Starting phenix.real_space_refine on Sun Aug 24 13:40:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8euv_28618/08_2025/8euv_28618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8euv_28618/08_2025/8euv_28618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8euv_28618/08_2025/8euv_28618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8euv_28618/08_2025/8euv_28618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8euv_28618/08_2025/8euv_28618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8euv_28618/08_2025/8euv_28618.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 12486 2.51 5 N 3342 2.21 5 O 4181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20138 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "C" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "E" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "G" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "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: "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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "b" 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: "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: "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: 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "l" 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: 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: "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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 5.46, per 1000 atoms: 0.27 Number of scatterers: 20138 At special positions: 0 Unit cell: (153.55, 142.76, 121.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 4181 8.00 N 3342 7.00 C 12486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.05 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 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=2.04 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 C 501 " - pdb=" SG CYS D 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=1.85 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.05 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 R 4 " - " MAN R 5 " " MAN b 4 " - " MAN b 5 " " MAN m 4 " - " MAN m 5 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA b 3 " - " MAN b 4 " " BMA m 3 " - " MAN m 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG 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 b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 133 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 133 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 392 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 133 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 363 " " NAG V 1 " - " ASN C 448 " " NAG W 1 " - " ASN C 160 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 276 " " NAG Z 1 " - " ASN C 386 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 295 " " NAG d 1 " - " ASN C 156 " " NAG e 1 " - " ASN C 332 " " NAG f 1 " - " ASN C 363 " " NAG g 1 " - " ASN E 295 " " NAG h 1 " - " ASN E 448 " " NAG i 1 " - " ASN E 160 " " NAG j 1 " - " ASN E 88 " " NAG k 1 " - " ASN E 276 " " NAG l 1 " - " ASN E 386 " " NAG m 1 " - " ASN E 262 " " NAG n 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 332 " " NAG p 1 " - " ASN E 363 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 884.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 45 sheets defined 17.9% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.940A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.941A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.505A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.640A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 639 through 662 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.929A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.065A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.508A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.619A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 595 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 639 through 662 Processing helix chain 'E' and resid 98 through 116 removed outlier: 3.940A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.011A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.504A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.978A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.719A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 595 Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 639 through 662 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.997A pdb=" N ASN G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.992A pdb=" N ASN I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.990A pdb=" N ASN K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.344A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.602A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.788A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.419A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.377A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.930A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.956A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.070A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.191A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 11.070A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.956A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.930A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.521A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.501A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.589A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.810A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.418A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.378A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.921A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.947A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.781A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.067A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 12.195A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 12.195A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 11.067A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.781A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.947A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.921A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.522A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.209A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.590A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.790A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.416A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.378A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.957A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.068A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.075A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 12.193A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 273 removed outlier: 12.193A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 11.075A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 11.068A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.957A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.522A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.512A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.767A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 7 removed outlier: 12.015A pdb=" N CYS H 23 " --> pdb=" O THR H 74 " (cutoff:3.500A) removed outlier: 10.985A pdb=" N THR H 74 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 12.093A pdb=" N ALA H 25 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 11.730A pdb=" N THR H 72 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N GLN H 27 " --> pdb=" O HIS H 70 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N HIS H 70 " --> pdb=" O GLN H 27 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.706A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.758A pdb=" N THR H 97 " --> pdb=" O HIS H 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.525A pdb=" N LEU I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.749A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 7 removed outlier: 12.005A pdb=" N CYS J 23 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N THR J 74 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 12.105A pdb=" N ALA J 25 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR J 72 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N GLN J 27 " --> pdb=" O HIS J 70 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N HIS J 70 " --> pdb=" O GLN J 27 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.717A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.766A pdb=" N THR J 97 " --> pdb=" O HIS J 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.511A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.759A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 4 through 7 removed outlier: 12.055A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 12.142A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.762A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.136A pdb=" N GLN L 27 " --> pdb=" O HIS L 70 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N HIS L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.724A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.768A pdb=" N THR L 97 " --> pdb=" O HIS L 90 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2070 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: 4.86 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.61: 20158 1.61 - 1.99: 176 1.99 - 2.37: 1 2.37 - 2.75: 0 2.75 - 3.14: 2 Bond restraints: 20337 Sorted by residual: bond pdb=" N PRO H 8 " pdb=" CD PRO H 8 " ideal model delta sigma weight residual 1.474 3.137 -1.663 1.40e-02 5.10e+03 1.41e+04 bond pdb=" N PRO J 8 " pdb=" CD PRO J 8 " ideal model delta sigma weight residual 1.474 2.946 -1.472 1.40e-02 5.10e+03 1.11e+04 bond pdb=" CB PRO H 8 " pdb=" CG PRO H 8 " ideal model delta sigma weight residual 1.506 2.053 -0.547 3.90e-02 6.57e+02 1.96e+02 bond pdb=" CB PRO J 8 " pdb=" CG PRO J 8 " ideal model delta sigma weight residual 1.506 1.933 -0.427 3.90e-02 6.57e+02 1.20e+02 bond pdb=" N PRO H 59 " pdb=" CD PRO H 59 " ideal model delta sigma weight residual 1.473 1.622 -0.149 1.40e-02 5.10e+03 1.13e+02 ... (remaining 20332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.55: 27594 16.55 - 33.11: 7 33.11 - 49.66: 0 49.66 - 66.21: 0 66.21 - 82.77: 2 Bond angle restraints: 27603 Sorted by residual: angle pdb=" N PRO H 8 " pdb=" CD PRO H 8 " pdb=" CG PRO H 8 " ideal model delta sigma weight residual 103.80 21.03 82.77 1.20e+00 6.94e-01 4.76e+03 angle pdb=" N PRO J 8 " pdb=" CD PRO J 8 " pdb=" CG PRO J 8 " ideal model delta sigma weight residual 103.80 36.76 67.04 1.20e+00 6.94e-01 3.12e+03 angle pdb=" CA PRO H 8 " pdb=" N PRO H 8 " pdb=" CD PRO H 8 " ideal model delta sigma weight residual 111.50 86.14 25.36 1.40e+00 5.10e-01 3.28e+02 angle pdb=" CA PRO J 8 " pdb=" N PRO J 8 " pdb=" CD PRO J 8 " ideal model delta sigma weight residual 111.50 88.42 23.08 1.40e+00 5.10e-01 2.72e+02 angle pdb=" CB PRO H 8 " pdb=" CG PRO H 8 " pdb=" CD PRO H 8 " ideal model delta sigma weight residual 105.40 78.06 27.34 2.30e+00 1.89e-01 1.41e+02 ... (remaining 27598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.29: 12499 27.29 - 54.58: 639 54.58 - 81.87: 110 81.87 - 109.17: 28 109.17 - 136.46: 2 Dihedral angle restraints: 13278 sinusoidal: 6393 harmonic: 6885 Sorted by residual: dihedral pdb=" CA ASN D 618 " pdb=" C ASN D 618 " pdb=" N LEU D 619 " pdb=" CA LEU D 619 " ideal model delta harmonic sigma weight residual -180.00 -135.65 -44.35 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 -6.74 -79.26 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CA ASN B 618 " pdb=" C ASN B 618 " pdb=" N LEU B 619 " pdb=" CA LEU B 619 " ideal model delta harmonic sigma weight residual -180.00 -136.28 -43.72 0 5.00e+00 4.00e-02 7.64e+01 ... (remaining 13275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2729 0.060 - 0.120: 501 0.120 - 0.180: 110 0.180 - 0.240: 3 0.240 - 0.299: 8 Chirality restraints: 3351 Sorted by residual: chirality pdb=" C1 MAN R 4 " pdb=" O3 BMA R 3 " pdb=" C2 MAN R 4 " pdb=" O5 MAN R 4 " both_signs ideal model delta sigma weight residual False 2.40 2.43 -0.03 2.00e-02 2.50e+03 2.76e+00 chirality pdb=" C5 BMA m 3 " pdb=" C4 BMA m 3 " pdb=" C6 BMA m 3 " pdb=" O5 BMA m 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C5 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" C6 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 3348 not shown) Planarity restraints: 3447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K 13 " -0.085 5.00e-02 4.00e+02 1.28e-01 2.60e+01 pdb=" N PRO K 14 " 0.221 5.00e-02 4.00e+02 pdb=" CA PRO K 14 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO K 14 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 7 " -0.060 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO H 8 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO H 8 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 8 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 75 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO E 76 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO E 76 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 76 " -0.029 5.00e-02 4.00e+02 ... (remaining 3444 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 425 2.68 - 3.24: 17949 3.24 - 3.79: 31436 3.79 - 4.35: 46106 4.35 - 4.90: 73105 Nonbonded interactions: 169021 Sorted by model distance: nonbonded pdb=" OG SER C 56 " pdb=" OG1 THR C 71 " model vdw 2.127 3.040 nonbonded pdb=" OG SER A 56 " pdb=" OG1 THR A 71 " model vdw 2.130 3.040 nonbonded pdb=" OG SER E 56 " pdb=" OG1 THR E 71 " model vdw 2.131 3.040 nonbonded pdb=" O GLN E 293 " pdb=" O HOH E 701 " model vdw 2.168 3.040 nonbonded pdb=" O GLN A 293 " pdb=" O HOH A 701 " model vdw 2.181 3.040 ... (remaining 169016 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'j' } ncs_group { reference = chain 'R' selection = chain 'b' selection = chain 'm' } 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: 8.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.050 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:9.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.017 1.663 20466 Z= 1.152 Angle : 1.145 82.766 27948 Z= 0.705 Chirality : 0.053 0.299 3351 Planarity : 0.005 0.128 3402 Dihedral : 16.363 136.457 8718 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.62 % Allowed : 10.17 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.17), residues: 2352 helix: 0.50 (0.27), residues: 408 sheet: 0.59 (0.18), residues: 765 loop : -0.28 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 30 TYR 0.010 0.002 TYR F 638 PHE 0.024 0.002 PHE A 53 TRP 0.013 0.001 TRP E 69 HIS 0.006 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.01742 (20337) covalent geometry : angle 1.10763 (27603) SS BOND : bond 0.02911 ( 42) SS BOND : angle 2.38360 ( 84) hydrogen bonds : bond 0.10861 ( 723) hydrogen bonds : angle 5.95066 ( 2070) link_ALPHA1-2 : bond 0.00202 ( 3) link_ALPHA1-2 : angle 2.01553 ( 9) link_ALPHA1-3 : bond 0.00233 ( 3) link_ALPHA1-3 : angle 2.09442 ( 9) link_BETA1-4 : bond 0.00343 ( 36) link_BETA1-4 : angle 2.10428 ( 108) link_NAG-ASN : bond 0.00373 ( 45) link_NAG-ASN : angle 3.62570 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 254 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8579 (mtp-110) cc_final: 0.7439 (mtm110) REVERT: G 75 ILE cc_start: 0.8202 (pt) cc_final: 0.7959 (pp) REVERT: I 75 ILE cc_start: 0.8316 (pt) cc_final: 0.7933 (pp) outliers start: 13 outliers final: 11 residues processed: 267 average time/residue: 0.6648 time to fit residues: 200.7123 Evaluate side-chains 246 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 235 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain K residue 11 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 137 ASN D 611 ASN E 67 ASN E 137 ASN F 591 GLN F 651 ASN L 6 GLN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.176762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.123398 restraints weight = 21426.482| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.26 r_work: 0.3305 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20466 Z= 0.156 Angle : 0.671 10.679 27948 Z= 0.327 Chirality : 0.046 0.294 3351 Planarity : 0.004 0.082 3402 Dihedral : 9.590 71.096 4370 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.25 % Allowed : 10.02 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.18), residues: 2352 helix: 1.04 (0.27), residues: 405 sheet: 0.79 (0.18), residues: 795 loop : 0.10 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.011 0.001 TYR C 318 PHE 0.015 0.002 PHE E 53 TRP 0.017 0.001 TRP A 427 HIS 0.004 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00357 (20337) covalent geometry : angle 0.62097 (27603) SS BOND : bond 0.00279 ( 42) SS BOND : angle 0.86069 ( 84) hydrogen bonds : bond 0.04405 ( 723) hydrogen bonds : angle 5.02782 ( 2070) link_ALPHA1-2 : bond 0.00395 ( 3) link_ALPHA1-2 : angle 1.78289 ( 9) link_ALPHA1-3 : bond 0.00789 ( 3) link_ALPHA1-3 : angle 1.95866 ( 9) link_BETA1-4 : bond 0.00521 ( 36) link_BETA1-4 : angle 1.82409 ( 108) link_NAG-ASN : bond 0.00399 ( 45) link_NAG-ASN : angle 3.26450 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8477 (mtp-110) cc_final: 0.7102 (mtm110) REVERT: B 658 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6531 (tm-30) REVERT: C 103 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: D 542 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7669 (mtt90) REVERT: E 103 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: E 327 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7830 (ptt-90) REVERT: F 530 MET cc_start: 0.8470 (mtp) cc_final: 0.8211 (mtp) REVERT: G 75 ILE cc_start: 0.7939 (pt) cc_final: 0.7708 (pp) REVERT: L 79 GLN cc_start: 0.5257 (OUTLIER) cc_final: 0.4827 (tp40) outliers start: 47 outliers final: 19 residues processed: 291 average time/residue: 0.6689 time to fit residues: 219.5746 Evaluate side-chains 272 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 248 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 198 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 151 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 137 ASN B 658 GLN C 136 ASN C 137 ASN D 543 ASN D 611 ASN E 137 ASN E 315 GLN E 422 GLN G 76 ASN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN K 76 ASN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.175078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121225 restraints weight = 21409.341| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.21 r_work: 0.3285 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20466 Z= 0.190 Angle : 0.679 9.251 27948 Z= 0.331 Chirality : 0.046 0.281 3351 Planarity : 0.004 0.064 3402 Dihedral : 7.716 58.801 4361 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.07 % Allowed : 11.08 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.18), residues: 2352 helix: 1.08 (0.27), residues: 405 sheet: 0.76 (0.18), residues: 771 loop : 0.15 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 178 TYR 0.014 0.002 TYR C 318 PHE 0.014 0.002 PHE E 53 TRP 0.018 0.002 TRP C 427 HIS 0.004 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00443 (20337) covalent geometry : angle 0.62598 (27603) SS BOND : bond 0.00337 ( 42) SS BOND : angle 1.26354 ( 84) hydrogen bonds : bond 0.04461 ( 723) hydrogen bonds : angle 4.87665 ( 2070) link_ALPHA1-2 : bond 0.00257 ( 3) link_ALPHA1-2 : angle 1.68037 ( 9) link_ALPHA1-3 : bond 0.00760 ( 3) link_ALPHA1-3 : angle 1.50517 ( 9) link_BETA1-4 : bond 0.00429 ( 36) link_BETA1-4 : angle 1.81283 ( 108) link_NAG-ASN : bond 0.00455 ( 45) link_NAG-ASN : angle 3.35229 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 258 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8246 (tp30) cc_final: 0.8012 (mm-30) REVERT: A 103 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7685 (tt0) REVERT: A 178 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.8010 (tpt170) REVERT: A 502 LYS cc_start: 0.7773 (ttpt) cc_final: 0.7243 (tttt) REVERT: B 530 MET cc_start: 0.8566 (mtp) cc_final: 0.8304 (mtp) REVERT: B 542 ARG cc_start: 0.8507 (mtp-110) cc_final: 0.7183 (mtt90) REVERT: B 632 ASP cc_start: 0.8478 (t0) cc_final: 0.8258 (t0) REVERT: C 66 HIS cc_start: 0.6232 (OUTLIER) cc_final: 0.5982 (m90) REVERT: C 103 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7569 (tt0) REVERT: C 173 TYR cc_start: 0.8811 (p90) cc_final: 0.8593 (p90) REVERT: E 95 MET cc_start: 0.9021 (ptm) cc_final: 0.8738 (ptm) REVERT: E 103 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: E 178 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7899 (tpt170) REVERT: E 327 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7739 (ptt-90) REVERT: E 412 ASP cc_start: 0.8380 (p0) cc_final: 0.8169 (p0) REVERT: H 79 GLN cc_start: 0.4950 (OUTLIER) cc_final: 0.4294 (tp40) REVERT: I 100 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6335 (mtt) REVERT: L 79 GLN cc_start: 0.5233 (OUTLIER) cc_final: 0.4917 (tp40) outliers start: 64 outliers final: 29 residues processed: 294 average time/residue: 0.6774 time to fit residues: 224.4321 Evaluate side-chains 278 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 137 ASN B 658 GLN C 136 ASN C 137 ASN C 422 GLN D 611 ASN E 136 ASN E 137 ASN F 611 ASN G 76 ASN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN J 45 ASN K 76 ASN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.174765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125494 restraints weight = 21547.336| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.97 r_work: 0.3316 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20466 Z= 0.193 Angle : 0.676 10.047 27948 Z= 0.329 Chirality : 0.046 0.281 3351 Planarity : 0.004 0.058 3402 Dihedral : 7.109 59.500 4361 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.84 % Allowed : 11.41 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.18), residues: 2352 helix: 1.29 (0.27), residues: 387 sheet: 0.80 (0.18), residues: 795 loop : 0.12 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 178 TYR 0.014 0.002 TYR A 318 PHE 0.014 0.002 PHE E 383 TRP 0.018 0.002 TRP C 427 HIS 0.003 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00452 (20337) covalent geometry : angle 0.62309 (27603) SS BOND : bond 0.00342 ( 42) SS BOND : angle 1.47287 ( 84) hydrogen bonds : bond 0.04411 ( 723) hydrogen bonds : angle 4.80608 ( 2070) link_ALPHA1-2 : bond 0.00244 ( 3) link_ALPHA1-2 : angle 1.69328 ( 9) link_ALPHA1-3 : bond 0.00705 ( 3) link_ALPHA1-3 : angle 1.72334 ( 9) link_BETA1-4 : bond 0.00444 ( 36) link_BETA1-4 : angle 1.79507 ( 108) link_NAG-ASN : bond 0.00461 ( 45) link_NAG-ASN : angle 3.28171 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 246 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8676 (t) REVERT: A 92 GLU cc_start: 0.8249 (tp30) cc_final: 0.8047 (mm-30) REVERT: A 103 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: A 178 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.8004 (tpt170) REVERT: A 501 CYS cc_start: 0.7614 (OUTLIER) cc_final: 0.6964 (p) REVERT: A 502 LYS cc_start: 0.7632 (ttpt) cc_final: 0.7161 (tttt) REVERT: B 530 MET cc_start: 0.8599 (mtp) cc_final: 0.8368 (mtp) REVERT: B 542 ARG cc_start: 0.8532 (mtp-110) cc_final: 0.7249 (mtt90) REVERT: B 632 ASP cc_start: 0.8487 (t70) cc_final: 0.8173 (t0) REVERT: B 655 LYS cc_start: 0.6904 (mttt) cc_final: 0.5311 (pttt) REVERT: C 103 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: C 173 TYR cc_start: 0.8821 (p90) cc_final: 0.8604 (p90) REVERT: D 632 ASP cc_start: 0.8363 (t70) cc_final: 0.7967 (t0) REVERT: E 95 MET cc_start: 0.8999 (ptm) cc_final: 0.8672 (ptm) REVERT: E 97 LYS cc_start: 0.8495 (mmpt) cc_final: 0.7856 (mptt) REVERT: E 103 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: E 178 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7861 (tpt170) REVERT: E 327 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7782 (ptt-90) REVERT: E 412 ASP cc_start: 0.8346 (p0) cc_final: 0.8087 (p0) REVERT: F 530 MET cc_start: 0.8609 (mtp) cc_final: 0.8391 (mtp) REVERT: F 637 ASN cc_start: 0.5715 (OUTLIER) cc_final: 0.5390 (p0) REVERT: H 79 GLN cc_start: 0.4948 (OUTLIER) cc_final: 0.4317 (tp40) REVERT: I 100 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6536 (mtt) REVERT: L 79 GLN cc_start: 0.5119 (OUTLIER) cc_final: 0.4796 (tp40) outliers start: 80 outliers final: 39 residues processed: 297 average time/residue: 0.6676 time to fit residues: 223.9900 Evaluate side-chains 291 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 148 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 100 optimal weight: 0.0570 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 137 ASN B 591 GLN B 658 GLN C 136 ASN C 137 ASN D 611 ASN E 136 ASN E 137 ASN E 315 GLN F 611 ASN F 651 ASN G 76 ASN I 76 ASN K 76 ASN L 45 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.175471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122366 restraints weight = 21494.935| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.13 r_work: 0.3330 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20466 Z= 0.190 Angle : 0.675 12.670 27948 Z= 0.329 Chirality : 0.046 0.278 3351 Planarity : 0.004 0.055 3402 Dihedral : 6.758 59.675 4361 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.50 % Allowed : 12.85 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.17), residues: 2352 helix: 1.29 (0.27), residues: 390 sheet: 0.76 (0.18), residues: 771 loop : 0.07 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 23 TYR 0.014 0.002 TYR A 318 PHE 0.016 0.002 PHE A 383 TRP 0.018 0.002 TRP C 427 HIS 0.004 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00446 (20337) covalent geometry : angle 0.62376 (27603) SS BOND : bond 0.00331 ( 42) SS BOND : angle 1.54852 ( 84) hydrogen bonds : bond 0.04350 ( 723) hydrogen bonds : angle 4.76160 ( 2070) link_ALPHA1-2 : bond 0.00233 ( 3) link_ALPHA1-2 : angle 1.71588 ( 9) link_ALPHA1-3 : bond 0.00662 ( 3) link_ALPHA1-3 : angle 1.59078 ( 9) link_BETA1-4 : bond 0.00429 ( 36) link_BETA1-4 : angle 1.74685 ( 108) link_NAG-ASN : bond 0.00465 ( 45) link_NAG-ASN : angle 3.24112 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 251 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 51 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8719 (t) REVERT: A 92 GLU cc_start: 0.8209 (tp30) cc_final: 0.8002 (mm-30) REVERT: A 103 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: A 178 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.8008 (tpt170) REVERT: A 501 CYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6611 (p) REVERT: A 502 LYS cc_start: 0.7623 (ttpt) cc_final: 0.7174 (tttt) REVERT: B 530 MET cc_start: 0.8632 (mtp) cc_final: 0.8385 (mtp) REVERT: B 542 ARG cc_start: 0.8511 (mtp-110) cc_final: 0.7278 (mtt90) REVERT: B 632 ASP cc_start: 0.8472 (t70) cc_final: 0.8101 (t0) REVERT: B 655 LYS cc_start: 0.6922 (mttt) cc_final: 0.5301 (pttt) REVERT: C 66 HIS cc_start: 0.6261 (OUTLIER) cc_final: 0.5955 (m90) REVERT: C 103 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: C 173 TYR cc_start: 0.8806 (p90) cc_final: 0.8580 (p90) REVERT: C 327 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7863 (ptt-90) REVERT: D 632 ASP cc_start: 0.8350 (t70) cc_final: 0.7992 (t0) REVERT: D 658 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6313 (tt0) REVERT: E 95 MET cc_start: 0.9033 (ptm) cc_final: 0.8697 (ptm) REVERT: E 97 LYS cc_start: 0.8509 (mmpt) cc_final: 0.7927 (mptt) REVERT: E 103 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: E 178 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7838 (tpt170) REVERT: E 327 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7763 (ptt-90) REVERT: H 79 GLN cc_start: 0.4972 (OUTLIER) cc_final: 0.4404 (tp40) REVERT: I 100 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6594 (mtt) REVERT: K 71 ARG cc_start: 0.8478 (ppt170) cc_final: 0.8180 (ppt170) REVERT: L 79 GLN cc_start: 0.5081 (OUTLIER) cc_final: 0.4817 (tp40) REVERT: L 90 HIS cc_start: 0.6601 (OUTLIER) cc_final: 0.5413 (p-80) outliers start: 73 outliers final: 38 residues processed: 296 average time/residue: 0.6616 time to fit residues: 221.2501 Evaluate side-chains 298 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 245 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 90 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 86 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 100 optimal weight: 0.0170 chunk 119 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 137 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 137 ASN D 611 ASN E 136 ASN E 137 ASN E 315 GLN F 611 ASN F 651 ASN G 76 ASN I 76 ASN K 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.176085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.122559 restraints weight = 21286.765| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.05 r_work: 0.3351 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20466 Z= 0.165 Angle : 0.638 10.264 27948 Z= 0.312 Chirality : 0.045 0.273 3351 Planarity : 0.004 0.052 3402 Dihedral : 6.388 59.760 4361 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.26 % Allowed : 13.72 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.18), residues: 2352 helix: 1.38 (0.27), residues: 390 sheet: 0.81 (0.18), residues: 762 loop : 0.13 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 178 TYR 0.013 0.002 TYR A 318 PHE 0.014 0.002 PHE A 383 TRP 0.017 0.002 TRP C 427 HIS 0.006 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00383 (20337) covalent geometry : angle 0.58921 (27603) SS BOND : bond 0.00362 ( 42) SS BOND : angle 1.35124 ( 84) hydrogen bonds : bond 0.04111 ( 723) hydrogen bonds : angle 4.69552 ( 2070) link_ALPHA1-2 : bond 0.00250 ( 3) link_ALPHA1-2 : angle 1.68634 ( 9) link_ALPHA1-3 : bond 0.00721 ( 3) link_ALPHA1-3 : angle 1.53328 ( 9) link_BETA1-4 : bond 0.00419 ( 36) link_BETA1-4 : angle 1.69143 ( 108) link_NAG-ASN : bond 0.00402 ( 45) link_NAG-ASN : angle 3.08868 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 245 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 51 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8804 (t) REVERT: A 92 GLU cc_start: 0.8208 (tp30) cc_final: 0.7998 (mm-30) REVERT: A 103 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: A 178 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7941 (tpt170) REVERT: B 530 MET cc_start: 0.8672 (mtp) cc_final: 0.8446 (mtp) REVERT: B 542 ARG cc_start: 0.8568 (mtp-110) cc_final: 0.7398 (mtt90) REVERT: B 632 ASP cc_start: 0.8450 (t70) cc_final: 0.8092 (t0) REVERT: B 655 LYS cc_start: 0.6976 (mtmt) cc_final: 0.5366 (pttt) REVERT: C 103 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: C 327 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7898 (ptt-90) REVERT: D 632 ASP cc_start: 0.8335 (t70) cc_final: 0.8011 (t0) REVERT: D 658 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6419 (tt0) REVERT: E 95 MET cc_start: 0.9050 (ptm) cc_final: 0.8710 (ptm) REVERT: E 97 LYS cc_start: 0.8532 (mmpt) cc_final: 0.8017 (mptt) REVERT: E 103 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: E 178 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7833 (tpt170) REVERT: E 327 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7878 (ptt-90) REVERT: F 530 MET cc_start: 0.8710 (mtp) cc_final: 0.8485 (mtp) REVERT: H 79 GLN cc_start: 0.5190 (OUTLIER) cc_final: 0.4693 (tp40) REVERT: H 90 HIS cc_start: 0.6586 (OUTLIER) cc_final: 0.5124 (p-80) REVERT: I 100 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6622 (mtt) REVERT: J 20 THR cc_start: 0.7242 (m) cc_final: 0.6719 (p) REVERT: L 79 GLN cc_start: 0.5213 (OUTLIER) cc_final: 0.4964 (tp40) REVERT: L 90 HIS cc_start: 0.6775 (OUTLIER) cc_final: 0.5576 (p-80) outliers start: 68 outliers final: 36 residues processed: 291 average time/residue: 0.6093 time to fit residues: 200.9538 Evaluate side-chains 288 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 90 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 173 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 137 ASN E 136 ASN E 137 ASN E 352 HIS F 611 ASN F 651 ASN G 76 ASN I 76 ASN K 76 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.174428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121338 restraints weight = 21470.407| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.10 r_work: 0.3314 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 20466 Z= 0.230 Angle : 0.714 12.559 27948 Z= 0.347 Chirality : 0.048 0.274 3351 Planarity : 0.004 0.052 3402 Dihedral : 6.798 59.594 4361 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.17 % Allowed : 14.20 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.17), residues: 2352 helix: 0.86 (0.26), residues: 408 sheet: 0.72 (0.18), residues: 738 loop : 0.05 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 178 TYR 0.017 0.002 TYR E 384 PHE 0.018 0.002 PHE A 383 TRP 0.017 0.002 TRP C 427 HIS 0.006 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00541 (20337) covalent geometry : angle 0.66158 (27603) SS BOND : bond 0.00384 ( 42) SS BOND : angle 1.62923 ( 84) hydrogen bonds : bond 0.04631 ( 723) hydrogen bonds : angle 4.82345 ( 2070) link_ALPHA1-2 : bond 0.00206 ( 3) link_ALPHA1-2 : angle 1.72141 ( 9) link_ALPHA1-3 : bond 0.00549 ( 3) link_ALPHA1-3 : angle 1.56766 ( 9) link_BETA1-4 : bond 0.00438 ( 36) link_BETA1-4 : angle 1.80382 ( 108) link_NAG-ASN : bond 0.00565 ( 45) link_NAG-ASN : angle 3.38199 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 253 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 51 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8712 (t) REVERT: A 92 GLU cc_start: 0.8242 (tp30) cc_final: 0.8018 (mm-30) REVERT: A 103 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: A 178 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7976 (tpt170) REVERT: A 501 CYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6804 (p) REVERT: A 502 LYS cc_start: 0.7603 (ttpt) cc_final: 0.7137 (tttt) REVERT: B 530 MET cc_start: 0.8655 (mtp) cc_final: 0.8382 (mtp) REVERT: B 542 ARG cc_start: 0.8528 (mtp-110) cc_final: 0.7298 (mtm110) REVERT: B 632 ASP cc_start: 0.8456 (t70) cc_final: 0.8065 (t0) REVERT: B 655 LYS cc_start: 0.6860 (mtmt) cc_final: 0.5290 (pttt) REVERT: C 103 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: D 632 ASP cc_start: 0.8330 (t70) cc_final: 0.8008 (t0) REVERT: D 658 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.6303 (tt0) REVERT: E 95 MET cc_start: 0.9052 (ptm) cc_final: 0.8678 (ptm) REVERT: E 103 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: E 178 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7896 (tpt170) REVERT: E 327 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7813 (ptt-90) REVERT: H 79 GLN cc_start: 0.5053 (OUTLIER) cc_final: 0.4553 (tp40) REVERT: H 90 HIS cc_start: 0.6616 (OUTLIER) cc_final: 0.5255 (p-80) REVERT: J 20 THR cc_start: 0.7232 (m) cc_final: 0.6773 (p) REVERT: L 79 GLN cc_start: 0.5105 (OUTLIER) cc_final: 0.4821 (tp40) REVERT: L 90 HIS cc_start: 0.6733 (OUTLIER) cc_final: 0.5485 (p-80) outliers start: 66 outliers final: 41 residues processed: 295 average time/residue: 0.6640 time to fit residues: 221.2976 Evaluate side-chains 305 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 251 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 90 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 101 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 223 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 658 GLN C 136 ASN C 137 ASN E 136 ASN E 137 ASN E 315 GLN F 611 ASN F 658 GLN G 76 ASN I 76 ASN K 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.175191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121439 restraints weight = 21517.577| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.06 r_work: 0.3337 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 20466 Z= 0.195 Angle : 0.675 11.825 27948 Z= 0.329 Chirality : 0.046 0.271 3351 Planarity : 0.004 0.051 3402 Dihedral : 6.680 59.825 4361 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.31 % Allowed : 14.34 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.17), residues: 2352 helix: 0.88 (0.26), residues: 408 sheet: 0.73 (0.18), residues: 762 loop : 0.08 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 178 TYR 0.014 0.002 TYR A 318 PHE 0.015 0.002 PHE A 383 TRP 0.018 0.002 TRP I 50 HIS 0.006 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00456 (20337) covalent geometry : angle 0.62497 (27603) SS BOND : bond 0.00342 ( 42) SS BOND : angle 1.42084 ( 84) hydrogen bonds : bond 0.04346 ( 723) hydrogen bonds : angle 4.78806 ( 2070) link_ALPHA1-2 : bond 0.00235 ( 3) link_ALPHA1-2 : angle 1.69940 ( 9) link_ALPHA1-3 : bond 0.00612 ( 3) link_ALPHA1-3 : angle 1.50368 ( 9) link_BETA1-4 : bond 0.00418 ( 36) link_BETA1-4 : angle 1.73723 ( 108) link_NAG-ASN : bond 0.00472 ( 45) link_NAG-ASN : angle 3.21383 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 242 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 51 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8772 (t) REVERT: A 92 GLU cc_start: 0.8223 (tp30) cc_final: 0.8008 (mm-30) REVERT: A 103 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: A 178 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7980 (tpt170) REVERT: A 502 LYS cc_start: 0.7391 (ttpt) cc_final: 0.6968 (tttt) REVERT: B 530 MET cc_start: 0.8653 (mtp) cc_final: 0.8392 (mtp) REVERT: B 542 ARG cc_start: 0.8613 (mtp-110) cc_final: 0.7374 (mtm110) REVERT: B 632 ASP cc_start: 0.8467 (t70) cc_final: 0.8069 (t0) REVERT: B 655 LYS cc_start: 0.6908 (mtmt) cc_final: 0.5325 (pttt) REVERT: C 103 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7725 (tt0) REVERT: C 327 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7897 (ptt-90) REVERT: D 632 ASP cc_start: 0.8348 (t70) cc_final: 0.8035 (t0) REVERT: D 658 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6346 (tt0) REVERT: E 95 MET cc_start: 0.9060 (ptm) cc_final: 0.8688 (ptm) REVERT: E 97 LYS cc_start: 0.8505 (mmpt) cc_final: 0.7984 (mptt) REVERT: E 103 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: E 178 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7841 (tpt170) REVERT: E 246 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: E 327 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7830 (ptt-90) REVERT: H 79 GLN cc_start: 0.5155 (OUTLIER) cc_final: 0.4688 (tp40) REVERT: H 90 HIS cc_start: 0.6634 (OUTLIER) cc_final: 0.5209 (p-80) REVERT: L 79 GLN cc_start: 0.5147 (OUTLIER) cc_final: 0.4850 (tp40) REVERT: L 90 HIS cc_start: 0.6781 (OUTLIER) cc_final: 0.5535 (p-80) outliers start: 69 outliers final: 44 residues processed: 290 average time/residue: 0.6822 time to fit residues: 223.1154 Evaluate side-chains 302 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 90 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 139 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C 136 ASN C 137 ASN E 136 ASN E 137 ASN F 611 ASN G 76 ASN I 76 ASN K 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.176049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.122482 restraints weight = 21258.094| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.06 r_work: 0.3348 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20466 Z= 0.159 Angle : 0.639 11.169 27948 Z= 0.313 Chirality : 0.045 0.268 3351 Planarity : 0.004 0.050 3402 Dihedral : 6.330 59.187 4361 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.26 % Allowed : 14.63 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.17), residues: 2352 helix: 0.97 (0.26), residues: 408 sheet: 0.76 (0.18), residues: 762 loop : 0.13 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 178 TYR 0.013 0.002 TYR A 40 PHE 0.014 0.002 PHE A 383 TRP 0.020 0.002 TRP I 50 HIS 0.006 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00369 (20337) covalent geometry : angle 0.59167 (27603) SS BOND : bond 0.00278 ( 42) SS BOND : angle 1.40682 ( 84) hydrogen bonds : bond 0.04058 ( 723) hydrogen bonds : angle 4.71395 ( 2070) link_ALPHA1-2 : bond 0.00254 ( 3) link_ALPHA1-2 : angle 1.67999 ( 9) link_ALPHA1-3 : bond 0.00679 ( 3) link_ALPHA1-3 : angle 1.41913 ( 9) link_BETA1-4 : bond 0.00409 ( 36) link_BETA1-4 : angle 1.66497 ( 108) link_NAG-ASN : bond 0.00399 ( 45) link_NAG-ASN : angle 3.02388 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 243 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: B 530 MET cc_start: 0.8606 (mtp) cc_final: 0.8360 (mtp) REVERT: B 542 ARG cc_start: 0.8561 (mtp-110) cc_final: 0.7269 (mtt90) REVERT: B 632 ASP cc_start: 0.8438 (t70) cc_final: 0.8013 (t0) REVERT: B 655 LYS cc_start: 0.6805 (mtmt) cc_final: 0.5210 (pttt) REVERT: C 103 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: C 327 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7776 (ptt-90) REVERT: C 499 THR cc_start: 0.8523 (p) cc_final: 0.8155 (p) REVERT: D 632 ASP cc_start: 0.8307 (t70) cc_final: 0.7981 (t0) REVERT: D 658 GLN cc_start: 0.6800 (OUTLIER) cc_final: 0.6288 (tt0) REVERT: E 95 MET cc_start: 0.9035 (ptm) cc_final: 0.8693 (ptm) REVERT: E 97 LYS cc_start: 0.8466 (mmpt) cc_final: 0.7900 (mptt) REVERT: E 178 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7815 (tpt170) REVERT: E 246 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: E 327 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7763 (ptt-90) REVERT: H 79 GLN cc_start: 0.5185 (OUTLIER) cc_final: 0.4733 (tp40) REVERT: H 90 HIS cc_start: 0.6569 (OUTLIER) cc_final: 0.5136 (p-80) REVERT: L 79 GLN cc_start: 0.5048 (OUTLIER) cc_final: 0.4798 (tp40) REVERT: L 90 HIS cc_start: 0.6735 (OUTLIER) cc_final: 0.5560 (p-80) outliers start: 68 outliers final: 41 residues processed: 292 average time/residue: 0.6807 time to fit residues: 223.8762 Evaluate side-chains 290 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 238 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 90 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 207 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 187 optimal weight: 0.6980 chunk 201 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C 136 ASN C 137 ASN E 136 ASN E 137 ASN F 611 ASN F 651 ASN I 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.175814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122052 restraints weight = 21423.787| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.07 r_work: 0.3349 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20466 Z= 0.170 Angle : 0.651 10.814 27948 Z= 0.318 Chirality : 0.045 0.269 3351 Planarity : 0.004 0.050 3402 Dihedral : 6.244 58.202 4361 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.73 % Allowed : 15.06 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.17), residues: 2352 helix: 0.93 (0.26), residues: 408 sheet: 0.77 (0.18), residues: 762 loop : 0.11 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 178 TYR 0.013 0.002 TYR A 318 PHE 0.014 0.002 PHE A 383 TRP 0.022 0.002 TRP I 50 HIS 0.006 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00397 (20337) covalent geometry : angle 0.60410 (27603) SS BOND : bond 0.00290 ( 42) SS BOND : angle 1.42191 ( 84) hydrogen bonds : bond 0.04134 ( 723) hydrogen bonds : angle 4.72976 ( 2070) link_ALPHA1-2 : bond 0.00243 ( 3) link_ALPHA1-2 : angle 1.68091 ( 9) link_ALPHA1-3 : bond 0.00645 ( 3) link_ALPHA1-3 : angle 1.40614 ( 9) link_BETA1-4 : bond 0.00411 ( 36) link_BETA1-4 : angle 1.67620 ( 108) link_NAG-ASN : bond 0.00421 ( 45) link_NAG-ASN : angle 3.05952 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 239 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: B 530 MET cc_start: 0.8643 (mtp) cc_final: 0.8407 (mtp) REVERT: B 542 ARG cc_start: 0.8606 (mtp-110) cc_final: 0.7358 (mtt90) REVERT: B 632 ASP cc_start: 0.8467 (t70) cc_final: 0.8056 (t0) REVERT: B 655 LYS cc_start: 0.6862 (mtmt) cc_final: 0.5309 (pttt) REVERT: C 103 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: C 327 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7847 (ptt-90) REVERT: C 499 THR cc_start: 0.8538 (p) cc_final: 0.8204 (p) REVERT: D 632 ASP cc_start: 0.8364 (t70) cc_final: 0.8067 (t0) REVERT: D 658 GLN cc_start: 0.6866 (OUTLIER) cc_final: 0.6351 (tt0) REVERT: E 95 MET cc_start: 0.9057 (ptm) cc_final: 0.8724 (ptm) REVERT: E 103 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: E 178 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7827 (tpt170) REVERT: E 246 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: E 327 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7785 (ptt-90) REVERT: H 79 GLN cc_start: 0.5224 (OUTLIER) cc_final: 0.4802 (tp40) REVERT: H 90 HIS cc_start: 0.6662 (OUTLIER) cc_final: 0.5198 (p-80) REVERT: L 90 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.5649 (p-80) outliers start: 57 outliers final: 40 residues processed: 282 average time/residue: 0.6907 time to fit residues: 219.4694 Evaluate side-chains 287 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 175 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C 136 ASN C 137 ASN E 136 ASN E 137 ASN F 611 ASN F 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.175564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121737 restraints weight = 21333.902| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.07 r_work: 0.3346 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20466 Z= 0.180 Angle : 0.661 10.941 27948 Z= 0.323 Chirality : 0.046 0.271 3351 Planarity : 0.004 0.077 3402 Dihedral : 6.231 56.495 4361 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.73 % Allowed : 15.01 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.17), residues: 2352 helix: 0.90 (0.26), residues: 408 sheet: 0.77 (0.18), residues: 762 loop : 0.08 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.015 0.002 TYR A 40 PHE 0.014 0.002 PHE A 383 TRP 0.028 0.002 TRP I 50 HIS 0.006 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00420 (20337) covalent geometry : angle 0.61409 (27603) SS BOND : bond 0.00302 ( 42) SS BOND : angle 1.43584 ( 84) hydrogen bonds : bond 0.04191 ( 723) hydrogen bonds : angle 4.74003 ( 2070) link_ALPHA1-2 : bond 0.00242 ( 3) link_ALPHA1-2 : angle 1.67764 ( 9) link_ALPHA1-3 : bond 0.00617 ( 3) link_ALPHA1-3 : angle 1.39800 ( 9) link_BETA1-4 : bond 0.00405 ( 36) link_BETA1-4 : angle 1.68115 ( 108) link_NAG-ASN : bond 0.00448 ( 45) link_NAG-ASN : angle 3.08381 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8943.61 seconds wall clock time: 153 minutes 19.84 seconds (9199.84 seconds total)