.7772 (pttp) REVERT: F 635 ILE cc_start: 0.7762 (pt) cc_final: 0.7545 (pt) REVERT: G 267 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6300 (mt-10) REVERT: G 423 ILE cc_start: 0.8379 (mm) cc_final: 0.8162 (mt) REVERT: I 95 MET cc_start: 0.8169 (ptm) cc_final: 0.7943 (ttp) REVERT: I 151 ARG cc_start: 0.7814 (tpm170) cc_final: 0.7514 (tpp80) REVERT: I 161 MET cc_start: 0.7594 (mmm) cc_final: 0.7391 (tpp) REVERT: H 38 ARG cc_start: 0.7442 (ptt180) cc_final: 0.7204 (ptt180) REVERT: L 36 TYR cc_start: 0.7903 (m-80) cc_final: 0.7512 (m-80) outliers start: 57 outliers final: 39 residues processed: 232 average time/residue: 0.2950 time to fit residues: 102.6361 Evaluate side-chains 225 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 267 GLU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.0170 chunk 174 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 chunk 173 optimal weight: 0.2980 chunk 114 optimal weight: 0.6980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 ASN I 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17300 Z= 0.176 Angle : 0.597 12.448 23480 Z= 0.281 Chirality : 0.049 1.023 2959 Planarity : 0.003 0.040 2840 Dihedral : 7.735 58.033 4403 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.77 % Allowed : 13.34 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 1932 helix: 1.43 (0.29), residues: 359 sheet: 0.66 (0.23), residues: 514 loop : -0.43 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 35 HIS 0.003 0.001 HIS G 352 PHE 0.014 0.001 PHE C 53 TYR 0.017 0.001 TYR F 638 ARG 0.004 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 191 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 523 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8123 (tt) REVERT: B 536 THR cc_start: 0.8751 (t) cc_final: 0.8392 (p) REVERT: B 544 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8075 (mt) REVERT: C 38 VAL cc_start: 0.8739 (p) cc_final: 0.8480 (m) REVERT: C 46 LYS cc_start: 0.8049 (pttm) cc_final: 0.7790 (pttp) REVERT: C 95 MET cc_start: 0.8345 (ptm) cc_final: 0.8099 (ttp) REVERT: G 95 MET cc_start: 0.7944 (ptm) cc_final: 0.7649 (ttp) REVERT: G 96 TRP cc_start: 0.8208 (m100) cc_final: 0.7887 (m100) REVERT: G 267 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6370 (mt-10) REVERT: G 423 ILE cc_start: 0.8372 (mm) cc_final: 0.8155 (mt) REVERT: I 151 ARG cc_start: 0.7852 (tpm170) cc_final: 0.7525 (tpp80) REVERT: I 308 ARG cc_start: 0.7507 (mmm-85) cc_final: 0.7297 (ttp-110) REVERT: H 107 THR cc_start: 0.7443 (p) cc_final: 0.7208 (p) REVERT: L 36 TYR cc_start: 0.7922 (m-80) cc_final: 0.7528 (m-80) outliers start: 48 outliers final: 40 residues processed: 230 average time/residue: 0.2980 time to fit residues: 102.4410 Evaluate side-chains 229 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 186 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 267 GLU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 177 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 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 577 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17300 Z= 0.245 Angle : 0.627 12.053 23480 Z= 0.298 Chirality : 0.048 0.678 2959 Planarity : 0.004 0.040 2840 Dihedral : 7.645 58.013 4403 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.66 % Allowed : 13.81 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 1932 helix: 1.33 (0.29), residues: 359 sheet: 0.58 (0.23), residues: 517 loop : -0.53 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 631 HIS 0.004 0.001 HIS G 374 PHE 0.014 0.001 PHE C 53 TYR 0.015 0.001 TYR G 384 ARG 0.005 0.000 ARG L 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 191 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 523 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8179 (tt) REVERT: B 536 THR cc_start: 0.8777 (t) cc_final: 0.8409 (p) REVERT: B 544 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8189 (mt) REVERT: B 656 ASN cc_start: 0.8089 (t0) cc_final: 0.7680 (t0) REVERT: C 38 VAL cc_start: 0.8718 (p) cc_final: 0.8484 (m) REVERT: C 46 LYS cc_start: 0.8056 (pttm) cc_final: 0.7799 (pttp) REVERT: C 434 MET cc_start: 0.7731 (tmm) cc_final: 0.6962 (ttp) REVERT: F 636 SER cc_start: 0.7960 (m) cc_final: 0.7647 (m) REVERT: G 95 MET cc_start: 0.8071 (ptm) cc_final: 0.7482 (ttp) REVERT: G 96 TRP cc_start: 0.8416 (m100) cc_final: 0.8014 (m100) REVERT: G 267 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6324 (mt-10) REVERT: I 151 ARG cc_start: 0.7828 (tpm170) cc_final: 0.7505 (tpp80) REVERT: H 107 THR cc_start: 0.7451 (p) cc_final: 0.7221 (p) REVERT: L 36 TYR cc_start: 0.7936 (m-80) cc_final: 0.7580 (m-80) outliers start: 46 outliers final: 41 residues processed: 227 average time/residue: 0.2947 time to fit residues: 99.9218 Evaluate side-chains 230 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 186 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 267 GLU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 154 optimal weight: 0.9980 chunk 64 optimal weight: 0.0010 chunk 158 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.186093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.159201 restraints weight = 20234.287| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.05 r_work: 0.3637 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17300 Z= 0.174 Angle : 0.587 12.329 23480 Z= 0.279 Chirality : 0.047 0.617 2959 Planarity : 0.003 0.040 2840 Dihedral : 7.322 57.903 4403 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.00 % Allowed : 13.81 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 1932 helix: 1.46 (0.29), residues: 360 sheet: 0.63 (0.23), residues: 509 loop : -0.46 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 395 HIS 0.003 0.001 HIS C 105 PHE 0.016 0.001 PHE C 53 TYR 0.012 0.001 TYR G 173 ARG 0.004 0.000 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3618.25 seconds wall clock time: 66 minutes 41.28 seconds (4001.28 seconds total)