Starting phenix.real_space_refine on Sat Jul 4 01:37:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jtd_36641/07_2026/8jtd_36641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtd_36641/07_2026/8jtd_36641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8jtd_36641/07_2026/8jtd_36641.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jtd_36641/07_2026/8jtd_36641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jtd_36641/07_2026/8jtd_36641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtd_36641/07_2026/8jtd_36641.map" model { file = "/net/cci-nas-00/data/ceres_data/8jtd_36641/07_2026/8jtd_36641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtd_36641/07_2026/8jtd_36641.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic. 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 111 5.16 5 C 10755 2.51 5 N 2830 2.21 5 O 3579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17275 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3545 Classifications: {'peptide': 450} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 426} Chain breaks: 2 Chain: "B" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "D" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3562 Classifications: {'peptide': 452} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "E" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "J" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1094 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} 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 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 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 chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" 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 chiralities: 3 Chain: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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 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 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 chiralities: 3 Chain: "Y" 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 chiralities: 5 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 chiralities: 2 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 chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "d" 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 chiralities: 3 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 chiralities: 2 Chain: "f" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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 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 chiralities: 2 Chain: "j" 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 chiralities: 2 Chain: "k" 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 chiralities: 5 Chain: "l" 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 chiralities: 3 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 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 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 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 chiralities: 2 Chain: "q" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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 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 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 chiralities: 2 Chain: "x" 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 chiralities: 5 Chain: "y" 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 chiralities: 3 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 chiralities: 2 Chain: "0" 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 chiralities: 2 Chain: "1" 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 chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" 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 chiralities: 5 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 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 chiralities: 2 Residues with excluded nonbonded symmetry interactions: 63 residue: pdb=" C1 NAG P 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG P 1 " occ=0.00 residue: pdb=" C1 NAG P 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG P 2 " occ=0.00 residue: pdb=" C1 NAG R 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG R 1 " occ=0.00 residue: pdb=" C1 NAG R 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG R 2 " occ=0.00 residue: pdb=" C1 NAG S 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG S 1 " occ=0.00 residue: pdb=" C1 NAG S 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG S 2 " occ=0.00 residue: pdb=" C1 BMA S 3 " occ=0.00 ... (9 atoms not shown) pdb=" O6 BMA S 3 " occ=0.00 residue: pdb=" C1 NAG T 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG T 1 " occ=0.00 residue: pdb=" C1 NAG T 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG T 2 " occ=0.00 residue: pdb=" C1 BMA T 3 " occ=0.00 ... (9 atoms not shown) pdb=" O6 BMA T 3 " occ=0.00 residue: pdb=" C1 MAN T 4 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN T 4 " occ=0.00 residue: pdb=" C1 MAN T 5 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN T 5 " occ=0.00 ... (remaining 51 not shown) Time building chain proxies: 3.95, per 1000 atoms: 0.23 Number of scatterers: 17275 At special positions: 0 Unit cell: (129, 137.6, 166.84, 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 111 16.00 O 3579 8.00 N 2830 7.00 C 10755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 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 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=2.03 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=2.04 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 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.04 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM17035 O5 NAG A 603 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN T 4 " - " MAN T 5 " " MAN f 4 " - " MAN f 5 " " MAN q 4 " - " MAN q 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA T 3 " - " MAN T 4 " " BMA Y 3 " - " MAN Y 4 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " " BMA k 3 " - " MAN k 4 " " BMA q 3 " - " MAN q 4 " " MAN q 6 " - " MAN q 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " " BMA x 3 " - " MAN x 4 " ALPHA1-6 " BMA T 3 " - " MAN T 6 " " BMA Y 3 " - " MAN Y 5 " " BMA f 3 " - " MAN f 6 " " BMA k 3 " - " MAN k 5 " " BMA q 3 " - " MAN q 6 " " MAN q 6 " - " MAN q 8 " " BMA s 3 " - " MAN s 6 " " BMA x 3 " - " MAN x 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " 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 Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " 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 y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN E 637 " " NAG 1 1 " - " ASN F 611 " " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 355 " " NAG A 604 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 339 " " NAG C 604 " - " ASN C 355 " " NAG D 601 " - " ASN D 133 " " NAG D 602 " - " ASN D 234 " " NAG D 603 " - " ASN D 339 " " NAG D 604 " - " ASN D 355 " " NAG D 605 " - " ASN D 392 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 618 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 133 " " NAG Q 1 " - " ASN A 156 " " NAG R 1 " - " ASN A 160 " " NAG S 1 " - " ASN A 197 " " NAG T 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 295 " " NAG W 1 " - " ASN A 301 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN A 363 " " NAG Z 1 " - " ASN A 386 " " NAG a 1 " - " ASN A 448 " " NAG b 1 " - " ASN C 133 " " NAG c 1 " - " ASN C 156 " " NAG d 1 " - " ASN C 160 " " NAG e 1 " - " ASN C 197 " " NAG f 1 " - " ASN C 262 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 301 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN C 363 " " NAG l 1 " - " ASN C 386 " " NAG m 1 " - " ASN C 392 " " NAG n 1 " - " ASN C 448 " " NAG o 1 " - " ASN D 88 " " NAG p 1 " - " ASN D 156 " " NAG q 1 " - " ASN D 160 " " NAG r 1 " - " ASN D 197 " " NAG s 1 " - " ASN D 262 " " NAG u 1 " - " ASN D 295 " " NAG v 1 " - " ASN D 301 " " NAG w 1 " - " ASN D 332 " " NAG x 1 " - " ASN D 363 " " NAG y 1 " - " ASN D 386 " " NAG z 1 " - " ASN D 448 " Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 685.5 milliseconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3686 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 33 sheets defined 27.1% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 59 through 64 removed outlier: 3.695A pdb=" N THR A 63 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.646A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 484 removed outlier: 4.654A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.654A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.422A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 597 Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.841A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 4.219A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.886A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 3.922A pdb=" N THR C 63 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.927A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 127 " --> pdb=" O PRO C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 127' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 removed outlier: 3.667A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 460 through 464 removed outlier: 3.682A pdb=" N SER C 463 " --> pdb=" O SER C 460 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR C 464 " --> pdb=" O THR C 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 460 through 464' Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 99 through 117 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 removed outlier: 3.505A pdb=" N ARG D 151 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 377 through 381 removed outlier: 3.668A pdb=" N GLU D 381 " --> pdb=" O CYS D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 392 removed outlier: 3.660A pdb=" N PHE D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN D 392 " --> pdb=" O GLY D 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 392' Processing helix chain 'D' and resid 474 through 484 removed outlier: 3.918A pdb=" N ASN D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 3.705A pdb=" N ALA E 526 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 535 removed outlier: 3.954A pdb=" N MET E 535 " --> pdb=" O ALA E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 543 removed outlier: 4.303A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 596 Processing helix chain 'E' and resid 618 through 624 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 649 Processing helix chain 'E' and resid 650 through 664 removed outlier: 3.728A pdb=" N ASP E 664 " --> pdb=" O LEU E 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 3.614A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 3.882A pdb=" N SER F 534 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 531 through 535' Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.170A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 597 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 650 removed outlier: 4.111A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 664 removed outlier: 3.596A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 31 removed outlier: 5.831A pdb=" N PHE J 29 " --> pdb=" O GLY J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 62 removed outlier: 3.791A pdb=" N GLN J 62 " --> pdb=" O GLN J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 59 through 62' Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.603A pdb=" N VAL N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.655A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS A 218 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.120A pdb=" N ILE A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 244 " --> pdb=" O ILE A 84 " (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 172 through 177 removed outlier: 3.691A pdb=" N VAL A 172 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 159 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 130 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.404A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.414A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 361 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AB2, first strand: chain 'C' and resid 46 through 47 removed outlier: 3.632A pdb=" N VAL C 489 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 224 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 55 through 56 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 172 through 177 removed outlier: 4.179A pdb=" N GLN C 130 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.853A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.032A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.085A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS C 331 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 416 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 333 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.050A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.085A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.032A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE C 361 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AB9, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AC1, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=AC2, first strand: chain 'D' and resid 76 through 77 removed outlier: 7.381A pdb=" N THR D 77 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER D 56 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 84 through 86 removed outlier: 4.302A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA D 224 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 489 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 487 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 177 removed outlier: 3.700A pdb=" N MET D 161 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL D 172 " --> pdb=" O PHE D 159 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE D 159 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN D 156 " --> pdb=" O THR D 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 202 through 203 removed outlier: 6.843A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.521A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.521A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 359 " --> pdb=" O TRP D 395 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 374 through 376 removed outlier: 3.900A pdb=" N HIS D 330 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR D 297 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN D 295 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 304 through 308 Processing sheet with id=AD2, first strand: chain 'J' and resid 4 through 6 removed outlier: 5.814A pdb=" N SER J 16 " --> pdb=" O GLY J 82B" (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU J 81 " --> pdb=" O THR J 68 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.168A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.168A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N CYS J 92 " --> pdb=" O TRP J 108 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TRP J 108 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR J 94 " --> pdb=" O ASP J 106 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N HIS J 98 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU J 102 " --> pdb=" O HIS J 98 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU J 100 " --> pdb=" O ASP J 100R" (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASP J 100R" --> pdb=" O LEU J 100 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP J 100B" --> pdb=" O TRP J 100P" (cutoff:3.500A) removed outlier: 7.580A pdb=" N TRP J 100P" --> pdb=" O ASP J 100B" (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE J 100D" --> pdb=" O GLU J 100N" (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU J 100N" --> pdb=" O PHE J 100D" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 4 through 7 removed outlier: 5.139A pdb=" N GLU N 17 " --> pdb=" O ARG N 77 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG N 77 " --> pdb=" O GLU N 17 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.509A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS N 53 " --> pdb=" O HIS N 49 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1542 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: 3.30 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5323 1.34 - 1.47: 4536 1.47 - 1.60: 7588 1.60 - 1.73: 0 1.73 - 1.85: 151 Bond restraints: 17598 Sorted by residual: bond pdb=" C1 NAG D 603 " pdb=" O5 NAG D 603 " ideal model delta sigma weight residual 1.406 1.506 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C1 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C1 NAG B 703 " pdb=" O5 NAG B 703 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C1 NAG l 1 " pdb=" O5 NAG l 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" C1 NAG A 604 " pdb=" O5 NAG A 604 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.07e+00 ... (remaining 17593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 23207 2.53 - 5.06: 586 5.06 - 7.59: 88 7.59 - 10.12: 6 10.12 - 12.65: 3 Bond angle restraints: 23890 Sorted by residual: angle pdb=" C LYS C 65 " pdb=" N HIS C 66 " pdb=" CA HIS C 66 " ideal model delta sigma weight residual 121.70 134.35 -12.65 1.80e+00 3.09e-01 4.94e+01 angle pdb=" CA ASN A 355 " pdb=" CB ASN A 355 " pdb=" CG ASN A 355 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.00e+00 1.00e+00 3.06e+01 angle pdb=" C LYS A 65 " pdb=" N HIS A 66 " pdb=" CA HIS A 66 " ideal model delta sigma weight residual 121.70 131.26 -9.56 1.80e+00 3.09e-01 2.82e+01 angle pdb=" C TRP A 427 " pdb=" CA TRP A 427 " pdb=" CB TRP A 427 " ideal model delta sigma weight residual 115.79 109.67 6.12 1.19e+00 7.06e-01 2.65e+01 angle pdb=" N ALA D 362 " pdb=" CA ALA D 362 " pdb=" C ALA D 362 " ideal model delta sigma weight residual 108.24 114.96 -6.72 1.32e+00 5.74e-01 2.59e+01 ... (remaining 23885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8812 17.99 - 35.97: 632 35.97 - 53.96: 121 53.96 - 71.95: 20 71.95 - 89.94: 12 Dihedral angle restraints: 9597 sinusoidal: 3893 harmonic: 5704 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 5.43 87.57 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -6.88 -79.12 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CA CYS C 385 " pdb=" C CYS C 385 " pdb=" N ASN C 386 " pdb=" CA ASN C 386 " ideal model delta harmonic sigma weight residual -180.00 -137.97 -42.03 0 5.00e+00 4.00e-02 7.07e+01 ... (remaining 9594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.226: 3040 0.226 - 0.451: 23 0.451 - 0.677: 4 0.677 - 0.902: 2 0.902 - 1.128: 1 Chirality restraints: 3070 Sorted by residual: chirality pdb=" C1 NAG s 1 " pdb=" ND2 ASN D 262 " pdb=" C2 NAG s 1 " pdb=" O5 NAG s 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.27 -1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN A 301 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN A 262 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 ... (remaining 3067 not shown) Planarity restraints: 2917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 355 " 0.083 2.00e-02 2.50e+03 7.33e-02 6.71e+01 pdb=" CG ASN A 355 " -0.085 2.00e-02 2.50e+03 pdb=" OD1 ASN A 355 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 355 " -0.073 2.00e-02 2.50e+03 pdb=" C1 NAG A 603 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 637 " -0.007 2.00e-02 2.50e+03 4.88e-02 2.97e+01 pdb=" CG ASN B 637 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN B 637 " -0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN B 637 " 0.054 2.00e-02 2.50e+03 pdb=" C1 NAG B 703 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 339 " 0.005 2.00e-02 2.50e+03 4.68e-02 2.74e+01 pdb=" CG ASN D 339 " -0.072 2.00e-02 2.50e+03 pdb=" OD1 ASN D 339 " 0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN D 339 " -0.030 2.00e-02 2.50e+03 pdb=" C1 NAG D 603 " 0.040 2.00e-02 2.50e+03 ... (remaining 2914 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 360 2.62 - 3.19: 16069 3.19 - 3.76: 27137 3.76 - 4.33: 35865 4.33 - 4.90: 56131 Nonbonded interactions: 135562 Sorted by model distance: nonbonded pdb=" O ILE F 595 " pdb=" ND2 ASN F 651 " model vdw 2.048 3.120 nonbonded pdb=" O ILE C 491 " pdb=" NH2 ARG F 585 " model vdw 2.068 3.120 nonbonded pdb=" OE1 GLU C 102 " pdb=" NH1 ARG C 476 " model vdw 2.168 3.120 nonbonded pdb=" OG1 THR J 83 " pdb=" OD1 ASP J 85 " model vdw 2.184 3.040 nonbonded pdb=" OG1 THR J 70 " pdb=" O TYR J 79 " model vdw 2.185 3.040 ... (remaining 135557 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 '0' selection = chain '1' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 32 through 398 or resid 412 through 604)) selection = (chain 'D' and (resid 32 through 185 or resid 189 through 398 or resid 412 throu \ gh 604)) } ncs_group { reference = (chain 'B' and (resid 520 through 545 or resid 569 through 702)) selection = (chain 'E' and (resid 520 through 545 or resid 569 through 702)) selection = (chain 'F' and (resid 520 through 545 or resid 569 through 702)) } ncs_group { reference = chain 'S' selection = chain 'X' selection = chain 'd' selection = chain 'l' selection = chain 'y' } ncs_group { reference = (chain 'T' and (resid 1 or resid 4 through 6)) selection = (chain 'f' and (resid 2 or resid 5 through 7)) selection = (chain 's' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'Y' selection = chain 'k' selection = chain 'x' } 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=0.00 max=1.00 mean=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.730 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5454 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 17761 Z= 0.267 Angle : 1.116 27.182 24344 Z= 0.488 Chirality : 0.067 1.128 3070 Planarity : 0.004 0.054 2860 Dihedral : 12.897 89.935 5806 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1944 helix: 0.11 (0.26), residues: 418 sheet: 0.00 (0.22), residues: 509 loop : -0.31 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 585 TYR 0.030 0.002 TYR F 643 PHE 0.041 0.002 PHE D 288 TRP 0.053 0.002 TRP D 45 HIS 0.007 0.001 HIS N 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.27 (17598) covalent geometry : angle 0.92955 / 0.44 (23890) SS BOND : bond 0.00564 / 0.36 ( 35) SS BOND : angle 1.86257 / 1.22 ( 70) hydrogen bonds : bond 0.21968 / 14.22 ( 571) hydrogen bonds : angle 8.74648 / 6.14 ( 1542) link_ALPHA1-2 : bond 0.00286 / 0.14 ( 4) link_ALPHA1-2 : angle 1.87362 / 0.95 ( 12) link_ALPHA1-3 : bond 0.00542 / 0.30 ( 10) link_ALPHA1-3 : angle 1.58806 / 0.98 ( 30) link_ALPHA1-6 : bond 0.00450 / 0.27 ( 8) link_ALPHA1-6 : angle 1.72791 / 1.10 ( 24) link_BETA1-4 : bond 0.00628 / 0.44 ( 49) link_BETA1-4 : angle 2.59209 / 1.82 ( 147) link_NAG-ASN : bond 0.00681 / 0.41 ( 57) link_NAG-ASN : angle 6.95287 / 4.45 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7063 (p-80) cc_final: 0.6653 (p-80) REVERT: A 108 ILE cc_start: 0.8499 (mp) cc_final: 0.7592 (mp) REVERT: A 117 LYS cc_start: 0.9052 (tttt) cc_final: 0.8740 (ptmt) REVERT: A 190 GLU cc_start: 0.6156 (pm20) cc_final: 0.5270 (pm20) REVERT: B 646 LEU cc_start: 0.9119 (mt) cc_final: 0.8877 (mt) REVERT: C 271 MET cc_start: 0.4814 (tpt) cc_final: 0.4499 (mmm) REVERT: C 298 ARG cc_start: 0.7662 (tmm-80) cc_final: 0.7321 (tmm-80) REVERT: C 423 ILE cc_start: 0.7946 (mt) cc_final: 0.7676 (mt) REVERT: D 216 HIS cc_start: 0.6996 (m-70) cc_final: 0.6427 (m170) REVERT: D 391 PHE cc_start: 0.7661 (m-80) cc_final: 0.7393 (m-80) REVERT: D 434 MET cc_start: 0.5241 (ptm) cc_final: 0.4427 (ppp) REVERT: D 484 TYR cc_start: 0.7944 (p90) cc_final: 0.7485 (p90) REVERT: F 590 GLN cc_start: 0.8914 (tt0) cc_final: 0.8457 (pt0) REVERT: F 591 GLN cc_start: 0.9049 (mt0) cc_final: 0.8825 (mt0) REVERT: F 601 LYS cc_start: 0.7682 (mppt) cc_final: 0.7418 (mmtm) REVERT: F 606 THR cc_start: 0.8112 (m) cc_final: 0.7839 (m) REVERT: F 642 ILE cc_start: 0.8420 (mt) cc_final: 0.8049 (mt) REVERT: F 643 TYR cc_start: 0.8122 (m-80) cc_final: 0.7573 (m-80) REVERT: F 656 ASN cc_start: 0.9130 (t0) cc_final: 0.8880 (t0) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.1191 time to fit residues: 68.7166 Evaluate side-chains 301 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN A 428 GLN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN C 72 HIS ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 374 HIS D 103 GLN D 315 GLN E 540 GLN E 651 ASN F 540 GLN F 575 GLN F 591 GLN F 650 GLN J 32 HIS ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 HIS ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.145085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.110716 restraints weight = 54854.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.114382 restraints weight = 40888.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.116409 restraints weight = 31220.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.117854 restraints weight = 26021.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.119058 restraints weight = 23399.008| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17761 Z= 0.147 Angle : 0.870 19.841 24344 Z= 0.395 Chirality : 0.053 0.771 3070 Planarity : 0.004 0.062 2860 Dihedral : 5.528 36.521 2108 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.40 % Allowed : 5.46 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.18), residues: 1944 helix: 0.19 (0.26), residues: 424 sheet: 0.03 (0.21), residues: 512 loop : -0.45 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 588 TYR 0.028 0.002 TYR F 643 PHE 0.022 0.002 PHE C 159 TRP 0.030 0.002 TRP D 45 HIS 0.006 0.001 HIS N 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (17598) covalent geometry : angle 0.73237 / 0.36 (23890) SS BOND : bond 0.00398 / 0.24 ( 35) SS BOND : angle 1.30886 / 0.93 ( 70) hydrogen bonds : bond 0.05124 / 3.44 ( 571) hydrogen bonds : angle 6.79750 / 4.74 ( 1542) link_ALPHA1-2 : bond 0.00226 / 0.11 ( 4) link_ALPHA1-2 : angle 1.79183 / 0.91 ( 12) link_ALPHA1-3 : bond 0.00607 / 0.35 ( 10) link_ALPHA1-3 : angle 1.48364 / 0.88 ( 30) link_ALPHA1-6 : bond 0.00593 / 0.37 ( 8) link_ALPHA1-6 : angle 1.35731 / 0.85 ( 24) link_BETA1-4 : bond 0.00583 / 0.36 ( 49) link_BETA1-4 : angle 1.98117 / 1.33 ( 147) link_NAG-ASN : bond 0.00766 / 0.48 ( 57) link_NAG-ASN : angle 5.28896 / 3.60 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 390 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8088 (p-80) cc_final: 0.7620 (p-80) REVERT: A 104 MET cc_start: 0.8595 (tpt) cc_final: 0.7932 (tpp) REVERT: A 108 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.7417 (mp) REVERT: A 190 GLU cc_start: 0.7694 (pm20) cc_final: 0.6805 (pm20) REVERT: A 271 MET cc_start: -0.1541 (ttt) cc_final: -0.2071 (ttt) REVERT: A 298 ARG cc_start: 0.8994 (ptm160) cc_final: 0.8402 (ptm160) REVERT: A 423 ILE cc_start: 0.7560 (mm) cc_final: 0.7304 (mm) REVERT: B 635 ILE cc_start: 0.7622 (tt) cc_final: 0.6836 (tt) REVERT: C 47 ASP cc_start: 0.8644 (t0) cc_final: 0.8317 (t0) REVERT: C 271 MET cc_start: 0.5667 (tpt) cc_final: 0.5294 (mmm) REVERT: C 288 PHE cc_start: 0.7288 (m-10) cc_final: 0.6871 (m-80) REVERT: C 298 ARG cc_start: 0.8462 (tmm-80) cc_final: 0.7762 (tmm-80) REVERT: C 423 ILE cc_start: 0.8153 (mt) cc_final: 0.7886 (mt) REVERT: C 434 MET cc_start: 0.4998 (tmm) cc_final: 0.3415 (ttm) REVERT: D 45 TRP cc_start: 0.6460 (p90) cc_final: 0.6172 (p90) REVERT: D 130 GLN cc_start: 0.9279 (mp10) cc_final: 0.8951 (pm20) REVERT: D 159 PHE cc_start: 0.4491 (p90) cc_final: 0.4144 (p90) REVERT: D 176 PHE cc_start: 0.8407 (m-10) cc_final: 0.8065 (m-10) REVERT: D 191 TYR cc_start: 0.8622 (m-10) cc_final: 0.8174 (m-80) REVERT: D 216 HIS cc_start: 0.8249 (m-70) cc_final: 0.7804 (m170) REVERT: D 260 LEU cc_start: 0.8458 (mt) cc_final: 0.8133 (mt) REVERT: D 271 MET cc_start: 0.7380 (tmm) cc_final: 0.6141 (ttt) REVERT: D 342 LEU cc_start: 0.9152 (mp) cc_final: 0.8856 (mt) REVERT: D 391 PHE cc_start: 0.9278 (m-80) cc_final: 0.8622 (m-80) REVERT: D 475 MET cc_start: 0.8470 (pmm) cc_final: 0.8255 (pmm) REVERT: F 588 ARG cc_start: 0.7763 (mmt180) cc_final: 0.7547 (mmt180) REVERT: F 591 GLN cc_start: 0.9137 (mt0) cc_final: 0.8797 (mt0) REVERT: F 643 TYR cc_start: 0.8990 (m-80) cc_final: 0.8241 (m-80) REVERT: J 51 MET cc_start: 0.8315 (ttt) cc_final: 0.7859 (mmm) REVERT: N 27 HIS cc_start: 0.8653 (t-90) cc_final: 0.8245 (t-90) REVERT: N 39 ARG cc_start: 0.7009 (mmt180) cc_final: 0.6558 (mmt180) REVERT: N 87 TYR cc_start: 0.8575 (m-80) cc_final: 0.8294 (m-80) outliers start: 7 outliers final: 3 residues processed: 394 average time/residue: 0.1118 time to fit residues: 67.7799 Evaluate side-chains 311 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 307 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 87 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS D 203 GLN E 651 ASN F 540 GLN F 575 GLN ** J 52AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 HIS ** N 90 GLN ** 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 = 0.4184 r_free = 0.4184 target = 0.138122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.104038 restraints weight = 56786.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.107671 restraints weight = 42057.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.109304 restraints weight = 31601.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.111273 restraints weight = 26890.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.111285 restraints weight = 24937.274| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17761 Z= 0.212 Angle : 0.926 19.818 24344 Z= 0.426 Chirality : 0.052 0.692 3070 Planarity : 0.005 0.053 2860 Dihedral : 5.754 39.392 2108 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.29 % Allowed : 4.82 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.18), residues: 1944 helix: -0.03 (0.25), residues: 428 sheet: -0.17 (0.21), residues: 506 loop : -0.59 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 588 TYR 0.023 0.002 TYR F 643 PHE 0.021 0.002 PHE C 159 TRP 0.022 0.002 TRP B 631 HIS 0.011 0.002 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 (17598) covalent geometry : angle 0.80188 / 0.40 (23890) SS BOND : bond 0.00783 / 0.50 ( 35) SS BOND : angle 1.59861 / 1.08 ( 70) hydrogen bonds : bond 0.04947 / 3.35 ( 571) hydrogen bonds : angle 6.84901 / 4.75 ( 1542) link_ALPHA1-2 : bond 0.00313 / 0.16 ( 4) link_ALPHA1-2 : angle 1.71467 / 0.83 ( 12) link_ALPHA1-3 : bond 0.00703 / 0.43 ( 10) link_ALPHA1-3 : angle 1.46791 / 0.87 ( 30) link_ALPHA1-6 : bond 0.00632 / 0.43 ( 8) link_ALPHA1-6 : angle 1.45167 / 0.94 ( 24) link_BETA1-4 : bond 0.00662 / 0.44 ( 49) link_BETA1-4 : angle 1.98375 / 1.30 ( 147) link_NAG-ASN : bond 0.00910 / 0.57 ( 57) link_NAG-ASN : angle 5.18110 / 3.54 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 384 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8700 (p-80) cc_final: 0.8471 (p-80) REVERT: A 104 MET cc_start: 0.8777 (tpt) cc_final: 0.8159 (tpp) REVERT: A 108 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.7539 (mp) REVERT: A 190 GLU cc_start: 0.7737 (pm20) cc_final: 0.7062 (pm20) REVERT: A 216 HIS cc_start: 0.8740 (m-70) cc_final: 0.8190 (m-70) REVERT: A 271 MET cc_start: -0.0694 (ttt) cc_final: -0.1440 (ttt) REVERT: A 339 ASN cc_start: 0.5585 (p0) cc_final: 0.5285 (p0) REVERT: A 383 PHE cc_start: 0.9074 (m-10) cc_final: 0.8730 (m-80) REVERT: A 391 PHE cc_start: 0.8746 (m-80) cc_final: 0.8515 (m-80) REVERT: A 423 ILE cc_start: 0.7751 (mm) cc_final: 0.7445 (mm) REVERT: A 435 TYR cc_start: 0.8122 (t80) cc_final: 0.7811 (t80) REVERT: C 47 ASP cc_start: 0.8709 (t0) cc_final: 0.8426 (t0) REVERT: C 99 ASN cc_start: 0.7580 (t0) cc_final: 0.7328 (t0) REVERT: C 150 MET cc_start: 0.5164 (tmm) cc_final: 0.4677 (ppp) REVERT: C 271 MET cc_start: 0.5924 (tpt) cc_final: 0.5497 (tpt) REVERT: C 288 PHE cc_start: 0.7628 (m-10) cc_final: 0.7185 (m-10) REVERT: C 298 ARG cc_start: 0.8593 (tmm-80) cc_final: 0.7984 (tmm-80) REVERT: C 423 ILE cc_start: 0.8074 (mt) cc_final: 0.7848 (mt) REVERT: C 446 VAL cc_start: 0.7244 (p) cc_final: 0.7005 (t) REVERT: D 52 LEU cc_start: 0.7514 (pt) cc_final: 0.7213 (pp) REVERT: D 130 GLN cc_start: 0.9413 (mp10) cc_final: 0.9069 (pm20) REVERT: D 176 PHE cc_start: 0.7883 (m-10) cc_final: 0.7445 (m-10) REVERT: D 191 TYR cc_start: 0.8643 (m-10) cc_final: 0.8011 (m-80) REVERT: D 216 HIS cc_start: 0.8855 (m-70) cc_final: 0.8596 (m-70) REVERT: D 271 MET cc_start: 0.7431 (tmm) cc_final: 0.7152 (tmm) REVERT: D 288 PHE cc_start: 0.8235 (m-10) cc_final: 0.7896 (m-10) REVERT: D 302 ASN cc_start: 0.9243 (m110) cc_final: 0.9006 (m-40) REVERT: D 318 TYR cc_start: 0.7958 (m-10) cc_final: 0.7519 (m-80) REVERT: D 342 LEU cc_start: 0.9207 (mp) cc_final: 0.8927 (mp) REVERT: D 384 TYR cc_start: 0.8437 (m-10) cc_final: 0.8190 (m-10) REVERT: D 391 PHE cc_start: 0.9299 (m-80) cc_final: 0.8747 (m-80) REVERT: D 453 ILE cc_start: 0.8829 (tp) cc_final: 0.8617 (tp) REVERT: D 475 MET cc_start: 0.8690 (pmm) cc_final: 0.8348 (pmm) REVERT: D 484 TYR cc_start: 0.8232 (p90) cc_final: 0.7980 (p90) REVERT: D 487 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7866 (mttt) REVERT: F 601 LYS cc_start: 0.7443 (mppt) cc_final: 0.6636 (pttt) REVERT: F 643 TYR cc_start: 0.8851 (m-80) cc_final: 0.8218 (m-80) REVERT: J 51 MET cc_start: 0.8516 (ttt) cc_final: 0.8208 (ttt) REVERT: J 69 ILE cc_start: 0.7346 (tp) cc_final: 0.5903 (tp) REVERT: N 27 LEU cc_start: 0.8327 (tp) cc_final: 0.8110 (tp) REVERT: N 27 HIS cc_start: 0.8856 (t-90) cc_final: 0.8370 (t-90) REVERT: N 87 TYR cc_start: 0.8612 (m-80) cc_final: 0.8354 (m-80) outliers start: 5 outliers final: 1 residues processed: 387 average time/residue: 0.1205 time to fit residues: 71.3291 Evaluate side-chains 309 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 307 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 74 optimal weight: 0.4980 chunk 92 optimal weight: 0.0770 chunk 70 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 72 HIS C 82 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 540 GLN ** J 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 HIS ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.142346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.107034 restraints weight = 55295.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.110565 restraints weight = 40697.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.113491 restraints weight = 30180.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.115132 restraints weight = 24319.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.115368 restraints weight = 21887.505| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17761 Z= 0.135 Angle : 0.858 18.923 24344 Z= 0.387 Chirality : 0.051 0.662 3070 Planarity : 0.004 0.060 2860 Dihedral : 5.528 38.109 2108 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.23 % Allowed : 3.27 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 1944 helix: 0.24 (0.26), residues: 428 sheet: -0.03 (0.21), residues: 527 loop : -0.56 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 588 TYR 0.021 0.001 TYR F 643 PHE 0.020 0.002 PHE A 159 TRP 0.047 0.002 TRP B 596 HIS 0.007 0.001 HIS N 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (17598) covalent geometry : angle 0.72905 / 0.36 (23890) SS BOND : bond 0.00577 / 0.36 ( 35) SS BOND : angle 1.46330 / 1.02 ( 70) hydrogen bonds : bond 0.04236 / 2.88 ( 571) hydrogen bonds : angle 6.38308 / 4.45 ( 1542) link_ALPHA1-2 : bond 0.00353 / 0.18 ( 4) link_ALPHA1-2 : angle 1.62023 / 0.80 ( 12) link_ALPHA1-3 : bond 0.00760 / 0.44 ( 10) link_ALPHA1-3 : angle 1.30897 / 0.76 ( 30) link_ALPHA1-6 : bond 0.00605 / 0.38 ( 8) link_ALPHA1-6 : angle 1.36664 / 0.87 ( 24) link_BETA1-4 : bond 0.00549 / 0.35 ( 49) link_BETA1-4 : angle 1.83908 / 1.21 ( 147) link_NAG-ASN : bond 0.00703 / 0.46 ( 57) link_NAG-ASN : angle 5.10826 / 3.57 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 386 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8771 (tpt) cc_final: 0.8066 (tpp) REVERT: A 108 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.7419 (mp) REVERT: A 190 GLU cc_start: 0.7840 (pm20) cc_final: 0.7194 (pm20) REVERT: A 216 HIS cc_start: 0.8939 (m-70) cc_final: 0.8462 (m-70) REVERT: A 271 MET cc_start: -0.0914 (ttt) cc_final: -0.1678 (ttt) REVERT: A 298 ARG cc_start: 0.8965 (ptm160) cc_final: 0.8450 (ptm-80) REVERT: A 317 PHE cc_start: 0.7137 (t80) cc_final: 0.6787 (t80) REVERT: A 370 GLU cc_start: 0.7218 (pt0) cc_final: 0.6980 (tt0) REVERT: A 383 PHE cc_start: 0.9009 (m-10) cc_final: 0.8655 (m-80) REVERT: B 586 TYR cc_start: 0.8723 (t80) cc_final: 0.8483 (t80) REVERT: C 47 ASP cc_start: 0.8698 (t0) cc_final: 0.8342 (t0) REVERT: C 59 LYS cc_start: 0.7082 (tppt) cc_final: 0.6840 (tptt) REVERT: C 80 ASN cc_start: 0.7125 (p0) cc_final: 0.6901 (p0) REVERT: C 100 MET cc_start: 0.7224 (mpp) cc_final: 0.6853 (mpp) REVERT: C 122 LEU cc_start: 0.9652 (tt) cc_final: 0.9436 (tt) REVERT: C 150 MET cc_start: 0.4788 (tmm) cc_final: 0.4543 (ppp) REVERT: C 271 MET cc_start: 0.6084 (tpt) cc_final: 0.5651 (tpt) REVERT: C 288 PHE cc_start: 0.7683 (m-10) cc_final: 0.7469 (m-10) REVERT: C 298 ARG cc_start: 0.8569 (tmm-80) cc_final: 0.7844 (tmm-80) REVERT: C 419 ARG cc_start: 0.7567 (mtp180) cc_final: 0.7088 (mmm160) REVERT: C 423 ILE cc_start: 0.8040 (mt) cc_final: 0.7776 (mt) REVERT: C 434 MET cc_start: 0.5179 (tmm) cc_final: 0.4167 (ttm) REVERT: C 446 VAL cc_start: 0.7224 (p) cc_final: 0.6957 (t) REVERT: D 45 TRP cc_start: 0.7146 (p90) cc_final: 0.6898 (p90) REVERT: D 52 LEU cc_start: 0.7458 (pt) cc_final: 0.7255 (pp) REVERT: D 93 PHE cc_start: 0.8812 (m-10) cc_final: 0.8510 (m-10) REVERT: D 130 GLN cc_start: 0.9443 (mp10) cc_final: 0.9035 (pm20) REVERT: D 176 PHE cc_start: 0.7815 (m-10) cc_final: 0.7400 (m-10) REVERT: D 191 TYR cc_start: 0.8702 (m-10) cc_final: 0.7865 (m-80) REVERT: D 244 THR cc_start: 0.8902 (t) cc_final: 0.8533 (t) REVERT: D 288 PHE cc_start: 0.8262 (m-10) cc_final: 0.7972 (m-10) REVERT: D 384 TYR cc_start: 0.8445 (m-10) cc_final: 0.8234 (m-10) REVERT: D 391 PHE cc_start: 0.9264 (m-80) cc_final: 0.8715 (m-80) REVERT: D 434 MET cc_start: 0.3431 (ptm) cc_final: 0.2742 (ppp) REVERT: D 475 MET cc_start: 0.8498 (pmm) cc_final: 0.8204 (pmm) REVERT: E 587 LEU cc_start: 0.9506 (mm) cc_final: 0.9297 (mm) REVERT: F 575 GLN cc_start: 0.8447 (pp30) cc_final: 0.7640 (mp10) REVERT: F 643 TYR cc_start: 0.8957 (m-80) cc_final: 0.8512 (m-80) REVERT: J 51 MET cc_start: 0.8480 (ttt) cc_final: 0.8212 (mmm) REVERT: N 27 LEU cc_start: 0.8285 (tp) cc_final: 0.8080 (tp) REVERT: N 27 HIS cc_start: 0.8879 (t-90) cc_final: 0.8344 (t-90) REVERT: N 39 ARG cc_start: 0.6368 (mmt180) cc_final: 0.5728 (mmt180) REVERT: N 53 HIS cc_start: 0.8584 (t-90) cc_final: 0.8334 (t70) REVERT: N 87 TYR cc_start: 0.8608 (m-80) cc_final: 0.8387 (m-80) outliers start: 4 outliers final: 2 residues processed: 388 average time/residue: 0.1232 time to fit residues: 72.7528 Evaluate side-chains 311 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 308 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 117 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 190 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 140 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN D 348 GLN E 651 ASN F 540 GLN ** J 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.141860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.107410 restraints weight = 55985.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.110736 restraints weight = 40364.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.112985 restraints weight = 30818.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.114658 restraints weight = 25617.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.114863 restraints weight = 23216.901| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17761 Z= 0.139 Angle : 0.835 18.483 24344 Z= 0.379 Chirality : 0.050 0.611 3070 Planarity : 0.004 0.076 2860 Dihedral : 5.428 39.192 2108 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.11 % Allowed : 3.22 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.19), residues: 1944 helix: 0.34 (0.26), residues: 423 sheet: 0.07 (0.21), residues: 531 loop : -0.57 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 588 TYR 0.021 0.001 TYR A 484 PHE 0.017 0.002 PHE A 159 TRP 0.024 0.002 TRP B 596 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (17598) covalent geometry : angle 0.71535 / 0.35 (23890) SS BOND : bond 0.00498 / 0.29 ( 35) SS BOND : angle 1.48561 / 1.04 ( 70) hydrogen bonds : bond 0.04109 / 2.80 ( 571) hydrogen bonds : angle 6.19825 / 4.32 ( 1542) link_ALPHA1-2 : bond 0.00341 / 0.17 ( 4) link_ALPHA1-2 : angle 1.61341 / 0.79 ( 12) link_ALPHA1-3 : bond 0.00681 / 0.40 ( 10) link_ALPHA1-3 : angle 1.35138 / 0.79 ( 30) link_ALPHA1-6 : bond 0.00502 / 0.30 ( 8) link_ALPHA1-6 : angle 1.37975 / 0.89 ( 24) link_BETA1-4 : bond 0.00562 / 0.36 ( 49) link_BETA1-4 : angle 1.78739 / 1.19 ( 147) link_NAG-ASN : bond 0.00676 / 0.43 ( 57) link_NAG-ASN : angle 4.83014 / 3.33 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 382 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.7812 (pm20) cc_final: 0.7157 (pm20) REVERT: A 216 HIS cc_start: 0.8772 (m-70) cc_final: 0.8213 (m-70) REVERT: A 271 MET cc_start: 0.0913 (ttt) cc_final: -0.0076 (ttt) REVERT: A 298 ARG cc_start: 0.8835 (ptm160) cc_final: 0.8582 (ptm-80) REVERT: A 381 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7629 (mm-30) REVERT: A 383 PHE cc_start: 0.8707 (m-10) cc_final: 0.8434 (m-80) REVERT: A 423 ILE cc_start: 0.8018 (mm) cc_final: 0.7795 (mm) REVERT: A 480 ARG cc_start: 0.8426 (mtp180) cc_final: 0.7667 (ptm160) REVERT: A 483 LEU cc_start: 0.9407 (mp) cc_final: 0.8769 (mp) REVERT: A 487 LYS cc_start: 0.8161 (tmmt) cc_final: 0.7938 (tmtt) REVERT: B 586 TYR cc_start: 0.8698 (t80) cc_final: 0.8496 (t80) REVERT: C 47 ASP cc_start: 0.8633 (t0) cc_final: 0.8287 (t0) REVERT: C 99 ASN cc_start: 0.7747 (t0) cc_final: 0.7380 (t0) REVERT: C 150 MET cc_start: 0.4819 (tmm) cc_final: 0.4543 (ppp) REVERT: C 271 MET cc_start: 0.6592 (tpt) cc_final: 0.6343 (tpt) REVERT: C 298 ARG cc_start: 0.8524 (tmm-80) cc_final: 0.7854 (tmm-80) REVERT: C 423 ILE cc_start: 0.7883 (mt) cc_final: 0.7593 (mt) REVERT: C 434 MET cc_start: 0.5435 (tmm) cc_final: 0.4467 (ttm) REVERT: C 446 VAL cc_start: 0.7346 (p) cc_final: 0.7113 (t) REVERT: D 93 PHE cc_start: 0.8658 (m-10) cc_final: 0.8295 (m-10) REVERT: D 130 GLN cc_start: 0.9469 (mp10) cc_final: 0.9053 (pm20) REVERT: D 176 PHE cc_start: 0.7872 (m-10) cc_final: 0.7528 (m-10) REVERT: D 191 TYR cc_start: 0.8702 (m-10) cc_final: 0.8053 (m-80) REVERT: D 216 HIS cc_start: 0.8148 (m-70) cc_final: 0.7836 (m-70) REVERT: D 244 THR cc_start: 0.8947 (t) cc_final: 0.8580 (t) REVERT: D 288 PHE cc_start: 0.8235 (m-10) cc_final: 0.7881 (m-10) REVERT: D 361 PHE cc_start: 0.7145 (m-80) cc_final: 0.6886 (m-80) REVERT: D 383 PHE cc_start: 0.8693 (m-80) cc_final: 0.8407 (m-80) REVERT: D 384 TYR cc_start: 0.8492 (m-10) cc_final: 0.8268 (m-10) REVERT: D 391 PHE cc_start: 0.9344 (m-80) cc_final: 0.8785 (m-80) REVERT: D 434 MET cc_start: 0.3292 (ptm) cc_final: 0.2342 (tmm) REVERT: D 475 MET cc_start: 0.8493 (pmm) cc_final: 0.8191 (pmm) REVERT: E 585 ARG cc_start: 0.9419 (mmm-85) cc_final: 0.9207 (mmm-85) REVERT: E 635 ILE cc_start: 0.9244 (mm) cc_final: 0.8792 (tp) REVERT: F 575 GLN cc_start: 0.8445 (pp30) cc_final: 0.7555 (mp10) REVERT: F 584 GLU cc_start: 0.9240 (pt0) cc_final: 0.9000 (pt0) REVERT: F 588 ARG cc_start: 0.8261 (mmt180) cc_final: 0.7997 (mmt180) REVERT: F 643 TYR cc_start: 0.8929 (m-80) cc_final: 0.8501 (m-80) REVERT: J 37 VAL cc_start: 0.8227 (t) cc_final: 0.7856 (t) REVERT: N 27 HIS cc_start: 0.8882 (t-90) cc_final: 0.8438 (t-90) REVERT: N 39 ARG cc_start: 0.6347 (mmt180) cc_final: 0.5693 (mmt180) REVERT: N 53 HIS cc_start: 0.8545 (t-90) cc_final: 0.8298 (t70) outliers start: 2 outliers final: 0 residues processed: 384 average time/residue: 0.1199 time to fit residues: 70.3990 Evaluate side-chains 300 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 302 ASN C 315 GLN C 422 GLN C 425 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 ASN E 651 ASN F 540 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** 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 = 0.4193 r_free = 0.4193 target = 0.138558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.104136 restraints weight = 56602.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.107698 restraints weight = 40635.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.109579 restraints weight = 30250.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.111237 restraints weight = 25842.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.111277 restraints weight = 24261.283| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17761 Z= 0.166 Angle : 0.879 18.131 24344 Z= 0.400 Chirality : 0.052 0.632 3070 Planarity : 0.004 0.046 2860 Dihedral : 5.555 40.600 2108 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.17 % Allowed : 2.70 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 1944 helix: 0.35 (0.27), residues: 418 sheet: -0.06 (0.22), residues: 512 loop : -0.57 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 273 TYR 0.013 0.002 TYR F 643 PHE 0.018 0.002 PHE A 159 TRP 0.034 0.002 TRP J 47 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (17598) covalent geometry : angle 0.75710 / 0.37 (23890) SS BOND : bond 0.00482 / 0.29 ( 35) SS BOND : angle 1.68581 / 1.14 ( 70) hydrogen bonds : bond 0.04248 / 2.95 ( 571) hydrogen bonds : angle 6.30348 / 4.39 ( 1542) link_ALPHA1-2 : bond 0.00291 / 0.15 ( 4) link_ALPHA1-2 : angle 1.60143 / 0.79 ( 12) link_ALPHA1-3 : bond 0.00686 / 0.41 ( 10) link_ALPHA1-3 : angle 1.37569 / 0.80 ( 30) link_ALPHA1-6 : bond 0.00668 / 0.46 ( 8) link_ALPHA1-6 : angle 1.40041 / 0.90 ( 24) link_BETA1-4 : bond 0.00581 / 0.38 ( 49) link_BETA1-4 : angle 1.92484 / 1.27 ( 147) link_NAG-ASN : bond 0.00709 / 0.46 ( 57) link_NAG-ASN : angle 4.97449 / 3.38 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 369 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8826 (mp) cc_final: 0.8619 (mp) REVERT: A 176 PHE cc_start: 0.8653 (m-80) cc_final: 0.8092 (m-80) REVERT: A 190 GLU cc_start: 0.7892 (pm20) cc_final: 0.7212 (pm20) REVERT: A 216 HIS cc_start: 0.8780 (m-70) cc_final: 0.8224 (m-70) REVERT: A 225 ILE cc_start: 0.7554 (mt) cc_final: 0.7324 (mt) REVERT: A 252 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8367 (mmtt) REVERT: A 271 MET cc_start: 0.1480 (ttt) cc_final: 0.0470 (ttt) REVERT: A 298 ARG cc_start: 0.8852 (ptm160) cc_final: 0.8571 (ptm-80) REVERT: A 383 PHE cc_start: 0.8753 (m-10) cc_final: 0.8485 (m-80) REVERT: A 423 ILE cc_start: 0.8080 (mm) cc_final: 0.7835 (mm) REVERT: B 586 TYR cc_start: 0.8764 (t80) cc_final: 0.8495 (t80) REVERT: C 47 ASP cc_start: 0.8740 (t0) cc_final: 0.8407 (t0) REVERT: C 93 PHE cc_start: 0.6653 (m-80) cc_final: 0.6352 (m-80) REVERT: C 271 MET cc_start: 0.6849 (tpt) cc_final: 0.6471 (tpt) REVERT: C 298 ARG cc_start: 0.8525 (tmm-80) cc_final: 0.7888 (tmm-80) REVERT: C 302 ASN cc_start: 0.7373 (OUTLIER) cc_final: 0.7024 (p0) REVERT: C 423 ILE cc_start: 0.7971 (mt) cc_final: 0.7696 (mt) REVERT: C 434 MET cc_start: 0.5587 (tmm) cc_final: 0.4776 (ttm) REVERT: D 93 PHE cc_start: 0.8780 (m-10) cc_final: 0.8415 (m-10) REVERT: D 109 ILE cc_start: 0.9490 (pt) cc_final: 0.9057 (pt) REVERT: D 111 LEU cc_start: 0.9328 (mt) cc_final: 0.8909 (mt) REVERT: D 130 GLN cc_start: 0.9507 (mp10) cc_final: 0.9156 (pm20) REVERT: D 176 PHE cc_start: 0.7974 (m-80) cc_final: 0.7546 (m-10) REVERT: D 216 HIS cc_start: 0.8405 (m-70) cc_final: 0.8173 (m-70) REVERT: D 271 MET cc_start: 0.5442 (tmm) cc_final: 0.5173 (tmm) REVERT: D 288 PHE cc_start: 0.8289 (m-10) cc_final: 0.7903 (m-10) REVERT: D 302 ASN cc_start: 0.9234 (m110) cc_final: 0.9024 (m110) REVERT: D 361 PHE cc_start: 0.7237 (m-80) cc_final: 0.6995 (m-80) REVERT: D 383 PHE cc_start: 0.8850 (m-80) cc_final: 0.8532 (m-80) REVERT: D 391 PHE cc_start: 0.9267 (m-80) cc_final: 0.8552 (m-80) REVERT: D 434 MET cc_start: 0.3451 (ptm) cc_final: 0.2528 (tmm) REVERT: D 475 MET cc_start: 0.8618 (pmm) cc_final: 0.8348 (pmm) REVERT: E 581 LEU cc_start: 0.9444 (mm) cc_final: 0.9108 (mm) REVERT: E 585 ARG cc_start: 0.9479 (mmm-85) cc_final: 0.9257 (mmm-85) REVERT: E 635 ILE cc_start: 0.9116 (mm) cc_final: 0.8670 (tp) REVERT: F 575 GLN cc_start: 0.8310 (pp30) cc_final: 0.7156 (mp10) REVERT: F 584 GLU cc_start: 0.9266 (pt0) cc_final: 0.9024 (pt0) REVERT: F 588 ARG cc_start: 0.8029 (mmt180) cc_final: 0.7822 (mmt180) REVERT: F 643 TYR cc_start: 0.9006 (m-80) cc_final: 0.8625 (m-80) REVERT: J 37 VAL cc_start: 0.8244 (t) cc_final: 0.8029 (t) REVERT: J 51 MET cc_start: 0.8745 (tpt) cc_final: 0.8459 (tpt) REVERT: N 27 HIS cc_start: 0.8962 (t-90) cc_final: 0.8428 (t-90) REVERT: N 39 ARG cc_start: 0.6504 (mmt180) cc_final: 0.5788 (mmt180) REVERT: N 53 HIS cc_start: 0.8599 (t-90) cc_final: 0.8347 (t70) REVERT: N 79 GLU cc_start: 0.5685 (pp20) cc_final: 0.5365 (pm20) outliers start: 3 outliers final: 0 residues processed: 372 average time/residue: 0.1241 time to fit residues: 70.3376 Evaluate side-chains 296 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 187 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 177 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 315 GLN C 425 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 ASN D 377 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** J 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.140683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.106714 restraints weight = 56198.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.109631 restraints weight = 43944.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.112503 restraints weight = 31947.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.113256 restraints weight = 26702.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.113499 restraints weight = 24780.274| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17761 Z= 0.136 Angle : 0.856 17.504 24344 Z= 0.389 Chirality : 0.050 0.554 3070 Planarity : 0.004 0.051 2860 Dihedral : 5.380 40.697 2108 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.06 % Allowed : 1.49 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.19), residues: 1944 helix: 0.26 (0.27), residues: 417 sheet: 0.02 (0.22), residues: 503 loop : -0.56 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 273 TYR 0.029 0.001 TYR C 486 PHE 0.017 0.002 PHE C 233 TRP 0.026 0.002 TRP B 631 HIS 0.009 0.001 HIS J 52A Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (17598) covalent geometry : angle 0.73982 / 0.36 (23890) SS BOND : bond 0.00608 / 0.37 ( 35) SS BOND : angle 1.45772 / 0.99 ( 70) hydrogen bonds : bond 0.04047 / 2.78 ( 571) hydrogen bonds : angle 6.11527 / 4.26 ( 1542) link_ALPHA1-2 : bond 0.00267 / 0.14 ( 4) link_ALPHA1-2 : angle 1.67084 / 0.84 ( 12) link_ALPHA1-3 : bond 0.00674 / 0.41 ( 10) link_ALPHA1-3 : angle 1.36687 / 0.79 ( 30) link_ALPHA1-6 : bond 0.00501 / 0.29 ( 8) link_ALPHA1-6 : angle 1.40601 / 0.90 ( 24) link_BETA1-4 : bond 0.00546 / 0.35 ( 49) link_BETA1-4 : angle 1.82550 / 1.21 ( 147) link_NAG-ASN : bond 0.00649 / 0.42 ( 57) link_NAG-ASN : angle 4.82049 / 3.26 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 376 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8734 (mp) cc_final: 0.8504 (mp) REVERT: A 216 HIS cc_start: 0.8621 (m-70) cc_final: 0.8102 (m-70) REVERT: A 225 ILE cc_start: 0.7194 (mt) cc_final: 0.6976 (mp) REVERT: A 271 MET cc_start: 0.1241 (ttt) cc_final: 0.0204 (ttt) REVERT: A 298 ARG cc_start: 0.8781 (ptm160) cc_final: 0.8513 (ptm-80) REVERT: A 423 ILE cc_start: 0.7969 (mm) cc_final: 0.7755 (mm) REVERT: A 480 ARG cc_start: 0.8396 (mtp180) cc_final: 0.7612 (ptm160) REVERT: B 586 TYR cc_start: 0.8689 (t80) cc_final: 0.8312 (t80) REVERT: B 590 GLN cc_start: 0.9206 (pm20) cc_final: 0.8800 (pm20) REVERT: C 47 ASP cc_start: 0.8630 (t0) cc_final: 0.8147 (t0) REVERT: C 176 PHE cc_start: 0.8753 (m-80) cc_final: 0.8548 (m-80) REVERT: C 271 MET cc_start: 0.6476 (tpt) cc_final: 0.6094 (tpt) REVERT: C 288 PHE cc_start: 0.7106 (m-10) cc_final: 0.6820 (m-10) REVERT: C 298 ARG cc_start: 0.8624 (tmm-80) cc_final: 0.7963 (tmm-80) REVERT: D 52 LEU cc_start: 0.8124 (pp) cc_final: 0.7831 (tp) REVERT: D 93 PHE cc_start: 0.8696 (m-10) cc_final: 0.8343 (m-10) REVERT: D 130 GLN cc_start: 0.9490 (mp10) cc_final: 0.9163 (pm20) REVERT: D 176 PHE cc_start: 0.7773 (m-80) cc_final: 0.7386 (m-80) REVERT: D 244 THR cc_start: 0.8757 (t) cc_final: 0.8316 (t) REVERT: D 271 MET cc_start: 0.5006 (tmm) cc_final: 0.4679 (tmm) REVERT: D 288 PHE cc_start: 0.8138 (m-10) cc_final: 0.7796 (m-10) REVERT: D 342 LEU cc_start: 0.9532 (mm) cc_final: 0.9290 (mp) REVERT: D 383 PHE cc_start: 0.8678 (m-80) cc_final: 0.8363 (m-80) REVERT: D 391 PHE cc_start: 0.9152 (m-80) cc_final: 0.8492 (m-80) REVERT: D 475 MET cc_start: 0.8522 (pmm) cc_final: 0.8260 (pmm) REVERT: E 581 LEU cc_start: 0.9367 (mm) cc_final: 0.9092 (mm) REVERT: E 635 ILE cc_start: 0.8992 (mm) cc_final: 0.8638 (tp) REVERT: F 584 GLU cc_start: 0.9163 (pt0) cc_final: 0.8944 (pt0) REVERT: F 623 TRP cc_start: 0.8519 (m-10) cc_final: 0.7929 (m-10) REVERT: F 643 TYR cc_start: 0.8899 (m-80) cc_final: 0.8528 (m-80) REVERT: J 51 MET cc_start: 0.8288 (tpt) cc_final: 0.7756 (tpt) REVERT: J 69 ILE cc_start: 0.7865 (tp) cc_final: 0.7646 (tp) REVERT: N 27 LEU cc_start: 0.8705 (tp) cc_final: 0.8477 (tp) REVERT: N 27 HIS cc_start: 0.8860 (t-90) cc_final: 0.8299 (t-90) REVERT: N 39 ARG cc_start: 0.6181 (mmt180) cc_final: 0.5376 (mmt180) REVERT: N 53 HIS cc_start: 0.8434 (t-90) cc_final: 0.8176 (t70) REVERT: N 87 TYR cc_start: 0.7251 (m-80) cc_final: 0.7002 (m-80) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.1234 time to fit residues: 70.5066 Evaluate side-chains 299 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.0010 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 315 GLN C 425 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.137692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.103969 restraints weight = 56554.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.107266 restraints weight = 41138.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.109384 restraints weight = 31118.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.110629 restraints weight = 26144.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.111454 restraints weight = 23521.812| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17761 Z= 0.161 Angle : 0.876 17.288 24344 Z= 0.400 Chirality : 0.051 0.594 3070 Planarity : 0.004 0.061 2860 Dihedral : 5.460 38.852 2108 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.06 % Allowed : 1.90 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.19), residues: 1944 helix: 0.01 (0.26), residues: 423 sheet: 0.08 (0.23), residues: 490 loop : -0.61 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 579 TYR 0.017 0.002 TYR C 486 PHE 0.014 0.002 PHE D 382 TRP 0.031 0.002 TRP B 631 HIS 0.005 0.001 HIS J 52A Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (17598) covalent geometry : angle 0.76660 / 0.38 (23890) SS BOND : bond 0.00405 / 0.25 ( 35) SS BOND : angle 1.39573 / 0.95 ( 70) hydrogen bonds : bond 0.04185 / 2.84 ( 571) hydrogen bonds : angle 6.22324 / 4.31 ( 1542) link_ALPHA1-2 : bond 0.00302 / 0.15 ( 4) link_ALPHA1-2 : angle 1.64271 / 0.81 ( 12) link_ALPHA1-3 : bond 0.00644 / 0.39 ( 10) link_ALPHA1-3 : angle 1.38091 / 0.81 ( 30) link_ALPHA1-6 : bond 0.00521 / 0.34 ( 8) link_ALPHA1-6 : angle 1.41923 / 0.91 ( 24) link_BETA1-4 : bond 0.00587 / 0.39 ( 49) link_BETA1-4 : angle 1.86548 / 1.23 ( 147) link_NAG-ASN : bond 0.00685 / 0.43 ( 57) link_NAG-ASN : angle 4.74324 / 3.21 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.7911 (pm20) cc_final: 0.7243 (pm20) REVERT: A 225 ILE cc_start: 0.7474 (mt) cc_final: 0.7272 (mt) REVERT: A 252 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8406 (mmtt) REVERT: A 271 MET cc_start: 0.1396 (ttt) cc_final: 0.1026 (ttt) REVERT: A 298 ARG cc_start: 0.8844 (ptm160) cc_final: 0.8382 (ptm-80) REVERT: A 383 PHE cc_start: 0.8890 (m-10) cc_final: 0.8567 (m-80) REVERT: A 395 TRP cc_start: 0.6101 (t-100) cc_final: 0.5882 (t-100) REVERT: A 423 ILE cc_start: 0.7953 (mm) cc_final: 0.7738 (mm) REVERT: B 586 TYR cc_start: 0.8760 (t80) cc_final: 0.8488 (t80) REVERT: C 180 ASP cc_start: 0.7640 (m-30) cc_final: 0.6978 (m-30) REVERT: C 271 MET cc_start: 0.6483 (tpt) cc_final: 0.6181 (tpt) REVERT: C 298 ARG cc_start: 0.8516 (tmm-80) cc_final: 0.7935 (tmm-80) REVERT: C 423 ILE cc_start: 0.7939 (mt) cc_final: 0.7069 (mt) REVERT: C 435 TYR cc_start: 0.7434 (t80) cc_final: 0.7191 (t80) REVERT: D 93 PHE cc_start: 0.8841 (m-10) cc_final: 0.8477 (m-10) REVERT: D 130 GLN cc_start: 0.9479 (mp10) cc_final: 0.9209 (mp10) REVERT: D 176 PHE cc_start: 0.7965 (m-80) cc_final: 0.7560 (m-80) REVERT: D 216 HIS cc_start: 0.8155 (m-70) cc_final: 0.7820 (m-70) REVERT: D 288 PHE cc_start: 0.8338 (m-10) cc_final: 0.8023 (m-10) REVERT: D 302 ASN cc_start: 0.9358 (m-40) cc_final: 0.9103 (m-40) REVERT: D 342 LEU cc_start: 0.9444 (mm) cc_final: 0.9115 (mt) REVERT: D 391 PHE cc_start: 0.9216 (m-80) cc_final: 0.8422 (m-80) REVERT: D 434 MET cc_start: 0.3615 (ptm) cc_final: 0.2703 (tmm) REVERT: D 475 MET cc_start: 0.8574 (pmm) cc_final: 0.8211 (pmm) REVERT: E 635 ILE cc_start: 0.8881 (mm) cc_final: 0.8582 (tp) REVERT: E 652 GLN cc_start: 0.8362 (mp10) cc_final: 0.8144 (mp10) REVERT: F 575 GLN cc_start: 0.8420 (pp30) cc_final: 0.7256 (mp10) REVERT: F 584 GLU cc_start: 0.9292 (pt0) cc_final: 0.9005 (pt0) REVERT: F 588 ARG cc_start: 0.8084 (mmt180) cc_final: 0.7722 (mmt180) REVERT: F 643 TYR cc_start: 0.8995 (m-80) cc_final: 0.8616 (m-80) REVERT: J 51 MET cc_start: 0.8819 (tpt) cc_final: 0.8425 (tpt) REVERT: J 69 ILE cc_start: 0.7719 (tp) cc_final: 0.7334 (tp) REVERT: N 27 LEU cc_start: 0.8762 (tp) cc_final: 0.8557 (tp) REVERT: N 27 HIS cc_start: 0.8957 (t-90) cc_final: 0.8410 (t-90) REVERT: N 39 ARG cc_start: 0.6176 (mmt180) cc_final: 0.5430 (mmt180) REVERT: N 53 HIS cc_start: 0.8578 (t-90) cc_final: 0.8302 (t70) REVERT: N 87 TYR cc_start: 0.7478 (m-80) cc_final: 0.7178 (m-80) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.1217 time to fit residues: 67.5391 Evaluate side-chains 289 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 134 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 315 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN D 103 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 540 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.137682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.104216 restraints weight = 56627.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.107266 restraints weight = 42775.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.110526 restraints weight = 30834.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.110821 restraints weight = 26263.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.111084 restraints weight = 23690.835| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 17761 Z= 0.163 Angle : 0.888 17.665 24344 Z= 0.408 Chirality : 0.051 0.512 3070 Planarity : 0.004 0.075 2860 Dihedral : 5.574 41.483 2108 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.06 % Allowed : 0.98 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.19), residues: 1944 helix: -0.15 (0.26), residues: 425 sheet: -0.08 (0.22), residues: 499 loop : -0.65 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 273 TYR 0.014 0.001 TYR J 100M PHE 0.013 0.002 PHE D 382 TRP 0.064 0.002 TRP B 596 HIS 0.003 0.001 HIS J 52A Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (17598) covalent geometry : angle 0.78280 / 0.38 (23890) SS BOND : bond 0.00712 / 0.49 ( 35) SS BOND : angle 1.91850 / 1.27 ( 70) hydrogen bonds : bond 0.04247 / 2.88 ( 571) hydrogen bonds : angle 6.21706 / 4.31 ( 1542) link_ALPHA1-2 : bond 0.00272 / 0.14 ( 4) link_ALPHA1-2 : angle 1.59619 / 0.80 ( 12) link_ALPHA1-3 : bond 0.00678 / 0.42 ( 10) link_ALPHA1-3 : angle 1.36218 / 0.80 ( 30) link_ALPHA1-6 : bond 0.00553 / 0.36 ( 8) link_ALPHA1-6 : angle 1.41331 / 0.90 ( 24) link_BETA1-4 : bond 0.00566 / 0.37 ( 49) link_BETA1-4 : angle 1.84266 / 1.21 ( 147) link_NAG-ASN : bond 0.00690 / 0.45 ( 57) link_NAG-ASN : angle 4.63013 / 3.14 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7608 (mp0) cc_final: 0.7218 (mp0) REVERT: A 107 ASP cc_start: 0.8313 (m-30) cc_final: 0.7903 (m-30) REVERT: A 225 ILE cc_start: 0.7490 (mt) cc_final: 0.7263 (mt) REVERT: A 298 ARG cc_start: 0.8821 (ptm160) cc_final: 0.8277 (ptm-80) REVERT: A 395 TRP cc_start: 0.6170 (t-100) cc_final: 0.5912 (t-100) REVERT: B 586 TYR cc_start: 0.8733 (t80) cc_final: 0.8403 (t80) REVERT: B 646 LEU cc_start: 0.9158 (mt) cc_final: 0.8940 (mt) REVERT: C 47 ASP cc_start: 0.8818 (t0) cc_final: 0.8557 (t0) REVERT: C 271 MET cc_start: 0.6596 (tpt) cc_final: 0.6289 (tpt) REVERT: C 298 ARG cc_start: 0.8585 (tmm-80) cc_final: 0.7958 (tmm-80) REVERT: C 317 PHE cc_start: 0.9231 (t80) cc_final: 0.8983 (t80) REVERT: C 395 TRP cc_start: 0.6501 (t-100) cc_final: 0.6225 (t-100) REVERT: D 45 TRP cc_start: 0.7435 (p90) cc_final: 0.7217 (p90) REVERT: D 93 PHE cc_start: 0.8874 (m-10) cc_final: 0.8542 (m-10) REVERT: D 130 GLN cc_start: 0.9466 (mp10) cc_final: 0.9172 (pm20) REVERT: D 169 LYS cc_start: 0.7461 (ttpp) cc_final: 0.7258 (tttt) REVERT: D 176 PHE cc_start: 0.7943 (m-80) cc_final: 0.7520 (m-80) REVERT: D 216 HIS cc_start: 0.8239 (m-70) cc_final: 0.7856 (m-70) REVERT: D 288 PHE cc_start: 0.8265 (m-10) cc_final: 0.7972 (m-10) REVERT: D 342 LEU cc_start: 0.9453 (mm) cc_final: 0.9098 (mt) REVERT: D 383 PHE cc_start: 0.8586 (m-80) cc_final: 0.8360 (m-80) REVERT: D 391 PHE cc_start: 0.9177 (m-80) cc_final: 0.8356 (m-80) REVERT: D 453 ILE cc_start: 0.9143 (mp) cc_final: 0.8795 (mp) REVERT: D 475 MET cc_start: 0.8495 (pmm) cc_final: 0.8203 (pmm) REVERT: E 536 THR cc_start: 0.9395 (p) cc_final: 0.8907 (p) REVERT: E 540 GLN cc_start: 0.7339 (mm-40) cc_final: 0.6690 (mm-40) REVERT: E 635 ILE cc_start: 0.8919 (mm) cc_final: 0.8606 (tp) REVERT: E 652 GLN cc_start: 0.8171 (mp10) cc_final: 0.7954 (mp10) REVERT: F 588 ARG cc_start: 0.8003 (mmt180) cc_final: 0.7546 (mmt180) REVERT: F 601 LYS cc_start: 0.6969 (mppt) cc_final: 0.6246 (pttt) REVERT: F 643 TYR cc_start: 0.8967 (m-80) cc_final: 0.8596 (m-80) REVERT: J 51 MET cc_start: 0.8624 (tpt) cc_final: 0.8089 (mmm) REVERT: J 69 ILE cc_start: 0.7711 (tp) cc_final: 0.7337 (tp) REVERT: N 27 HIS cc_start: 0.8946 (t-90) cc_final: 0.8386 (t-90) REVERT: N 39 ARG cc_start: 0.6027 (mmt180) cc_final: 0.5312 (mmt180) REVERT: N 53 HIS cc_start: 0.8608 (t-90) cc_final: 0.8309 (t70) REVERT: N 87 TYR cc_start: 0.7498 (m-80) cc_final: 0.7143 (m-80) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.1206 time to fit residues: 67.0853 Evaluate side-chains 290 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 96 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 157 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 315 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.133756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.100722 restraints weight = 56997.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.103558 restraints weight = 41969.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106107 restraints weight = 31868.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.107153 restraints weight = 26107.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.107554 restraints weight = 23802.879| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 17761 Z= 0.204 Angle : 0.944 17.282 24344 Z= 0.432 Chirality : 0.053 0.502 3070 Planarity : 0.005 0.074 2860 Dihedral : 5.792 41.687 2108 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.06 % Allowed : 0.46 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.18), residues: 1944 helix: -0.35 (0.25), residues: 427 sheet: -0.28 (0.22), residues: 494 loop : -0.73 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 273 TYR 0.015 0.002 TYR C 61 PHE 0.019 0.002 PHE C 93 TRP 0.054 0.003 TRP B 596 HIS 0.006 0.001 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (17598) covalent geometry : angle 0.83380 / 0.41 (23890) SS BOND : bond 0.00572 / 0.37 ( 35) SS BOND : angle 2.04058 / 1.37 ( 70) hydrogen bonds : bond 0.04522 / 3.12 ( 571) hydrogen bonds : angle 6.42578 / 4.46 ( 1542) link_ALPHA1-2 : bond 0.00282 / 0.14 ( 4) link_ALPHA1-2 : angle 1.68556 / 0.84 ( 12) link_ALPHA1-3 : bond 0.00683 / 0.44 ( 10) link_ALPHA1-3 : angle 1.41189 / 0.83 ( 30) link_ALPHA1-6 : bond 0.00661 / 0.46 ( 8) link_ALPHA1-6 : angle 1.44335 / 0.92 ( 24) link_BETA1-4 : bond 0.00637 / 0.42 ( 49) link_BETA1-4 : angle 1.97922 / 1.31 ( 147) link_NAG-ASN : bond 0.00765 / 0.47 ( 57) link_NAG-ASN : angle 4.87727 / 3.32 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7617 (mp0) cc_final: 0.6960 (mp0) REVERT: A 164 GLU cc_start: 0.7828 (mp0) cc_final: 0.7360 (tt0) REVERT: A 271 MET cc_start: 0.1527 (ttt) cc_final: 0.0342 (ttt) REVERT: A 298 ARG cc_start: 0.8869 (ptm160) cc_final: 0.8396 (ptm-80) REVERT: A 383 PHE cc_start: 0.9061 (m-80) cc_final: 0.8554 (m-80) REVERT: A 423 ILE cc_start: 0.8281 (mm) cc_final: 0.8032 (mm) REVERT: A 435 TYR cc_start: 0.8344 (t80) cc_final: 0.7968 (t80) REVERT: B 586 TYR cc_start: 0.8757 (t80) cc_final: 0.8439 (t80) REVERT: B 596 TRP cc_start: 0.9031 (m-90) cc_final: 0.8803 (m-90) REVERT: B 646 LEU cc_start: 0.9128 (mt) cc_final: 0.8871 (mt) REVERT: C 180 ASP cc_start: 0.7449 (m-30) cc_final: 0.6864 (m-30) REVERT: C 271 MET cc_start: 0.6548 (tpt) cc_final: 0.6246 (tpt) REVERT: C 298 ARG cc_start: 0.8533 (tmm-80) cc_final: 0.7945 (tmm-80) REVERT: C 395 TRP cc_start: 0.6386 (t-100) cc_final: 0.6092 (t-100) REVERT: C 423 ILE cc_start: 0.8064 (mt) cc_final: 0.7424 (mt) REVERT: D 93 PHE cc_start: 0.9000 (m-10) cc_final: 0.8674 (m-10) REVERT: D 130 GLN cc_start: 0.9469 (mp10) cc_final: 0.9246 (mp10) REVERT: D 176 PHE cc_start: 0.8057 (m-80) cc_final: 0.7651 (m-80) REVERT: D 180 ASP cc_start: 0.7373 (m-30) cc_final: 0.7058 (m-30) REVERT: D 216 HIS cc_start: 0.8199 (m-70) cc_final: 0.7857 (m-70) REVERT: D 288 PHE cc_start: 0.8325 (m-10) cc_final: 0.7995 (m-10) REVERT: D 342 LEU cc_start: 0.9495 (mm) cc_final: 0.9052 (mt) REVERT: D 391 PHE cc_start: 0.9132 (m-80) cc_final: 0.8328 (m-80) REVERT: D 434 MET cc_start: 0.3826 (ptm) cc_final: 0.2869 (tmm) REVERT: D 475 MET cc_start: 0.8556 (pmm) cc_final: 0.8315 (pmm) REVERT: E 581 LEU cc_start: 0.9477 (mm) cc_final: 0.9238 (mm) REVERT: E 588 ARG cc_start: 0.9235 (ptp-110) cc_final: 0.9005 (mtm110) REVERT: E 635 ILE cc_start: 0.9005 (mm) cc_final: 0.8670 (tp) REVERT: F 588 ARG cc_start: 0.8062 (mmt180) cc_final: 0.7857 (mmt180) REVERT: F 601 LYS cc_start: 0.6845 (mppt) cc_final: 0.6185 (pttt) REVERT: F 643 TYR cc_start: 0.8914 (m-80) cc_final: 0.8370 (m-80) REVERT: J 46 GLU cc_start: 0.8314 (mp0) cc_final: 0.7780 (pm20) REVERT: J 48 MET cc_start: 0.9205 (mtm) cc_final: 0.8358 (mmm) REVERT: J 51 MET cc_start: 0.8623 (tpt) cc_final: 0.8036 (mmm) REVERT: J 69 ILE cc_start: 0.7809 (tp) cc_final: 0.7548 (tp) REVERT: J 97 LYS cc_start: 0.9537 (pttp) cc_final: 0.9110 (pttp) REVERT: N 39 ARG cc_start: 0.6097 (mmt180) cc_final: 0.5417 (mmt180) REVERT: N 53 HIS cc_start: 0.8703 (t-90) cc_final: 0.8404 (t70) REVERT: N 87 TYR cc_start: 0.7568 (m-80) cc_final: 0.7075 (m-80) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.1278 time to fit residues: 69.3994 Evaluate side-chains 288 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 134 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 315 GLN C 348 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 540 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.137050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.103544 restraints weight = 54766.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.106775 restraints weight = 39421.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.109744 restraints weight = 29320.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.110605 restraints weight = 23677.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.111313 restraints weight = 21513.008| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 17761 Z= 0.143 Angle : 0.894 16.605 24344 Z= 0.406 Chirality : 0.052 0.534 3070 Planarity : 0.004 0.071 2860 Dihedral : 5.628 40.110 2108 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.06 % Allowed : 0.46 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1944 helix: -0.01 (0.26), residues: 423 sheet: -0.17 (0.22), residues: 488 loop : -0.70 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 273 TYR 0.015 0.001 TYR J 100M PHE 0.016 0.002 PHE D 382 TRP 0.061 0.002 TRP B 596 HIS 0.006 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (17598) covalent geometry : angle 0.78861 / 0.38 (23890) SS BOND : bond 0.00544 / 0.36 ( 35) SS BOND : angle 1.77543 / 1.18 ( 70) hydrogen bonds : bond 0.04228 / 2.92 ( 571) hydrogen bonds : angle 6.12751 / 4.25 ( 1542) link_ALPHA1-2 : bond 0.00316 / 0.16 ( 4) link_ALPHA1-2 : angle 1.59566 / 0.80 ( 12) link_ALPHA1-3 : bond 0.00714 / 0.43 ( 10) link_ALPHA1-3 : angle 1.34128 / 0.79 ( 30) link_ALPHA1-6 : bond 0.00557 / 0.35 ( 8) link_ALPHA1-6 : angle 1.40521 / 0.89 ( 24) link_BETA1-4 : bond 0.00538 / 0.35 ( 49) link_BETA1-4 : angle 1.84493 / 1.22 ( 147) link_NAG-ASN : bond 0.00761 / 0.50 ( 57) link_NAG-ASN : angle 4.67916 / 3.17 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2656.64 seconds wall clock time: 47 minutes 2.40 seconds (2822.40 seconds total)