Starting phenix.real_space_refine on Tue May 20 17:46:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8euv_28618/05_2025/8euv_28618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8euv_28618/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8euv_28618/05_2025/8euv_28618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8euv_28618/05_2025/8euv_28618.map" model { file = "/net/cci-nas-00/data/ceres_data/8euv_28618/05_2025/8euv_28618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8euv_28618/05_2025/8euv_28618.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.80, per 1000 atoms: 0.64 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: 5.56 Conformation dependent library (CDL) restraints added in 2.5 seconds 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 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: 2.97 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: 7.54 Time building geometry restraints manager: 6.45 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: 0.00 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: 5.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 48.120 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.160 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:11.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.130 ------------------------------------------------------------------------------- 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 : 2.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (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 TRP 0.013 0.001 TRP E 69 HIS 0.006 0.001 HIS K 35 PHE 0.024 0.002 PHE A 53 TYR 0.010 0.002 TYR F 638 ARG 0.005 0.000 ARG L 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 45) link_NAG-ASN : angle 3.62570 ( 135) link_BETA1-4 : bond 0.00343 ( 36) link_BETA1-4 : angle 2.10428 ( 108) 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) hydrogen bonds : bond 0.10861 ( 723) hydrogen bonds : angle 5.95066 ( 2070) SS BOND : bond 0.02911 ( 42) SS BOND : angle 2.38360 ( 84) covalent geometry : bond 0.01742 (20337) covalent geometry : angle 1.10763 (27603) *********************** 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 : 2.102 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: 1.2076 time to fit residues: 367.3267 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 : 2.094 ------------------------------------------------------------------------------- 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 200 optimal weight: 0.7980 chunk 179 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 185 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.176182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125027 restraints weight = 21393.188| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.01 r_work: 0.3316 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20466 Z= 0.168 Angle : 0.687 10.423 27948 Z= 0.335 Chirality : 0.046 0.292 3351 Planarity : 0.004 0.082 3402 Dihedral : 9.574 70.705 4370 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.49 % Allowed : 9.93 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2352 helix: 0.73 (0.26), residues: 423 sheet: 0.78 (0.18), residues: 759 loop : -0.03 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 427 HIS 0.003 0.001 HIS H 90 PHE 0.015 0.002 PHE E 53 TYR 0.012 0.002 TYR C 318 ARG 0.005 0.000 ARG H 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 45) link_NAG-ASN : angle 3.30847 ( 135) link_BETA1-4 : bond 0.00474 ( 36) link_BETA1-4 : angle 1.84498 ( 108) link_ALPHA1-2 : bond 0.00406 ( 3) link_ALPHA1-2 : angle 1.90082 ( 9) link_ALPHA1-3 : bond 0.00803 ( 3) link_ALPHA1-3 : angle 2.15478 ( 9) hydrogen bonds : bond 0.04472 ( 723) hydrogen bonds : angle 5.04246 ( 2070) SS BOND : bond 0.00348 ( 42) SS BOND : angle 0.92738 ( 84) covalent geometry : bond 0.00383 (20337) covalent geometry : angle 0.63688 (27603) *********************** 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 314 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8344 (m100) cc_final: 0.8137 (m100) REVERT: B 530 MET cc_start: 0.8479 (mtp) cc_final: 0.8254 (mtp) REVERT: B 542 ARG cc_start: 0.8486 (mtp-110) cc_final: 0.7152 (mtm110) REVERT: B 632 ASP cc_start: 0.8348 (t70) cc_final: 0.8133 (t0) REVERT: B 658 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6601 (tm-30) REVERT: C 103 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: D 542 ARG cc_start: 0.8022 (mtm-85) cc_final: 0.7682 (mtt90) REVERT: E 103 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: E 327 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7845 (ptt-90) REVERT: G 75 ILE cc_start: 0.7972 (pt) cc_final: 0.7745 (pp) REVERT: L 79 GLN cc_start: 0.5334 (OUTLIER) cc_final: 0.4899 (tp40) outliers start: 52 outliers final: 24 residues processed: 296 average time/residue: 1.3061 time to fit residues: 438.4633 Evaluate side-chains 276 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 247 time to evaluate : 2.385 ------------------------------------------------------------------------------- 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 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 641 ILE 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 C residue 499 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 394 THR 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 7 SER 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 110 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 205 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 177 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 E 422 GLN G 76 ASN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN K 76 ASN L 45 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 = 0.3999 r_free = 0.3999 target = 0.176666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121158 restraints weight = 21242.625| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.17 r_work: 0.3325 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20466 Z= 0.146 Angle : 0.621 8.433 27948 Z= 0.303 Chirality : 0.045 0.274 3351 Planarity : 0.004 0.063 3402 Dihedral : 7.642 58.626 4361 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.64 % Allowed : 11.70 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2352 helix: 1.43 (0.28), residues: 387 sheet: 0.82 (0.18), residues: 771 loop : 0.13 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 427 HIS 0.003 0.001 HIS C 352 PHE 0.015 0.002 PHE E 53 TYR 0.011 0.001 TYR C 318 ARG 0.004 0.000 ARG H 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 45) link_NAG-ASN : angle 3.06821 ( 135) link_BETA1-4 : bond 0.00440 ( 36) link_BETA1-4 : angle 1.73001 ( 108) link_ALPHA1-2 : bond 0.00313 ( 3) link_ALPHA1-2 : angle 1.63895 ( 9) link_ALPHA1-3 : bond 0.00806 ( 3) link_ALPHA1-3 : angle 1.40694 ( 9) hydrogen bonds : bond 0.04061 ( 723) hydrogen bonds : angle 4.79504 ( 2070) SS BOND : bond 0.00267 ( 42) SS BOND : angle 1.04440 ( 84) covalent geometry : bond 0.00340 (20337) covalent geometry : angle 0.57259 (27603) *********************** 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 310 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 255 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: A 178 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7913 (tpt170) REVERT: A 327 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7882 (ptt-90) REVERT: A 502 LYS cc_start: 0.7613 (ttpt) cc_final: 0.7107 (tttt) REVERT: B 542 ARG cc_start: 0.8529 (mtp-110) cc_final: 0.7217 (mtt90) REVERT: B 632 ASP cc_start: 0.8502 (t70) cc_final: 0.8201 (t0) REVERT: C 66 HIS cc_start: 0.6176 (OUTLIER) cc_final: 0.5917 (m90) REVERT: C 103 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: E 95 MET cc_start: 0.8999 (ptm) cc_final: 0.8704 (ptm) REVERT: E 103 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: E 178 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7833 (tpt170) REVERT: E 327 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7791 (ptt-90) REVERT: E 412 ASP cc_start: 0.8336 (p0) cc_final: 0.8126 (p0) REVERT: G 75 ILE cc_start: 0.8087 (pt) cc_final: 0.7844 (pp) REVERT: H 79 GLN cc_start: 0.5032 (OUTLIER) cc_final: 0.4346 (tp40) REVERT: L 79 GLN cc_start: 0.5262 (OUTLIER) cc_final: 0.4946 (tp40) outliers start: 55 outliers final: 23 residues processed: 283 average time/residue: 1.2953 time to fit residues: 415.3354 Evaluate side-chains 279 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 246 time to evaluate : 2.235 ------------------------------------------------------------------------------- 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 327 ARG 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 499 THR Chi-restraints excluded: chain C residue 501 CYS 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 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 74 THR 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 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 59 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 70 optimal weight: 0.0030 overall best weight: 1.9998 ------------------------------------------------------------------------------- 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 540 GLN B 653 GLN B 658 GLN C 136 ASN C 137 ASN D 611 ASN E 136 ASN E 137 ASN 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 = 0.3976 r_free = 0.3976 target = 0.173237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123434 restraints weight = 21545.216| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.99 r_work: 0.3285 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20466 Z= 0.263 Angle : 0.759 12.954 27948 Z= 0.368 Chirality : 0.049 0.293 3351 Planarity : 0.005 0.059 3402 Dihedral : 7.652 59.350 4361 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.88 % Allowed : 11.46 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.17), residues: 2352 helix: 0.89 (0.26), residues: 405 sheet: 0.71 (0.18), residues: 771 loop : 0.08 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 427 HIS 0.005 0.001 HIS C 352 PHE 0.017 0.002 PHE C 353 TYR 0.017 0.002 TYR E 384 ARG 0.005 0.001 ARG A 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00645 ( 45) link_NAG-ASN : angle 3.66792 ( 135) link_BETA1-4 : bond 0.00485 ( 36) link_BETA1-4 : angle 1.93821 ( 108) link_ALPHA1-2 : bond 0.00210 ( 3) link_ALPHA1-2 : angle 1.74402 ( 9) link_ALPHA1-3 : bond 0.00563 ( 3) link_ALPHA1-3 : angle 1.80949 ( 9) hydrogen bonds : bond 0.04971 ( 723) hydrogen bonds : angle 4.95930 ( 2070) SS BOND : bond 0.00421 ( 42) SS BOND : angle 1.45833 ( 84) covalent geometry : bond 0.00619 (20337) covalent geometry : angle 0.70325 (27603) *********************** 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 330 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 249 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8723 (t) REVERT: A 103 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: A 178 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.8032 (tpt170) REVERT: A 502 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7409 (tttt) REVERT: B 530 MET cc_start: 0.8628 (mtp) cc_final: 0.8342 (mtp) REVERT: B 542 ARG cc_start: 0.8553 (mtp-110) cc_final: 0.7281 (mtt90) REVERT: B 632 ASP cc_start: 0.8496 (t70) cc_final: 0.8111 (t0) REVERT: C 103 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: C 173 TYR cc_start: 0.8838 (p90) cc_final: 0.8623 (p90) REVERT: C 327 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7757 (ptt-90) REVERT: C 340 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7721 (pp20) REVERT: D 632 ASP cc_start: 0.8417 (t70) cc_final: 0.7998 (t0) REVERT: E 95 MET cc_start: 0.9011 (ptm) cc_final: 0.8718 (ptm) REVERT: E 103 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: E 178 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7871 (tpt170) REVERT: E 327 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7828 (ptt-90) REVERT: F 637 ASN cc_start: 0.5851 (OUTLIER) cc_final: 0.5501 (p0) REVERT: H 79 GLN cc_start: 0.4999 (OUTLIER) cc_final: 0.4339 (tp40) REVERT: I 75 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7909 (pp) REVERT: L 79 GLN cc_start: 0.5131 (OUTLIER) cc_final: 0.4809 (tp40) outliers start: 81 outliers final: 35 residues processed: 301 average time/residue: 1.1764 time to fit residues: 404.8976 Evaluate side-chains 293 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 2.181 ------------------------------------------------------------------------------- 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 641 ILE Chi-restraints excluded: chain C residue 42 VAL 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 340 GLU 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 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 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 H residue 12 SER Chi-restraints excluded: chain H residue 21 ILE 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 75 ILE Chi-restraints excluded: chain I residue 83 THR 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 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 139 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 611 ASN E 136 ASN E 137 ASN E 315 GLN F 611 ASN F 651 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 = 0.176008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122458 restraints weight = 21526.869| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.07 r_work: 0.3349 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20466 Z= 0.162 Angle : 0.648 11.608 27948 Z= 0.317 Chirality : 0.045 0.277 3351 Planarity : 0.004 0.054 3402 Dihedral : 6.876 59.849 4361 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.26 % Allowed : 12.81 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2352 helix: 1.29 (0.27), residues: 390 sheet: 0.79 (0.18), residues: 795 loop : 0.11 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 427 HIS 0.006 0.001 HIS L 90 PHE 0.015 0.002 PHE A 383 TYR 0.013 0.001 TYR A 318 ARG 0.003 0.000 ARG H 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 45) link_NAG-ASN : angle 3.17287 ( 135) link_BETA1-4 : bond 0.00423 ( 36) link_BETA1-4 : angle 1.73563 ( 108) link_ALPHA1-2 : bond 0.00268 ( 3) link_ALPHA1-2 : angle 1.68317 ( 9) link_ALPHA1-3 : bond 0.00757 ( 3) link_ALPHA1-3 : angle 1.60596 ( 9) hydrogen bonds : bond 0.04152 ( 723) hydrogen bonds : angle 4.75858 ( 2070) SS BOND : bond 0.00305 ( 42) SS BOND : angle 1.49167 ( 84) covalent geometry : bond 0.00377 (20337) covalent geometry : angle 0.59644 (27603) *********************** 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 319 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 251 time to evaluate : 2.122 Fit side-chains revert: symmetry clash REVERT: A 51 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8740 (t) REVERT: A 103 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: A 178 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7981 (tpt170) REVERT: A 502 LYS cc_start: 0.7491 (ttpt) cc_final: 0.7030 (tttt) REVERT: B 530 MET cc_start: 0.8632 (mtp) cc_final: 0.8419 (mtp) REVERT: B 542 ARG cc_start: 0.8505 (mtp-110) cc_final: 0.7296 (mtt90) REVERT: B 632 ASP cc_start: 0.8480 (t70) cc_final: 0.8078 (t0) REVERT: B 655 LYS cc_start: 0.7017 (mttt) cc_final: 0.5434 (pttt) REVERT: C 103 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: C 173 TYR cc_start: 0.8809 (p90) cc_final: 0.8590 (p90) REVERT: C 327 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7798 (ptt-90) REVERT: C 340 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7700 (pp20) REVERT: D 632 ASP cc_start: 0.8393 (t70) cc_final: 0.8061 (t70) REVERT: D 658 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6375 (tt0) REVERT: E 95 MET cc_start: 0.9028 (ptm) cc_final: 0.8692 (ptm) REVERT: E 103 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: E 178 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7808 (tpt170) REVERT: E 246 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: E 327 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7784 (ptt-90) REVERT: H 79 GLN cc_start: 0.5042 (OUTLIER) cc_final: 0.4495 (tp40) REVERT: L 79 GLN cc_start: 0.5194 (OUTLIER) cc_final: 0.4865 (tp40) REVERT: L 90 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.5536 (p-80) outliers start: 68 outliers final: 36 residues processed: 293 average time/residue: 1.2092 time to fit residues: 403.7025 Evaluate side-chains 294 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 244 time to evaluate : 2.343 ------------------------------------------------------------------------------- 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 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 340 GLU 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 246 GLN 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 455 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 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 89 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 79 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 183 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 206 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 543 ASN B 591 GLN B 658 GLN C 136 ASN C 137 ASN E 136 ASN E 137 ASN F 611 ASN F 651 ASN G 76 ASN I 76 ASN K 76 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.174842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126895 restraints weight = 21475.050| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.95 r_work: 0.3335 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1923 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= 0.210 Angle : 0.695 12.046 27948 Z= 0.338 Chirality : 0.047 0.279 3351 Planarity : 0.004 0.052 3402 Dihedral : 6.849 59.901 4361 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.60 % Allowed : 13.33 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.17), residues: 2352 helix: 1.18 (0.26), residues: 390 sheet: 0.73 (0.18), residues: 738 loop : 0.02 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 427 HIS 0.006 0.001 HIS L 90 PHE 0.016 0.002 PHE A 383 TYR 0.015 0.002 TYR A 318 ARG 0.003 0.000 ARG E 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 45) link_NAG-ASN : angle 3.35150 ( 135) link_BETA1-4 : bond 0.00439 ( 36) link_BETA1-4 : angle 1.80143 ( 108) link_ALPHA1-2 : bond 0.00253 ( 3) link_ALPHA1-2 : angle 1.73930 ( 9) link_ALPHA1-3 : bond 0.00610 ( 3) link_ALPHA1-3 : angle 1.64936 ( 9) hydrogen bonds : bond 0.04506 ( 723) hydrogen bonds : angle 4.80754 ( 2070) SS BOND : bond 0.00353 ( 42) SS BOND : angle 1.48949 ( 84) covalent geometry : bond 0.00493 (20337) covalent geometry : angle 0.64277 (27603) *********************** 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 321 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 246 time to evaluate : 2.211 Fit side-chains revert: symmetry clash REVERT: A 51 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8681 (t) REVERT: A 103 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: A 178 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7972 (tpt170) REVERT: A 501 CYS cc_start: 0.7467 (OUTLIER) cc_final: 0.6603 (p) REVERT: A 502 LYS cc_start: 0.7640 (ttpt) cc_final: 0.7175 (tttt) REVERT: B 530 MET cc_start: 0.8622 (mtp) cc_final: 0.8366 (mtp) REVERT: B 542 ARG cc_start: 0.8491 (mtp-110) cc_final: 0.7247 (mtt90) REVERT: B 632 ASP cc_start: 0.8392 (t70) cc_final: 0.7987 (t0) REVERT: B 655 LYS cc_start: 0.7030 (mttt) cc_final: 0.5419 (pttt) REVERT: C 66 HIS cc_start: 0.6197 (OUTLIER) cc_final: 0.5904 (m90) REVERT: C 103 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: C 327 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7705 (ptt-90) REVERT: C 340 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7626 (pp20) REVERT: C 501 CYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6812 (p) REVERT: D 632 ASP cc_start: 0.8347 (t70) cc_final: 0.7987 (t0) REVERT: D 658 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6309 (tt0) REVERT: E 95 MET cc_start: 0.9028 (ptm) cc_final: 0.8658 (ptm) REVERT: E 103 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: E 178 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7805 (tpt170) REVERT: E 246 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7180 (tm-30) REVERT: E 327 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7757 (ptt-90) REVERT: H 79 GLN cc_start: 0.5044 (OUTLIER) cc_final: 0.4578 (tp40) REVERT: H 90 HIS cc_start: 0.6551 (OUTLIER) cc_final: 0.4988 (p-80) REVERT: L 79 GLN cc_start: 0.5060 (OUTLIER) cc_final: 0.4792 (tp40) REVERT: L 90 HIS cc_start: 0.6695 (OUTLIER) cc_final: 0.5526 (p-80) outliers start: 75 outliers final: 37 residues processed: 294 average time/residue: 1.2209 time to fit residues: 408.2661 Evaluate side-chains 297 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 2.072 ------------------------------------------------------------------------------- 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 340 GLU 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 246 GLN 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 125 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 94 optimal weight: 0.0010 chunk 13 optimal weight: 1.9990 chunk 225 optimal weight: 0.0050 chunk 38 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- 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 E 136 ASN E 137 ASN F 611 ASN F 651 ASN 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 = 0.4041 r_free = 0.4041 target = 0.178295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.130590 restraints weight = 21378.011| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.86 r_work: 0.3391 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 20466 Z= 0.110 Angle : 0.577 9.339 27948 Z= 0.284 Chirality : 0.044 0.266 3351 Planarity : 0.004 0.050 3402 Dihedral : 5.967 59.262 4361 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.83 % Allowed : 14.34 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2352 helix: 1.67 (0.28), residues: 384 sheet: 0.86 (0.18), residues: 762 loop : 0.21 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 427 HIS 0.006 0.001 HIS L 90 PHE 0.012 0.001 PHE E 53 TYR 0.011 0.001 TYR A 40 ARG 0.002 0.000 ARG H 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 45) link_NAG-ASN : angle 2.78848 ( 135) link_BETA1-4 : bond 0.00423 ( 36) link_BETA1-4 : angle 1.57494 ( 108) link_ALPHA1-2 : bond 0.00262 ( 3) link_ALPHA1-2 : angle 1.64083 ( 9) link_ALPHA1-3 : bond 0.00865 ( 3) link_ALPHA1-3 : angle 1.38410 ( 9) hydrogen bonds : bond 0.03569 ( 723) hydrogen bonds : angle 4.58801 ( 2070) SS BOND : bond 0.00393 ( 42) SS BOND : angle 1.27072 ( 84) covalent geometry : bond 0.00247 (20337) covalent geometry : angle 0.53185 (27603) *********************** 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 314 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 255 time to evaluate : 2.288 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8096 (tp30) cc_final: 0.7892 (mm-30) REVERT: A 103 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: B 542 ARG cc_start: 0.8471 (mtp-110) cc_final: 0.7277 (mtt90) REVERT: B 632 ASP cc_start: 0.8399 (t70) cc_final: 0.7959 (t0) REVERT: B 655 LYS cc_start: 0.6874 (mttt) cc_final: 0.5316 (pttt) REVERT: C 327 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7673 (ptt-90) REVERT: C 340 GLU cc_start: 0.7807 (pt0) cc_final: 0.7553 (pp20) REVERT: C 499 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7607 (p) REVERT: D 632 ASP cc_start: 0.8331 (t70) cc_final: 0.7983 (t0) REVERT: E 95 MET cc_start: 0.8995 (ptm) cc_final: 0.8647 (ptm) REVERT: E 97 LYS cc_start: 0.8462 (mmpt) cc_final: 0.7907 (mptt) REVERT: E 246 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: E 327 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7708 (ptt-90) REVERT: E 455 THR cc_start: 0.8567 (m) cc_final: 0.8365 (p) REVERT: H 79 GLN cc_start: 0.5117 (OUTLIER) cc_final: 0.4627 (tp40) REVERT: J 20 THR cc_start: 0.7165 (m) cc_final: 0.6636 (p) REVERT: L 79 GLN cc_start: 0.5192 (OUTLIER) cc_final: 0.4925 (tp40) REVERT: L 90 HIS cc_start: 0.6635 (OUTLIER) cc_final: 0.5403 (p-80) outliers start: 59 outliers final: 31 residues processed: 294 average time/residue: 1.2822 time to fit residues: 426.6977 Evaluate side-chains 281 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 2.190 ------------------------------------------------------------------------------- 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 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 641 ILE Chi-restraints excluded: chain C residue 71 THR 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 635 ILE Chi-restraints excluded: chain E residue 51 THR 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 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 J residue 12 SER Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 89 ILE 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 22 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 139 optimal weight: 0.3980 chunk 90 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 C 422 GLN D 651 ASN E 136 ASN E 137 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 = 0.4015 r_free = 0.4015 target = 0.175886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128058 restraints weight = 21505.606| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.93 r_work: 0.3351 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20466 Z= 0.181 Angle : 0.652 11.076 27948 Z= 0.318 Chirality : 0.046 0.270 3351 Planarity : 0.004 0.081 3402 Dihedral : 6.188 59.207 4361 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.78 % Allowed : 14.68 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2352 helix: 1.42 (0.27), residues: 390 sheet: 0.82 (0.18), residues: 762 loop : 0.16 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 50 HIS 0.006 0.001 HIS L 90 PHE 0.016 0.002 PHE A 383 TYR 0.014 0.002 TYR A 318 ARG 0.003 0.000 ARG K 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 45) link_NAG-ASN : angle 3.10429 ( 135) link_BETA1-4 : bond 0.00425 ( 36) link_BETA1-4 : angle 1.68761 ( 108) link_ALPHA1-2 : bond 0.00228 ( 3) link_ALPHA1-2 : angle 1.68073 ( 9) link_ALPHA1-3 : bond 0.00667 ( 3) link_ALPHA1-3 : angle 1.45832 ( 9) hydrogen bonds : bond 0.04167 ( 723) hydrogen bonds : angle 4.67548 ( 2070) SS BOND : bond 0.00303 ( 42) SS BOND : angle 1.41639 ( 84) covalent geometry : bond 0.00425 (20337) covalent geometry : angle 0.60333 (27603) *********************** 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 302 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 2.318 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8139 (tp30) cc_final: 0.7936 (mm-30) REVERT: A 103 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7725 (tt0) REVERT: B 542 ARG cc_start: 0.8461 (mtp-110) cc_final: 0.7292 (mtm110) REVERT: B 632 ASP cc_start: 0.8409 (t70) cc_final: 0.7972 (t0) REVERT: B 655 LYS cc_start: 0.6801 (mttt) cc_final: 0.5210 (pttt) REVERT: C 327 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7702 (ptt-90) REVERT: C 340 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7568 (pp20) REVERT: D 632 ASP cc_start: 0.8322 (t70) cc_final: 0.7958 (t0) REVERT: E 95 MET cc_start: 0.9034 (ptm) cc_final: 0.8653 (ptm) REVERT: E 103 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: E 246 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7195 (tm-30) REVERT: E 327 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7711 (ptt-90) REVERT: H 79 GLN cc_start: 0.4998 (OUTLIER) cc_final: 0.4498 (tp40) REVERT: H 90 HIS cc_start: 0.6427 (OUTLIER) cc_final: 0.4909 (p-80) REVERT: J 20 THR cc_start: 0.7143 (m) cc_final: 0.6672 (p) REVERT: L 79 GLN cc_start: 0.5138 (OUTLIER) cc_final: 0.4871 (tp40) REVERT: L 90 HIS cc_start: 0.6669 (OUTLIER) cc_final: 0.5557 (p-80) outliers start: 58 outliers final: 36 residues processed: 281 average time/residue: 1.2825 time to fit residues: 411.3107 Evaluate side-chains 287 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL 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 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 71 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 340 GLU 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 635 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN 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 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 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 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 152 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 187 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 D 651 ASN E 136 ASN E 137 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 = 0.4028 r_free = 0.4028 target = 0.177053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123577 restraints weight = 21387.665| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.07 r_work: 0.3369 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20466 Z= 0.138 Angle : 0.606 9.863 27948 Z= 0.297 Chirality : 0.044 0.266 3351 Planarity : 0.004 0.067 3402 Dihedral : 5.958 58.071 4361 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.02 % Allowed : 14.68 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2352 helix: 1.24 (0.27), residues: 408 sheet: 0.86 (0.18), residues: 756 loop : 0.14 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 50 HIS 0.006 0.001 HIS L 90 PHE 0.013 0.001 PHE A 383 TYR 0.012 0.001 TYR A 40 ARG 0.002 0.000 ARG K 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 45) link_NAG-ASN : angle 2.92135 ( 135) link_BETA1-4 : bond 0.00407 ( 36) link_BETA1-4 : angle 1.59765 ( 108) link_ALPHA1-2 : bond 0.00273 ( 3) link_ALPHA1-2 : angle 1.64837 ( 9) link_ALPHA1-3 : bond 0.00735 ( 3) link_ALPHA1-3 : angle 1.34568 ( 9) hydrogen bonds : bond 0.03805 ( 723) hydrogen bonds : angle 4.61065 ( 2070) SS BOND : bond 0.00234 ( 42) SS BOND : angle 1.25867 ( 84) covalent geometry : bond 0.00319 (20337) covalent geometry : angle 0.56030 (27603) *********************** 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 306 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 243 time to evaluate : 2.041 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: B 542 ARG cc_start: 0.8514 (mtp-110) cc_final: 0.7348 (mtm110) REVERT: B 632 ASP cc_start: 0.8420 (t70) cc_final: 0.7975 (t0) REVERT: B 655 LYS cc_start: 0.6907 (mttt) cc_final: 0.5385 (pttt) REVERT: C 103 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: C 327 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7724 (ptt-90) REVERT: C 340 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7626 (pp20) REVERT: D 632 ASP cc_start: 0.8337 (t70) cc_final: 0.7979 (t0) REVERT: D 658 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6341 (tt0) REVERT: E 95 MET cc_start: 0.9041 (ptm) cc_final: 0.8669 (ptm) REVERT: E 103 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: E 246 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: E 327 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7743 (ptt-90) REVERT: H 79 GLN cc_start: 0.5161 (OUTLIER) cc_final: 0.4675 (tp40) REVERT: H 90 HIS cc_start: 0.6513 (OUTLIER) cc_final: 0.4999 (p-80) REVERT: L 79 GLN cc_start: 0.5182 (OUTLIER) cc_final: 0.4919 (tp40) REVERT: L 90 HIS cc_start: 0.6730 (OUTLIER) cc_final: 0.5620 (p-80) outliers start: 63 outliers final: 42 residues processed: 288 average time/residue: 1.3549 time to fit residues: 441.0543 Evaluate side-chains 291 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 237 time to evaluate : 2.323 ------------------------------------------------------------------------------- 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 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 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 340 GLU Chi-restraints excluded: chain C residue 499 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 635 ILE 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 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 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 173 optimal weight: 0.8980 chunk 217 optimal weight: 3.9990 chunk 216 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 D 651 ASN E 136 ASN E 137 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.175050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121143 restraints weight = 21360.241| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.06 r_work: 0.3331 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20466 Z= 0.214 Angle : 0.692 11.668 27948 Z= 0.337 Chirality : 0.047 0.275 3351 Planarity : 0.004 0.064 3402 Dihedral : 6.446 57.759 4361 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.83 % Allowed : 14.63 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2352 helix: 0.95 (0.26), residues: 408 sheet: 0.73 (0.18), residues: 738 loop : 0.08 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 50 HIS 0.006 0.001 HIS L 90 PHE 0.015 0.002 PHE A 383 TYR 0.016 0.002 TYR A 318 ARG 0.003 0.000 ARG C 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 45) link_NAG-ASN : angle 3.27789 ( 135) link_BETA1-4 : bond 0.00423 ( 36) link_BETA1-4 : angle 1.74970 ( 108) link_ALPHA1-2 : bond 0.00250 ( 3) link_ALPHA1-2 : angle 1.68192 ( 9) link_ALPHA1-3 : bond 0.00564 ( 3) link_ALPHA1-3 : angle 1.43273 ( 9) hydrogen bonds : bond 0.04432 ( 723) hydrogen bonds : angle 4.75964 ( 2070) SS BOND : bond 0.00345 ( 42) SS BOND : angle 1.49494 ( 84) covalent geometry : bond 0.00504 (20337) covalent geometry : angle 0.64144 (27603) ********************** 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 307 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 248 time to evaluate : 2.258 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: A 501 CYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6746 (p) REVERT: B 542 ARG cc_start: 0.8509 (mtp-110) cc_final: 0.7242 (mtt90) REVERT: B 632 ASP cc_start: 0.8398 (t70) cc_final: 0.7982 (t0) REVERT: B 655 LYS cc_start: 0.6855 (mtmt) cc_final: 0.5244 (pttt) REVERT: C 103 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: C 327 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7708 (ptt-90) REVERT: C 340 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7678 (pp20) REVERT: D 632 ASP cc_start: 0.8315 (t70) cc_final: 0.7984 (t0) REVERT: D 658 GLN cc_start: 0.6828 (OUTLIER) cc_final: 0.6321 (tt0) REVERT: E 95 MET cc_start: 0.9044 (ptm) cc_final: 0.8667 (ptm) REVERT: E 103 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: E 246 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: E 327 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7770 (ptt-90) REVERT: H 79 GLN cc_start: 0.5079 (OUTLIER) cc_final: 0.4647 (tp40) REVERT: L 20 THR cc_start: 0.7341 (m) cc_final: 0.6983 (p) REVERT: L 90 HIS cc_start: 0.6766 (OUTLIER) cc_final: 0.5701 (p-80) outliers start: 59 outliers final: 39 residues processed: 291 average time/residue: 1.3447 time to fit residues: 442.6052 Evaluate side-chains 294 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 244 time to evaluate : 2.241 ------------------------------------------------------------------------------- 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 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 340 GLU 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 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 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 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 50 optimal weight: 0.9980 chunk 151 optimal weight: 0.0870 chunk 81 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 198 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 F 651 ASN F 658 GLN I 76 ASN L 70 HIS ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.177470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130505 restraints weight = 21419.839| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.97 r_work: 0.3378 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20466 Z= 0.123 Angle : 0.602 10.087 27948 Z= 0.296 Chirality : 0.044 0.261 3351 Planarity : 0.004 0.062 3402 Dihedral : 5.924 54.101 4361 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.45 % Allowed : 15.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2352 helix: 1.21 (0.27), residues: 408 sheet: 0.86 (0.18), residues: 756 loop : 0.12 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 50 HIS 0.007 0.001 HIS H 90 PHE 0.013 0.001 PHE A 383 TYR 0.013 0.001 TYR A 40 ARG 0.004 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 45) link_NAG-ASN : angle 2.84909 ( 135) link_BETA1-4 : bond 0.00381 ( 36) link_BETA1-4 : angle 1.57417 ( 108) link_ALPHA1-2 : bond 0.00312 ( 3) link_ALPHA1-2 : angle 1.64702 ( 9) link_ALPHA1-3 : bond 0.00710 ( 3) link_ALPHA1-3 : angle 1.27526 ( 9) hydrogen bonds : bond 0.03694 ( 723) hydrogen bonds : angle 4.63011 ( 2070) SS BOND : bond 0.00220 ( 42) SS BOND : angle 1.25466 ( 84) covalent geometry : bond 0.00283 (20337) covalent geometry : angle 0.55785 (27603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16975.45 seconds wall clock time: 292 minutes 40.77 seconds (17560.77 seconds total)