Starting phenix.real_space_refine on Tue Jun 17 19:16:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8euv_28618/06_2025/8euv_28618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8euv_28618/06_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_28618/06_2025/8euv_28618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8euv_28618/06_2025/8euv_28618.map" model { file = "/net/cci-nas-00/data/ceres_data/8euv_28618/06_2025/8euv_28618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8euv_28618/06_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-5710/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: 14.08, per 1000 atoms: 0.70 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: 5.99 Conformation dependent library (CDL) restraints added in 2.7 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: 3.14 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: 8.23 Time building geometry restraints manager: 7.02 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: 5.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 51.840 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.680 ------------------------------------------------------------------------------- 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 : 2.106 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: 1.2420 time to fit residues: 377.6610 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 : 1.997 ------------------------------------------------------------------------------- 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 = 0.125028 restraints weight = 21393.187| |-----------------------------------------------------------------------------| 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: 0.8257 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 1.90081 ( 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 : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8348 (m100) cc_final: 0.8142 (m100) REVERT: B 530 MET cc_start: 0.8482 (mtp) cc_final: 0.8259 (mtp) REVERT: B 542 ARG cc_start: 0.8493 (mtp-110) cc_final: 0.7158 (mtm110) REVERT: B 632 ASP cc_start: 0.8348 (t70) cc_final: 0.8135 (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: 0.7534 (tt0) REVERT: D 542 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7688 (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: 0.7965 (pt) cc_final: 0.7738 (pp) REVERT: L 79 GLN cc_start: 0.5287 (OUTLIER) cc_final: 0.4854 (tp40) outliers start: 52 outliers final: 24 residues processed: 296 average time/residue: 1.2649 time to fit residues: 425.7040 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 : 2.186 ------------------------------------------------------------------------------- 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: 0.9990 chunk 205 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 177 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.176611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121099 restraints weight = 21245.474| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.16 r_work: 0.3327 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20466 Z= 0.149 Angle : 0.623 8.339 27948 Z= 0.304 Chirality : 0.045 0.274 3351 Planarity : 0.004 0.065 3402 Dihedral : 7.544 58.766 4361 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.54 % Allowed : 11.85 % Favored : 85.61 % 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: 0.79 (0.18), residues: 2352 helix: 1.42 (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 0.012 0.001 TYR C 318 ARG 0.004 0.000 ARG H 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 45) link_NAG-ASN : angle 3.07307 ( 135) link_BETA1-4 : bond 0.00452 ( 36) link_BETA1-4 : angle 1.72055 ( 108) link_ALPHA1-2 : bond 0.00284 ( 3) link_ALPHA1-2 : angle 1.63572 ( 9) link_ALPHA1-3 : bond 0.00805 ( 3) link_ALPHA1-3 : angle 1.39992 ( 9) hydrogen bonds : bond 0.04086 ( 723) hydrogen bonds : angle 4.79570 ( 2070) SS BOND : bond 0.00281 ( 42) SS BOND : angle 1.04039 ( 84) covalent geometry : bond 0.00346 (20337) covalent geometry : angle 0.57528 (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 309 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 256 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8203 (tp30) cc_final: 0.7961 (mm-30) REVERT: A 103 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: A 327 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7915 (ptt-90) REVERT: A 502 LYS cc_start: 0.7676 (ttpt) cc_final: 0.7189 (tttt) REVERT: B 542 ARG cc_start: 0.8553 (mtp-110) cc_final: 0.7261 (mtt90) REVERT: B 632 ASP cc_start: 0.8515 (t70) cc_final: 0.8224 (t0) REVERT: C 66 HIS cc_start: 0.6170 (OUTLIER) cc_final: 0.5919 (m90) REVERT: C 103 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: E 95 MET cc_start: 0.9017 (ptm) cc_final: 0.8731 (ptm) REVERT: E 103 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: E 178 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7835 (tpt170) REVERT: E 327 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7828 (ptt-90) REVERT: E 412 ASP cc_start: 0.8350 (p0) cc_final: 0.8140 (p0) REVERT: E 455 THR cc_start: 0.8557 (m) cc_final: 0.8324 (p) REVERT: G 75 ILE cc_start: 0.8149 (pt) cc_final: 0.7902 (pp) REVERT: H 79 GLN cc_start: 0.5116 (OUTLIER) cc_final: 0.4437 (tp40) REVERT: L 79 GLN cc_start: 0.5350 (OUTLIER) cc_final: 0.5023 (tp40) outliers start: 53 outliers final: 23 residues processed: 284 average time/residue: 1.2582 time to fit residues: 404.7249 Evaluate side-chains 280 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 2.9990 chunk 101 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 543 ASN 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 J 45 ASN K 76 ASN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.172045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121835 restraints weight = 21541.888| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.99 r_work: 0.3277 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 20466 Z= 0.347 Angle : 0.835 14.859 27948 Z= 0.405 Chirality : 0.053 0.298 3351 Planarity : 0.005 0.060 3402 Dihedral : 8.152 58.868 4361 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.03 % Allowed : 11.56 % Favored : 84.41 % 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: 0.34 (0.17), residues: 2352 helix: 0.41 (0.25), residues: 423 sheet: 0.71 (0.18), residues: 756 loop : -0.05 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 427 HIS 0.006 0.002 HIS C 352 PHE 0.019 0.003 PHE A 383 TYR 0.022 0.003 TYR E 384 ARG 0.006 0.001 ARG C 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00772 ( 45) link_NAG-ASN : angle 3.89879 ( 135) link_BETA1-4 : bond 0.00525 ( 36) link_BETA1-4 : angle 2.07842 ( 108) link_ALPHA1-2 : bond 0.00228 ( 3) link_ALPHA1-2 : angle 1.82045 ( 9) link_ALPHA1-3 : bond 0.00429 ( 3) link_ALPHA1-3 : angle 1.86240 ( 9) hydrogen bonds : bond 0.05418 ( 723) hydrogen bonds : angle 5.09593 ( 2070) SS BOND : bond 0.00680 ( 42) SS BOND : angle 1.70538 ( 84) covalent geometry : bond 0.00827 (20337) covalent geometry : angle 0.77733 (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 334 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 250 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8737 (t) REVERT: A 103 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: A 178 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8084 (tpt170) REVERT: A 502 LYS cc_start: 0.8053 (ttpt) cc_final: 0.7582 (tttt) REVERT: B 530 MET cc_start: 0.8616 (mtp) cc_final: 0.8318 (mtp) REVERT: B 542 ARG cc_start: 0.8538 (mtp-110) cc_final: 0.7266 (mtt90) REVERT: B 632 ASP cc_start: 0.8497 (t70) cc_final: 0.8123 (t0) REVERT: C 103 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: C 173 TYR cc_start: 0.8821 (p90) cc_final: 0.8599 (p90) REVERT: C 327 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7723 (ptt-90) REVERT: C 340 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7709 (pp20) REVERT: D 632 ASP cc_start: 0.8476 (t70) cc_final: 0.8070 (t0) REVERT: D 658 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6381 (tt0) REVERT: E 95 MET cc_start: 0.9017 (ptm) cc_final: 0.8721 (ptm) REVERT: E 97 LYS cc_start: 0.8532 (mmpt) cc_final: 0.7907 (mptt) REVERT: E 103 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: E 178 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7874 (tpt170) REVERT: E 327 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7837 (ptt-90) REVERT: F 637 ASN cc_start: 0.5859 (OUTLIER) cc_final: 0.5516 (p0) REVERT: H 79 GLN cc_start: 0.4950 (OUTLIER) cc_final: 0.4303 (tp40) REVERT: I 75 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7777 (pp) REVERT: L 79 GLN cc_start: 0.5075 (OUTLIER) cc_final: 0.4733 (tp40) outliers start: 84 outliers final: 38 residues processed: 305 average time/residue: 1.2497 time to fit residues: 433.8756 Evaluate side-chains 293 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 241 time to evaluate : 2.141 ------------------------------------------------------------------------------- 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 501 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 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 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 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 K residue 83 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 139 optimal weight: 0.8980 chunk 121 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 148 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 F 611 ASN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4026 r_free = 0.4026 target = 0.176865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123480 restraints weight = 21533.790| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.08 r_work: 0.3360 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20466 Z= 0.128 Angle : 0.620 10.202 27948 Z= 0.303 Chirality : 0.044 0.274 3351 Planarity : 0.004 0.054 3402 Dihedral : 6.900 59.333 4361 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.02 % Allowed : 13.24 % Favored : 83.74 % 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: 1.33 (0.27), residues: 390 sheet: 0.78 (0.18), residues: 795 loop : 0.11 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 427 HIS 0.006 0.001 HIS L 90 PHE 0.014 0.001 PHE E 383 TYR 0.013 0.001 TYR A 40 ARG 0.003 0.000 ARG H 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 45) link_NAG-ASN : angle 3.08682 ( 135) link_BETA1-4 : bond 0.00423 ( 36) link_BETA1-4 : angle 1.71455 ( 108) link_ALPHA1-2 : bond 0.00275 ( 3) link_ALPHA1-2 : angle 1.66035 ( 9) link_ALPHA1-3 : bond 0.00883 ( 3) link_ALPHA1-3 : angle 1.55580 ( 9) hydrogen bonds : bond 0.03910 ( 723) hydrogen bonds : angle 4.74540 ( 2070) SS BOND : bond 0.00275 ( 42) SS BOND : angle 1.30492 ( 84) covalent geometry : bond 0.00294 (20337) covalent geometry : angle 0.56962 (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 316 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 253 time to evaluate : 2.440 Fit side-chains revert: symmetry clash REVERT: A 51 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8697 (t) REVERT: A 92 GLU cc_start: 0.8142 (tp30) cc_final: 0.7938 (mm-30) REVERT: A 103 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: A 178 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7942 (tpt170) REVERT: A 502 LYS cc_start: 0.7401 (ttpt) cc_final: 0.6952 (tttt) REVERT: B 530 MET cc_start: 0.8592 (mtp) cc_final: 0.8365 (mtp) REVERT: B 542 ARG cc_start: 0.8478 (mtp-110) cc_final: 0.7234 (mtt90) REVERT: B 632 ASP cc_start: 0.8451 (t70) cc_final: 0.8041 (t0) REVERT: B 655 LYS cc_start: 0.6949 (mttt) cc_final: 0.5387 (pttt) REVERT: C 103 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: C 173 TYR cc_start: 0.8776 (p90) cc_final: 0.8571 (p90) REVERT: C 327 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7750 (ptt-90) REVERT: C 340 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7611 (pp20) REVERT: C 499 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7478 (p) REVERT: D 632 ASP cc_start: 0.8364 (t70) cc_final: 0.7977 (t0) REVERT: E 95 MET cc_start: 0.8994 (ptm) cc_final: 0.8646 (ptm) REVERT: E 97 LYS cc_start: 0.8473 (mmpt) cc_final: 0.7878 (mptt) REVERT: E 103 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: E 178 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7782 (tpt170) REVERT: E 246 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: E 327 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7700 (ptt-90) REVERT: H 79 GLN cc_start: 0.4918 (OUTLIER) cc_final: 0.4376 (tp40) REVERT: L 79 GLN cc_start: 0.5114 (OUTLIER) cc_final: 0.4798 (tp40) REVERT: L 90 HIS cc_start: 0.6672 (OUTLIER) cc_final: 0.5512 (p-80) outliers start: 63 outliers final: 30 residues processed: 292 average time/residue: 1.3211 time to fit residues: 439.5321 Evaluate side-chains 290 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 2.303 ------------------------------------------------------------------------------- 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 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 91 GLU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 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 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 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 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 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: 10.0000 chunk 93 optimal weight: 0.7980 chunk 229 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 206 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 137 ASN B 591 GLN B 658 GLN C 136 ASN C 137 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.174434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121190 restraints weight = 21491.905| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.15 r_work: 0.3324 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 20466 Z= 0.231 Angle : 0.722 13.603 27948 Z= 0.351 Chirality : 0.048 0.282 3351 Planarity : 0.004 0.053 3402 Dihedral : 7.062 58.503 4361 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.41 % Allowed : 13.48 % Favored : 83.12 % 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: 0.62 (0.17), residues: 2352 helix: 1.15 (0.26), residues: 390 sheet: 0.74 (0.18), residues: 762 loop : 0.05 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 427 HIS 0.006 0.001 HIS L 90 PHE 0.016 0.002 PHE A 383 TYR 0.018 0.002 TYR E 384 ARG 0.003 0.000 ARG C 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 45) link_NAG-ASN : angle 3.43213 ( 135) link_BETA1-4 : bond 0.00456 ( 36) link_BETA1-4 : angle 1.84685 ( 108) link_ALPHA1-2 : bond 0.00193 ( 3) link_ALPHA1-2 : angle 1.75244 ( 9) link_ALPHA1-3 : bond 0.00567 ( 3) link_ALPHA1-3 : angle 1.69371 ( 9) hydrogen bonds : bond 0.04658 ( 723) hydrogen bonds : angle 4.86937 ( 2070) SS BOND : bond 0.00402 ( 42) SS BOND : angle 1.76763 ( 84) covalent geometry : bond 0.00543 (20337) covalent geometry : angle 0.66734 (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 318 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 247 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8796 (t) REVERT: A 92 GLU cc_start: 0.8259 (tp30) cc_final: 0.8051 (mm-30) REVERT: A 103 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: A 178 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7962 (tpt170) REVERT: A 502 LYS cc_start: 0.7619 (ttpt) cc_final: 0.7163 (tttt) REVERT: B 530 MET cc_start: 0.8690 (mtp) cc_final: 0.8448 (mtp) REVERT: B 542 ARG cc_start: 0.8565 (mtp-110) cc_final: 0.7379 (mtt90) REVERT: B 632 ASP cc_start: 0.8445 (t70) cc_final: 0.8037 (t0) REVERT: B 655 LYS cc_start: 0.7164 (mttt) cc_final: 0.5592 (pttt) REVERT: C 103 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: C 327 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7850 (ptt-90) REVERT: C 340 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7765 (pp20) REVERT: D 632 ASP cc_start: 0.8384 (t70) cc_final: 0.8051 (t0) REVERT: E 95 MET cc_start: 0.9069 (ptm) cc_final: 0.8720 (ptm) REVERT: E 103 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: E 178 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7856 (tpt170) REVERT: E 246 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: E 327 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7894 (ptt-90) REVERT: H 79 GLN cc_start: 0.5125 (OUTLIER) cc_final: 0.4562 (tp40) REVERT: L 79 GLN cc_start: 0.5147 (OUTLIER) cc_final: 0.4875 (tp40) REVERT: L 90 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.5676 (p-80) outliers start: 71 outliers final: 40 residues processed: 293 average time/residue: 1.2633 time to fit residues: 420.9786 Evaluate side-chains 295 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 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 42 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 91 GLU 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 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 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 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 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: 0.8980 chunk 62 optimal weight: 0.7980 chunk 94 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 191 optimal weight: 9.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 E 315 GLN E 352 HIS F 651 ASN G 76 ASN I 76 ASN K 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.177239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130050 restraints weight = 21387.419| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.95 r_work: 0.3368 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20466 Z= 0.129 Angle : 0.604 10.000 27948 Z= 0.296 Chirality : 0.044 0.267 3351 Planarity : 0.004 0.051 3402 Dihedral : 6.269 58.456 4361 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.26 % Allowed : 14.10 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.84 (0.18), residues: 2352 helix: 1.44 (0.27), residues: 390 sheet: 0.82 (0.18), residues: 795 loop : 0.17 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 427 HIS 0.007 0.001 HIS H 90 PHE 0.014 0.001 PHE A 383 TYR 0.013 0.001 TYR F 638 ARG 0.002 0.000 ARG H 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 45) link_NAG-ASN : angle 2.92909 ( 135) link_BETA1-4 : bond 0.00428 ( 36) link_BETA1-4 : angle 1.62893 ( 108) link_ALPHA1-2 : bond 0.00279 ( 3) link_ALPHA1-2 : angle 1.67592 ( 9) link_ALPHA1-3 : bond 0.00825 ( 3) link_ALPHA1-3 : angle 1.46417 ( 9) hydrogen bonds : bond 0.03802 ( 723) hydrogen bonds : angle 4.65965 ( 2070) SS BOND : bond 0.00242 ( 42) SS BOND : angle 1.28732 ( 84) covalent geometry : bond 0.00294 (20337) covalent geometry : angle 0.55740 (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 317 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 249 time to evaluate : 2.258 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8118 (tp30) cc_final: 0.7900 (mm-30) REVERT: A 103 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: A 327 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7784 (ptt-90) REVERT: B 530 MET cc_start: 0.8611 (mtp) cc_final: 0.8402 (mtp) REVERT: B 542 ARG cc_start: 0.8481 (mtp-110) cc_final: 0.7257 (mtt90) REVERT: B 632 ASP cc_start: 0.8390 (t70) cc_final: 0.7967 (t0) REVERT: B 655 LYS cc_start: 0.6846 (mttt) cc_final: 0.5236 (pttt) REVERT: C 66 HIS cc_start: 0.6184 (OUTLIER) cc_final: 0.5875 (m90) REVERT: C 103 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: C 327 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7683 (ptt-90) REVERT: C 340 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7572 (pp20) REVERT: C 499 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7674 (p) REVERT: D 632 ASP cc_start: 0.8326 (t70) cc_final: 0.7977 (t0) REVERT: E 95 MET cc_start: 0.9007 (ptm) cc_final: 0.8650 (ptm) REVERT: E 97 LYS cc_start: 0.8473 (mmpt) cc_final: 0.7903 (mptt) REVERT: E 178 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7791 (tpt170) REVERT: E 246 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7153 (tm-30) REVERT: E 327 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7729 (ptt-90) REVERT: E 455 THR cc_start: 0.8574 (m) cc_final: 0.8356 (p) REVERT: H 79 GLN cc_start: 0.5078 (OUTLIER) cc_final: 0.4592 (tp40) REVERT: H 90 HIS cc_start: 0.6544 (OUTLIER) cc_final: 0.5210 (p-80) REVERT: I 95 ASP cc_start: 0.7531 (t70) cc_final: 0.7322 (t70) REVERT: J 20 THR cc_start: 0.7223 (m) cc_final: 0.6708 (p) REVERT: L 79 GLN cc_start: 0.5160 (OUTLIER) cc_final: 0.4891 (tp40) REVERT: L 90 HIS cc_start: 0.6658 (OUTLIER) cc_final: 0.5557 (p-80) outliers start: 68 outliers final: 35 residues processed: 291 average time/residue: 1.2553 time to fit residues: 415.5962 Evaluate side-chains 289 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 240 time to evaluate : 2.020 ------------------------------------------------------------------------------- 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 114 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 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 E residue 51 THR Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 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 74 THR 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 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 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: 9.9990 chunk 134 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 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: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 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 = 0.4012 r_free = 0.4012 target = 0.175617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121799 restraints weight = 21515.131| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.07 r_work: 0.3346 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20466 Z= 0.185 Angle : 0.664 11.420 27948 Z= 0.324 Chirality : 0.046 0.270 3351 Planarity : 0.004 0.050 3402 Dihedral : 6.406 57.293 4361 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.93 % Allowed : 14.29 % Favored : 82.78 % 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: 0.69 (0.17), residues: 2352 helix: 1.05 (0.27), residues: 408 sheet: 0.76 (0.18), residues: 771 loop : 0.15 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 50 HIS 0.007 0.001 HIS H 90 PHE 0.016 0.002 PHE A 383 TYR 0.013 0.002 TYR A 318 ARG 0.003 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 45) link_NAG-ASN : angle 3.15783 ( 135) link_BETA1-4 : bond 0.00420 ( 36) link_BETA1-4 : angle 1.71803 ( 108) link_ALPHA1-2 : bond 0.00239 ( 3) link_ALPHA1-2 : angle 1.70036 ( 9) link_ALPHA1-3 : bond 0.00656 ( 3) link_ALPHA1-3 : angle 1.49756 ( 9) hydrogen bonds : bond 0.04252 ( 723) hydrogen bonds : angle 4.72450 ( 2070) SS BOND : bond 0.00318 ( 42) SS BOND : angle 1.47306 ( 84) covalent geometry : bond 0.00433 (20337) covalent geometry : angle 0.61413 (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 307 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 246 time to evaluate : 2.011 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8189 (tp30) cc_final: 0.7984 (mm-30) REVERT: A 103 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: A 501 CYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6736 (p) REVERT: B 530 MET cc_start: 0.8651 (mtp) cc_final: 0.8428 (mtp) REVERT: B 542 ARG cc_start: 0.8529 (mtp-110) cc_final: 0.7309 (mtt90) REVERT: B 632 ASP cc_start: 0.8422 (t70) cc_final: 0.8009 (t0) REVERT: B 655 LYS cc_start: 0.6951 (mttt) cc_final: 0.5350 (pttt) REVERT: C 103 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: C 327 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7754 (ptt-90) REVERT: C 340 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7684 (pp20) REVERT: D 632 ASP cc_start: 0.8358 (t70) cc_final: 0.8033 (t0) REVERT: E 95 MET cc_start: 0.9052 (ptm) cc_final: 0.8688 (ptm) REVERT: E 103 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: E 178 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7828 (tpt170) REVERT: E 246 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: E 327 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7788 (ptt-90) REVERT: H 79 GLN cc_start: 0.5085 (OUTLIER) cc_final: 0.4583 (tp40) REVERT: H 90 HIS cc_start: 0.6647 (OUTLIER) cc_final: 0.5319 (p-80) REVERT: J 20 THR cc_start: 0.7236 (m) cc_final: 0.6768 (p) REVERT: L 79 GLN cc_start: 0.5203 (OUTLIER) cc_final: 0.4928 (tp40) REVERT: L 90 HIS cc_start: 0.6777 (OUTLIER) cc_final: 0.5665 (p-80) outliers start: 61 outliers final: 36 residues processed: 283 average time/residue: 1.3207 time to fit residues: 426.0466 Evaluate side-chains 292 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 2.161 ------------------------------------------------------------------------------- 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 114 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 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 501 CYS Chi-restraints excluded: chain D residue 518 VAL 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 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 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 74 THR 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 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 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: 0.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 187 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 175 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 G 76 ASN I 76 ASN K 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.177032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123599 restraints weight = 21383.148| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.06 r_work: 0.3368 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20466 Z= 0.134 Angle : 0.609 10.344 27948 Z= 0.298 Chirality : 0.044 0.264 3351 Planarity : 0.004 0.049 3402 Dihedral : 6.053 58.612 4361 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.07 % Allowed : 14.15 % Favored : 82.78 % 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: 0.77 (0.18), residues: 2352 helix: 1.20 (0.27), residues: 408 sheet: 0.79 (0.18), residues: 762 loop : 0.19 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 50 HIS 0.007 0.001 HIS H 90 PHE 0.013 0.001 PHE A 383 TYR 0.012 0.001 TYR A 40 ARG 0.004 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 45) link_NAG-ASN : angle 2.90260 ( 135) link_BETA1-4 : bond 0.00404 ( 36) link_BETA1-4 : angle 1.60232 ( 108) link_ALPHA1-2 : bond 0.00277 ( 3) link_ALPHA1-2 : angle 1.65971 ( 9) link_ALPHA1-3 : bond 0.00752 ( 3) link_ALPHA1-3 : angle 1.37613 ( 9) hydrogen bonds : bond 0.03804 ( 723) hydrogen bonds : angle 4.63502 ( 2070) SS BOND : bond 0.00245 ( 42) SS BOND : angle 1.27612 ( 84) covalent geometry : bond 0.00308 (20337) covalent geometry : angle 0.56335 (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 304 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 240 time to evaluate : 2.020 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: B 530 MET cc_start: 0.8619 (mtp) cc_final: 0.8413 (mtp) REVERT: B 542 ARG cc_start: 0.8542 (mtp-110) cc_final: 0.7353 (mtt90) REVERT: B 632 ASP cc_start: 0.8411 (t70) cc_final: 0.7988 (t0) REVERT: B 655 LYS cc_start: 0.6858 (mtmt) cc_final: 0.5294 (pttt) REVERT: C 103 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: C 327 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7710 (ptt-90) REVERT: C 340 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7618 (pp20) REVERT: D 632 ASP cc_start: 0.8312 (t70) cc_final: 0.7974 (t0) REVERT: D 655 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6811 (mtpt) REVERT: E 95 MET cc_start: 0.9035 (ptm) cc_final: 0.8702 (ptm) REVERT: E 178 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7798 (tpt170) REVERT: E 246 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: E 327 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7779 (ptt-90) REVERT: H 79 GLN cc_start: 0.5184 (OUTLIER) cc_final: 0.4668 (tp40) REVERT: H 90 HIS cc_start: 0.6622 (OUTLIER) cc_final: 0.5278 (p-80) REVERT: L 79 GLN cc_start: 0.5221 (OUTLIER) cc_final: 0.4959 (tp40) REVERT: L 90 HIS cc_start: 0.6744 (OUTLIER) cc_final: 0.5622 (p-80) outliers start: 64 outliers final: 39 residues processed: 285 average time/residue: 1.2905 time to fit residues: 417.2331 Evaluate side-chains 281 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 230 time to evaluate : 2.114 ------------------------------------------------------------------------------- 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 518 VAL 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 394 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 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 74 THR 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 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: 0.6980 chunk 217 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C 136 ASN C 137 ASN D 651 ASN E 136 ASN E 137 ASN F 651 ASN I 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.174598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.120553 restraints weight = 21362.021| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.06 r_work: 0.3328 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20466 Z= 0.230 Angle : 0.713 12.249 27948 Z= 0.348 Chirality : 0.048 0.275 3351 Planarity : 0.005 0.079 3402 Dihedral : 6.602 57.134 4361 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.73 % Allowed : 14.68 % Favored : 82.59 % 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: 0.54 (0.17), residues: 2352 helix: 0.83 (0.26), residues: 408 sheet: 0.72 (0.18), residues: 738 loop : 0.06 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 50 HIS 0.007 0.001 HIS H 90 PHE 0.017 0.002 PHE A 383 TYR 0.017 0.002 TYR E 384 ARG 0.005 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 45) link_NAG-ASN : angle 3.35230 ( 135) link_BETA1-4 : bond 0.00428 ( 36) link_BETA1-4 : angle 1.79093 ( 108) link_ALPHA1-2 : bond 0.00239 ( 3) link_ALPHA1-2 : angle 1.69984 ( 9) link_ALPHA1-3 : bond 0.00535 ( 3) link_ALPHA1-3 : angle 1.47210 ( 9) hydrogen bonds : bond 0.04579 ( 723) hydrogen bonds : angle 4.81103 ( 2070) SS BOND : bond 0.00370 ( 42) SS BOND : angle 1.57510 ( 84) covalent geometry : bond 0.00540 (20337) covalent geometry : angle 0.66236 (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 300 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 243 time to evaluate : 2.284 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: A 501 CYS cc_start: 0.7419 (OUTLIER) cc_final: 0.6784 (p) REVERT: A 502 LYS cc_start: 0.7240 (tmmt) cc_final: 0.6938 (tttt) REVERT: B 530 MET cc_start: 0.8668 (mtp) cc_final: 0.8411 (mtp) REVERT: B 542 ARG cc_start: 0.8610 (mtp-110) cc_final: 0.7317 (mtt90) REVERT: B 632 ASP cc_start: 0.8423 (t70) cc_final: 0.8000 (t0) REVERT: B 655 LYS cc_start: 0.7008 (mtmt) cc_final: 0.5422 (pttt) REVERT: C 103 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: C 327 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7766 (ptt-90) REVERT: C 340 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7693 (pp20) REVERT: C 499 THR cc_start: 0.8567 (p) cc_final: 0.8180 (p) REVERT: D 632 ASP cc_start: 0.8344 (t70) cc_final: 0.8018 (t0) REVERT: D 655 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6906 (mtpt) REVERT: E 95 MET cc_start: 0.9063 (ptm) cc_final: 0.8698 (ptm) REVERT: E 178 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7849 (tpt170) REVERT: E 246 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: E 327 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7819 (ptt-90) REVERT: H 79 GLN cc_start: 0.5083 (OUTLIER) cc_final: 0.4644 (tp40) REVERT: H 90 HIS cc_start: 0.6725 (OUTLIER) cc_final: 0.5386 (p-80) REVERT: L 90 HIS cc_start: 0.6829 (OUTLIER) cc_final: 0.5710 (p-80) outliers start: 57 outliers final: 39 residues processed: 285 average time/residue: 1.3485 time to fit residues: 434.3788 Evaluate side-chains 290 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 239 time to evaluate : 3.014 ------------------------------------------------------------------------------- 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 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 518 VAL 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 394 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 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 74 THR 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 90 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 50 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 198 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 352 HIS C 136 ASN C 137 ASN E 136 ASN E 137 ASN F 658 GLN I 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.177073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129311 restraints weight = 21403.992| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.04 r_work: 0.3362 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2193 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= 0.132 Angle : 0.612 9.972 27948 Z= 0.301 Chirality : 0.044 0.262 3351 Planarity : 0.004 0.068 3402 Dihedral : 6.006 54.016 4361 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.69 % Allowed : 14.82 % Favored : 82.49 % 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: 1.10 (0.27), residues: 408 sheet: 0.87 (0.18), residues: 756 loop : 0.15 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 50 HIS 0.007 0.001 HIS H 90 PHE 0.013 0.001 PHE A 383 TYR 0.014 0.001 TYR A 40 ARG 0.004 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 45) link_NAG-ASN : angle 2.88026 ( 135) link_BETA1-4 : bond 0.00387 ( 36) link_BETA1-4 : angle 1.59680 ( 108) link_ALPHA1-2 : bond 0.00273 ( 3) link_ALPHA1-2 : angle 1.64768 ( 9) link_ALPHA1-3 : bond 0.00719 ( 3) link_ALPHA1-3 : angle 1.32059 ( 9) hydrogen bonds : bond 0.03783 ( 723) hydrogen bonds : angle 4.64758 ( 2070) SS BOND : bond 0.00235 ( 42) SS BOND : angle 1.24550 ( 84) covalent geometry : bond 0.00302 (20337) covalent geometry : angle 0.56754 (27603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17446.11 seconds wall clock time: 298 minutes 29.67 seconds (17909.67 seconds total)