Starting phenix.real_space_refine on Mon Nov 18 18:34:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk5_29248/11_2024/8fk5_29248.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk5_29248/11_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_29248/11_2024/8fk5_29248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk5_29248/11_2024/8fk5_29248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk5_29248/11_2024/8fk5_29248.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk5_29248/11_2024/8fk5_29248.cif" } 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. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 10.79, per 1000 atoms: 0.64 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 - 3.00 Amino acid : True - 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: 5.38 Conformation dependent library (CDL) restraints added in 2.1 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... Secondary structure from input PDB file: 47 helices and 30 sheets defined 24.6% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.543A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 535 removed outlier: 4.158A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 542 removed outlier: 4.063A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 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) removed outlier: 3.684A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 664 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) removed outlier: 3.732A pdb=" N ALA A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.317A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.779A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.367A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 removed outlier: 3.758A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.930A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 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 57 through 64 removed outlier: 4.374A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 353 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 368 through 373 removed outlier: 3.630A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.018A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.267A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.547A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 removed outlier: 4.071A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.570A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 98 through 115 removed outlier: 4.041A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 139 through 151 removed outlier: 3.577A pdb=" N ARG G 151 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 350 removed outlier: 3.821A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.504A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 390 Processing helix chain 'G' and resid 474 through 484 removed outlier: 3.945A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 63 Processing helix chain 'I' and resid 98 through 115 removed outlier: 4.223A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 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 368 through 373 Processing helix chain 'I' and resid 475 through 481 removed outlier: 4.113A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.550A pdb=" N THR H 87 " --> pdb=" O VAL H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 4.102A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 4.871A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA3, 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=AA4, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AA5, 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=AA6, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.306A pdb=" N CYS C 201 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA8, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 309 removed outlier: 4.020A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR C 303 " --> pdb=" O ASP C 321A" (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP C 321A" --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AA9, first strand: chain 'F' and resid 603 through 609 removed outlier: 4.314A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR I 499 " --> pdb=" O TRP I 35 " (cutoff:3.500A) Processing sheet with id=AB1, 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=AB2, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.652A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AB3, 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=AB4, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AB5, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.469A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 260 current: chain 'G' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 287 current: chain 'G' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 393 through 395 current: chain 'G' and resid 465 through 470 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, 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: 4.001A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 304 through 312 removed outlier: 3.501A pdb=" N ILE G 309 " --> pdb=" O GLN G 315 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB9, 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=AC1, first strand: chain 'I' and resid 75 through 76 removed outlier: 4.078A pdb=" N VAL I 75 " --> pdb=" O CYS I 54 " (cutoff:3.500A) Processing sheet with id=AC2, 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=AC3, first strand: chain 'I' and resid 130 through 133 removed outlier: 4.705A pdb=" N PHE H 100J" --> pdb=" O LYS I 171 " (cutoff:3.500A) removed outlier: 9.822A pdb=" N TYR I 173 " --> pdb=" O PHE H 100J" (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AC5, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.477A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET I 434 " --> pdb=" O ILE I 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 292 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 284 through 292 current: chain 'I' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 393 through 395 current: chain 'I' and resid 466 through 470 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'I' and resid 374 through 378 removed outlier: 4.543A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 301 through 312 removed outlier: 3.985A pdb=" N ASN I 301 " --> pdb=" O ILE I 323 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP I 321A" --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS I 305 " --> pdb=" O THR I 320 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR I 320 " --> pdb=" O LYS I 305 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE I 307 " --> pdb=" O TYR I 318 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR I 318 " --> pdb=" O ILE I 307 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE I 309 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA I 316 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AC9, 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=AD1, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100O through 103 Processing sheet with id=AD2, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'L' and resid 19 through 24 484 hydrogen bonds defined for protein. 1314 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: 5.74 Time building geometry restraints manager: 6.05 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: 0.00 - 2.51: 23054 2.51 - 5.02: 365 5.02 - 7.52: 58 7.52 - 10.03: 2 10.03 - 12.54: 1 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: 203 2.62 - 3.19: 15011 3.19 - 3.76: 23718 3.76 - 4.33: 34615 4.33 - 4.90: 57220 Nonbonded interactions: 130767 Sorted by model distance: nonbonded pdb=" O ASP A 632 " pdb=" OG SER A 636 " model vdw 2.052 3.040 nonbonded pdb=" OD1 ASP C 457 " pdb=" OG1 THR C 467 " model vdw 2.090 3.040 nonbonded pdb=" NH2 ARG G 350 " pdb=" O ASN G 398 " model vdw 2.168 3.120 nonbonded pdb=" OG1 THR B 627 " pdb=" OE1 GLN B 630 " model vdw 2.168 3.040 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.198 3.040 ... (remaining 130762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 40.080 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.120 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.320 ------------------------------------------------------------------------------- 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= 0.309 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 to be fit. rotamer outliers: 2 poor density : 330 time to evaluate : 1.851 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: 0.3336 time to fit residues: 159.2956 Evaluate side-chains 190 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.719 ------------------------------------------------------------------------------- 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: 0.2980 chunk 147 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 0.0060 chunk 99 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 0.0060 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 overall best weight: 0.3612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN A 651 ASN B 540 GLN B 543 ASN C 105 HIS C 249 HIS C 478 ASN G 183 GLN G 249 HIS G 374 HIS I 99 ASN I 374 HIS ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100CASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17300 Z= 0.190 Angle : 0.645 11.597 23480 Z= 0.314 Chirality : 0.046 0.300 2959 Planarity : 0.004 0.046 2840 Dihedral : 12.244 112.864 4403 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.44 % Allowed : 7.11 % Favored : 91.45 % 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: 0.26 (0.19), residues: 1932 helix: 1.05 (0.27), residues: 383 sheet: 0.53 (0.23), residues: 505 loop : -0.27 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 35 HIS 0.004 0.001 HIS H 59 PHE 0.026 0.001 PHE C 53 TYR 0.014 0.001 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 238 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.7881 (pt0) cc_final: 0.7626 (mt-10) REVERT: B 536 THR cc_start: 0.8900 (t) cc_final: 0.8616 (p) REVERT: C 46 LYS cc_start: 0.8523 (pttp) cc_final: 0.8279 (pttp) REVERT: C 491 ILE cc_start: 0.8200 (mm) cc_final: 0.7680 (mt) REVERT: G 270 VAL cc_start: 0.8206 (p) cc_final: 0.7826 (t) REVERT: H 38 ARG cc_start: 0.7059 (ptt180) cc_final: 0.6835 (ptt180) REVERT: H 94 ARG cc_start: 0.7728 (ttp-170) cc_final: 0.7364 (ttt-90) REVERT: L 36 TYR cc_start: 0.7974 (m-80) cc_final: 0.7544 (m-80) outliers start: 25 outliers final: 17 residues processed: 231 average time/residue: 0.3246 time to fit residues: 110.3357 Evaluate side-chains 192 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 605 CYS 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 C residue 138 ILE Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 125 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 90 THR 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: 0.7980 chunk 54 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 190 optimal weight: 20.0000 chunk 157 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 141 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 GLN C 374 HIS C 478 ASN H 100CASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17300 Z= 0.232 Angle : 0.625 11.425 23480 Z= 0.301 Chirality : 0.047 0.363 2959 Planarity : 0.004 0.044 2840 Dihedral : 11.173 116.394 4403 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.54 % Allowed : 8.38 % Favored : 89.08 % 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: 0.23 (0.19), residues: 1932 helix: 1.01 (0.27), residues: 390 sheet: 0.65 (0.23), residues: 501 loop : -0.38 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 479 HIS 0.004 0.001 HIS C 105 PHE 0.026 0.002 PHE C 53 TYR 0.022 0.001 TYR C 484 ARG 0.006 0.001 ARG G 500 *********************** 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 236 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 THR cc_start: 0.8964 (t) cc_final: 0.8631 (p) REVERT: C 95 MET cc_start: 0.8632 (ptm) cc_final: 0.7734 (ttp) REVERT: C 491 ILE cc_start: 0.8267 (mm) cc_final: 0.7746 (mt) REVERT: G 100 MET cc_start: 0.8743 (mtp) cc_final: 0.8428 (mtp) REVERT: G 390 LEU cc_start: 0.7981 (mt) cc_final: 0.7778 (mp) REVERT: I 246 GLN cc_start: 0.6949 (pm20) cc_final: 0.6691 (pm20) REVERT: H 94 ARG cc_start: 0.7769 (ttp-170) cc_final: 0.7406 (ttt-90) REVERT: L 36 TYR cc_start: 0.7961 (m-80) cc_final: 0.7612 (m-80) outliers start: 44 outliers final: 29 residues processed: 226 average time/residue: 0.3096 time to fit residues: 104.3457 Evaluate side-chains 206 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 605 CYS 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 123 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 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 412 ASP Chi-restraints excluded: chain G residue 447 SER 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 371 VAL Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN C 82 GLN C 478 ASN G 183 GLN G 422 GLN I 422 GLN H 100CASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 17300 Z= 0.423 Angle : 0.755 13.307 23480 Z= 0.361 Chirality : 0.052 0.395 2959 Planarity : 0.005 0.057 2840 Dihedral : 10.550 114.069 4403 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.47 % Allowed : 10.05 % Favored : 86.48 % 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: -0.23 (0.19), residues: 1932 helix: 0.52 (0.27), residues: 395 sheet: 0.35 (0.23), residues: 504 loop : -0.64 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 35 HIS 0.009 0.002 HIS H 100R PHE 0.029 0.003 PHE C 391 TYR 0.021 0.002 TYR F 643 ARG 0.006 0.001 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 268 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.7903 (pt0) cc_final: 0.7579 (pt0) REVERT: A 655 LYS cc_start: 0.7255 (tptp) cc_final: 0.7012 (tptt) REVERT: B 536 THR cc_start: 0.9016 (t) cc_final: 0.8642 (p) REVERT: C 46 LYS cc_start: 0.8227 (pttm) cc_final: 0.7934 (pttp) REVERT: C 95 MET cc_start: 0.8699 (ptm) cc_final: 0.7711 (ttp) REVERT: C 292 VAL cc_start: 0.9086 (OUTLIER) cc_final: 0.8810 (m) REVERT: C 478 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7648 (m-40) REVERT: G 423 ILE cc_start: 0.8544 (mm) cc_final: 0.8328 (mt) REVERT: I 161 MET cc_start: 0.8037 (mmm) cc_final: 0.7664 (mmm) REVERT: I 246 GLN cc_start: 0.7020 (pm20) cc_final: 0.6389 (pm20) REVERT: H 94 ARG cc_start: 0.7685 (ttp-170) cc_final: 0.7217 (ttt-90) REVERT: H 100 TYR cc_start: 0.8218 (m-80) cc_final: 0.7737 (m-80) outliers start: 60 outliers final: 38 residues processed: 253 average time/residue: 0.3269 time to fit residues: 121.4651 Evaluate side-chains 226 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 1.770 ------------------------------------------------------------------------------- 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 B residue 648 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR 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 292 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 478 ASN 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 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 292 VAL 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 50 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 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 371 VAL 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 L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER 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: 0.8980 chunk 2 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 160 optimal weight: 0.5980 chunk 129 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 168 optimal weight: 0.0030 chunk 47 optimal weight: 0.7980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 67 ASN I 103 GLN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17300 Z= 0.179 Angle : 0.625 11.733 23480 Z= 0.298 Chirality : 0.048 0.558 2959 Planarity : 0.004 0.043 2840 Dihedral : 9.851 112.806 4403 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.12 % Allowed : 11.38 % Favored : 85.50 % 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: 0.03 (0.19), residues: 1932 helix: 0.96 (0.28), residues: 387 sheet: 0.42 (0.22), residues: 534 loop : -0.53 (0.19), residues: 1011 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 0.018 0.001 PHE C 53 TYR 0.012 0.001 TYR L 49 ARG 0.012 0.000 ARG A 585 *********************** 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 256 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 202 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 ASN cc_start: 0.7318 (t0) cc_final: 0.7042 (t0) REVERT: A 655 LYS cc_start: 0.7110 (tptp) cc_final: 0.6731 (tptt) REVERT: B 536 THR cc_start: 0.8986 (t) cc_final: 0.8613 (p) REVERT: B 540 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7100 (mt0) REVERT: B 544 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8116 (mt) REVERT: C 46 LYS cc_start: 0.8296 (pttm) cc_final: 0.8058 (pttp) REVERT: C 95 MET cc_start: 0.8774 (ptm) cc_final: 0.7716 (ttp) REVERT: G 100 MET cc_start: 0.8753 (mtp) cc_final: 0.8460 (mtp) REVERT: G 423 ILE cc_start: 0.8445 (mm) cc_final: 0.8240 (mt) REVERT: H 94 ARG cc_start: 0.7623 (ttp-170) cc_final: 0.7247 (ttt-90) REVERT: L 36 TYR cc_start: 0.8033 (m-80) cc_final: 0.7743 (m-80) outliers start: 54 outliers final: 37 residues processed: 241 average time/residue: 0.3091 time to fit residues: 111.5934 Evaluate side-chains 220 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN 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 B residue 636 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 641 ILE 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 270 VAL 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 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 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 32 SER 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: 1.9990 chunk 168 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 187 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 ASN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17300 Z= 0.248 Angle : 0.642 12.080 23480 Z= 0.303 Chirality : 0.049 0.626 2959 Planarity : 0.004 0.042 2840 Dihedral : 9.217 111.361 4403 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.64 % Allowed : 11.73 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.19), residues: 1932 helix: 0.97 (0.28), residues: 387 sheet: 0.34 (0.23), residues: 515 loop : -0.61 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 479 HIS 0.005 0.001 HIS H 100R PHE 0.015 0.001 PHE C 53 TYR 0.015 0.001 TYR H 100E ARG 0.006 0.000 ARG A 585 *********************** 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 255 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 192 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 ASN cc_start: 0.7296 (t0) cc_final: 0.7015 (t0) REVERT: B 536 THR cc_start: 0.8959 (t) cc_final: 0.8599 (p) REVERT: B 540 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7119 (mt0) REVERT: B 544 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8196 (mt) REVERT: C 46 LYS cc_start: 0.8278 (pttm) cc_final: 0.7941 (pttp) REVERT: C 207 LYS cc_start: 0.7067 (mmtm) cc_final: 0.6843 (mmtm) REVERT: C 292 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8805 (m) REVERT: G 100 MET cc_start: 0.8753 (mtp) cc_final: 0.8421 (mtp) REVERT: G 423 ILE cc_start: 0.8496 (mm) cc_final: 0.8289 (mt) REVERT: H 81 GLN cc_start: 0.6390 (OUTLIER) cc_final: 0.5532 (mp-120) outliers start: 63 outliers final: 47 residues processed: 242 average time/residue: 0.3076 time to fit residues: 112.2861 Evaluate side-chains 229 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 587 LEU 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 540 GLN 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 B residue 636 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 641 ILE 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 270 VAL 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 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 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 H residue 81 GLN Chi-restraints excluded: chain L residue 32 SER 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: 0.7980 chunk 106 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 67 ASN G 428 GLN H 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17300 Z= 0.246 Angle : 0.642 12.450 23480 Z= 0.302 Chirality : 0.049 0.649 2959 Planarity : 0.004 0.041 2840 Dihedral : 8.525 67.389 4403 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.16 % Allowed : 11.55 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.19), residues: 1932 helix: 1.01 (0.28), residues: 387 sheet: 0.52 (0.24), residues: 482 loop : -0.66 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 479 HIS 0.004 0.001 HIS H 100R PHE 0.014 0.001 PHE C 53 TYR 0.012 0.001 TYR L 49 ARG 0.005 0.000 ARG A 585 *********************** 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 256 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 184 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 ASN cc_start: 0.7272 (t0) cc_final: 0.6985 (t0) REVERT: B 536 THR cc_start: 0.8944 (t) cc_final: 0.8582 (p) REVERT: B 540 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7122 (mt0) REVERT: B 544 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8282 (mt) REVERT: C 46 LYS cc_start: 0.8298 (pttm) cc_final: 0.8078 (pttp) REVERT: C 95 MET cc_start: 0.8809 (ptm) cc_final: 0.7642 (ttp) REVERT: C 292 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8732 (m) REVERT: C 434 MET cc_start: 0.7739 (tmm) cc_final: 0.7004 (ttp) REVERT: F 540 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.6700 (mp-120) REVERT: G 67 ASN cc_start: 0.6747 (OUTLIER) cc_final: 0.6387 (p0) REVERT: I 151 ARG cc_start: 0.7786 (tpm170) cc_final: 0.7495 (tpp80) REVERT: I 161 MET cc_start: 0.7871 (mmm) cc_final: 0.7252 (tpp) REVERT: H 94 ARG cc_start: 0.7711 (ttp-170) cc_final: 0.7339 (ttt-90) outliers start: 72 outliers final: 56 residues processed: 241 average time/residue: 0.2999 time to fit residues: 109.7257 Evaluate side-chains 237 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 176 time to evaluate : 1.685 ------------------------------------------------------------------------------- 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 587 LEU 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 540 GLN 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 B residue 636 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 111 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 270 VAL 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 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 371 VAL 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 H residue 80 LEU Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain L residue 32 SER 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: 0.5980 chunk 111 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 118 optimal weight: 0.0070 chunk 127 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 17 optimal weight: 0.0040 chunk 146 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 overall best weight: 0.4610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 67 ASN G 103 GLN H 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17300 Z= 0.182 Angle : 0.609 12.508 23480 Z= 0.287 Chirality : 0.046 0.447 2959 Planarity : 0.003 0.041 2840 Dihedral : 7.879 58.493 4403 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.22 % Allowed : 11.90 % 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: 0.06 (0.19), residues: 1932 helix: 1.14 (0.28), residues: 387 sheet: 0.35 (0.22), residues: 559 loop : -0.54 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 479 HIS 0.004 0.001 HIS H 100R PHE 0.013 0.001 PHE C 53 TYR 0.011 0.001 TYR H 100E ARG 0.004 0.000 ARG A 585 *********************** 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 258 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 185 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 THR cc_start: 0.8937 (t) cc_final: 0.8584 (p) REVERT: B 540 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7072 (mt0) REVERT: B 544 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8270 (mt) REVERT: C 46 LYS cc_start: 0.8296 (pttm) cc_final: 0.8092 (pttp) REVERT: C 95 MET cc_start: 0.8808 (ptm) cc_final: 0.7645 (ttp) REVERT: F 540 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.6668 (mp-120) REVERT: G 95 MET cc_start: 0.8105 (ptm) cc_final: 0.7544 (ttp) REVERT: I 151 ARG cc_start: 0.7803 (tpm170) cc_final: 0.7490 (tpp80) REVERT: I 161 MET cc_start: 0.7747 (mmm) cc_final: 0.7166 (tpp) REVERT: L 36 TYR cc_start: 0.8057 (m-80) cc_final: 0.7810 (m-80) REVERT: L 95 HIS cc_start: 0.6585 (m170) cc_final: 0.6379 (m170) outliers start: 73 outliers final: 55 residues processed: 242 average time/residue: 0.3059 time to fit residues: 111.9960 Evaluate side-chains 236 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 1.995 ------------------------------------------------------------------------------- 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 587 LEU 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 540 GLN 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 B residue 636 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 294 ILE 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 F residue 535 MET Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL 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 120 VAL 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 371 VAL 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 H residue 81 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 ASN H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 17300 Z= 0.374 Angle : 0.696 12.535 23480 Z= 0.331 Chirality : 0.050 0.424 2959 Planarity : 0.004 0.041 2840 Dihedral : 8.010 59.971 4403 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.10 % Allowed : 11.90 % Favored : 84.00 % 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: -0.27 (0.19), residues: 1932 helix: 0.89 (0.28), residues: 387 sheet: 0.00 (0.21), residues: 584 loop : -0.68 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 96 HIS 0.004 0.001 HIS C 105 PHE 0.015 0.002 PHE C 53 TYR 0.017 0.002 TYR L 49 ARG 0.005 0.001 ARG A 585 *********************** 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 251 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 180 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.7844 (pt0) cc_final: 0.7580 (pt0) REVERT: A 651 ASN cc_start: 0.7337 (t0) cc_final: 0.7072 (t0) REVERT: B 540 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7173 (mt0) REVERT: B 544 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8508 (mt) REVERT: C 95 MET cc_start: 0.8960 (ptm) cc_final: 0.7814 (ttp) REVERT: C 434 MET cc_start: 0.7916 (tmm) cc_final: 0.7319 (ttp) REVERT: F 540 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.6886 (mp-120) REVERT: F 626 MET cc_start: 0.8293 (ttt) cc_final: 0.8075 (ttt) REVERT: G 95 MET cc_start: 0.8303 (ptm) cc_final: 0.7670 (ttp) REVERT: I 151 ARG cc_start: 0.7761 (tpm170) cc_final: 0.7515 (tpp80) REVERT: I 161 MET cc_start: 0.7869 (mmm) cc_final: 0.7281 (tpp) REVERT: H 81 GLN cc_start: 0.6521 (OUTLIER) cc_final: 0.6262 (tp40) outliers start: 71 outliers final: 58 residues processed: 238 average time/residue: 0.2895 time to fit residues: 103.9694 Evaluate side-chains 238 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 176 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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 587 LEU 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 540 GLN 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 B residue 636 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 294 ILE 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 F residue 535 MET Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS 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 270 VAL Chi-restraints excluded: chain G residue 292 VAL 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 52 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 120 VAL 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 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 356 ASN Chi-restraints excluded: chain I residue 371 VAL 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 H residue 81 GLN Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 32 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: 9.9990 chunk 112 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 177 optimal weight: 0.0370 chunk 153 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 118 optimal weight: 0.0070 chunk 94 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 428 GLN I 356 ASN H 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17300 Z= 0.177 Angle : 0.621 12.823 23480 Z= 0.294 Chirality : 0.046 0.414 2959 Planarity : 0.004 0.041 2840 Dihedral : 7.697 59.061 4403 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.41 % Allowed : 12.59 % Favored : 84.00 % 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: -0.11 (0.19), residues: 1932 helix: 1.14 (0.28), residues: 387 sheet: 0.08 (0.22), residues: 583 loop : -0.61 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 96 HIS 0.004 0.001 HIS H 100R PHE 0.013 0.001 PHE C 53 TYR 0.011 0.001 TYR L 49 ARG 0.007 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 247 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 188 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 540 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7093 (mt0) REVERT: B 544 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8428 (mt) REVERT: C 95 MET cc_start: 0.8841 (ptm) cc_final: 0.7701 (ttp) REVERT: C 434 MET cc_start: 0.7604 (tmm) cc_final: 0.7023 (ttp) REVERT: F 540 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.6476 (mp-120) REVERT: G 95 MET cc_start: 0.8156 (ptm) cc_final: 0.7829 (ttp) REVERT: G 96 TRP cc_start: 0.8319 (m100) cc_final: 0.7772 (m100) REVERT: I 151 ARG cc_start: 0.7725 (tpm170) cc_final: 0.7439 (tpp80) REVERT: I 161 MET cc_start: 0.7696 (mmm) cc_final: 0.7182 (tpp) outliers start: 59 outliers final: 53 residues processed: 234 average time/residue: 0.3477 time to fit residues: 125.9799 Evaluate side-chains 240 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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 587 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN 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 B residue 636 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 294 ILE 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 F residue 535 MET Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS 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 270 VAL Chi-restraints excluded: chain G residue 292 VAL 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 120 VAL 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 371 VAL 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 81 GLN Chi-restraints excluded: chain L residue 32 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 163 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.179908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.152538 restraints weight = 20045.487| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.01 r_work: 0.3594 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17300 Z= 0.259 Angle : 0.642 12.620 23480 Z= 0.303 Chirality : 0.047 0.393 2959 Planarity : 0.004 0.041 2840 Dihedral : 7.660 59.205 4403 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.52 % Allowed : 12.82 % Favored : 83.65 % 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: 1.10 (0.28), residues: 387 sheet: 0.03 (0.22), residues: 583 loop : -0.65 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 96 HIS 0.004 0.001 HIS H 100R PHE 0.013 0.001 PHE C 53 TYR 0.013 0.001 TYR L 49 ARG 0.006 0.000 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3684.06 seconds wall clock time: 68 minutes 15.12 seconds (4095.12 seconds total)