Starting phenix.real_space_refine on Sat Jul 4 01:25:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g9w_29880/07_2026/8g9w_29880.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9w_29880/07_2026/8g9w_29880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g9w_29880/07_2026/8g9w_29880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9w_29880/07_2026/8g9w_29880.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8g9w_29880/07_2026/8g9w_29880.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g9w_29880/07_2026/8g9w_29880.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g9w_29880/07_2026/8g9w_29880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9w_29880/07_2026/8g9w_29880.map" } resolution = 4.66 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= 0.010 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 10664 2.51 5 N 2809 2.21 5 O 3547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 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: 17135 Number of models: 1 Model: "" Number of chains: 53 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "E" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "G" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 100} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "P" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 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: "C" 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: "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 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: "Q" 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: "R" 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: "S" 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: "T" 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: "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: 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: "X" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: 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: 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: "f" 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: "g" 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: "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: 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: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 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: "r" 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: "s" 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: "t" 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: "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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" 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: "G" 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: "O" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" 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 Time building chain proxies: 2.96, per 1000 atoms: 0.17 Number of scatterers: 17135 At special positions: 0 Unit cell: (142.742, 138.449, 132.01, 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 115 16.00 O 3547 8.00 N 2809 7.00 C 10664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS P 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.02 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS O 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.02 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 598 " - pdb=" SG CYS O 604 " distance=2.02 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 74 " distance=2.03 Simple disulfide: pdb=" SG CYS P 119 " - pdb=" SG CYS P 205 " distance=2.04 Simple disulfide: pdb=" SG CYS P 126 " - pdb=" SG CYS P 196 " distance=2.03 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.03 Simple disulfide: pdb=" SG CYS P 201 " - pdb=" SG CYS P 433 " distance=2.03 Simple disulfide: pdb=" SG CYS P 218 " - pdb=" SG CYS P 247 " distance=2.02 Simple disulfide: pdb=" SG CYS P 228 " - pdb=" SG CYS P 239 " distance=2.02 Simple disulfide: pdb=" SG CYS P 296 " - pdb=" SG CYS P 331 " distance=2.02 Simple disulfide: pdb=" SG CYS P 378 " - pdb=" SG CYS P 445 " distance=2.03 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA S 3 " - " MAN S 4 " " BMA a 3 " - " MAN a 4 " " BMA f 3 " - " MAN f 4 " " BMA n 3 " - " MAN n 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA f 3 " - " MAN f 5 " " BMA s 3 " - " MAN s 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG F 1 " - " NAG F 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " 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 r 2 " - " BMA r 3 " " 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 u 1 " - " NAG u 2 " NAG-ASN " NAG A 1 " - " ASN E 88 " " NAG B 701 " - " ASN B 637 " " NAG C 1 " - " ASN E 156 " " NAG D 701 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 339 " " NAG E 603 " - " ASN E 355 " " NAG E 604 " - " ASN E 276 " " NAG F 1 " - " ASN E 160 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 339 " " NAG G 603 " - " ASN G 355 " " NAG G 604 " - " ASN G 276 " " NAG I 1 " - " ASN E 197 " " NAG J 1 " - " ASN E 234 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN E 295 " " NAG N 1 " - " ASN E 301 " " NAG O 701 " - " ASN O 637 " " NAG P 601 " - " ASN P 133 " " NAG P 602 " - " ASN P 339 " " NAG P 603 " - " ASN P 355 " " NAG P 604 " - " ASN P 276 " " NAG Q 1 " - " ASN E 332 " " NAG R 1 " - " ASN E 363 " " NAG S 1 " - " ASN E 386 " " NAG T 1 " - " ASN E 392 " " NAG U 1 " - " ASN E 448 " " NAG V 1 " - " ASN G 88 " " NAG W 1 " - " ASN G 156 " " NAG X 1 " - " ASN G 160 " " NAG Y 1 " - " ASN G 197 " " NAG Z 1 " - " ASN G 234 " " NAG a 1 " - " ASN G 262 " " NAG b 1 " - " ASN G 295 " " NAG c 1 " - " ASN G 301 " " NAG d 1 " - " ASN G 332 " " NAG e 1 " - " ASN G 363 " " NAG f 1 " - " ASN G 386 " " NAG g 1 " - " ASN G 392 " " NAG h 1 " - " ASN G 448 " " NAG i 1 " - " ASN P 88 " " NAG j 1 " - " ASN P 156 " " NAG k 1 " - " ASN P 160 " " NAG l 1 " - " ASN P 197 " " NAG m 1 " - " ASN P 234 " " NAG n 1 " - " ASN P 262 " " NAG o 1 " - " ASN P 295 " " NAG p 1 " - " ASN P 301 " " NAG q 1 " - " ASN P 332 " " NAG r 1 " - " ASN P 363 " " NAG s 1 " - " ASN P 386 " " NAG t 1 " - " ASN P 392 " " NAG u 1 " - " ASN P 448 " Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 698.0 milliseconds 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 42 sheets defined 20.8% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.865A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 removed outlier: 3.833A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 641 through 664 removed outlier: 3.694A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.566A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 removed outlier: 3.946A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.203A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.542A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 664 removed outlier: 3.641A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.748A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 115 removed outlier: 3.574A pdb=" N MET E 104 " --> pdb=" O MET E 100 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.915A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.614A pdb=" N LYS E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.279A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.830A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.711A pdb=" N GLU G 62 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.568A pdb=" N HIS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.827A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.801A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.294A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.776A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.522A pdb=" N PHE L 83 " --> pdb=" O THR L 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 534 Processing helix chain 'O' and resid 537 through 543 removed outlier: 3.535A pdb=" N ALA O 541 " --> pdb=" O LEU O 537 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN O 543 " --> pdb=" O VAL O 539 " (cutoff:3.500A) Processing helix chain 'O' and resid 572 through 595 removed outlier: 3.756A pdb=" N LEU O 581 " --> pdb=" O GLN O 577 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU O 584 " --> pdb=" O VAL O 580 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP O 589 " --> pdb=" O ARG O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 611 through 616 removed outlier: 4.381A pdb=" N SER O 615 " --> pdb=" O ASN O 611 " (cutoff:3.500A) Processing helix chain 'O' and resid 627 through 636 removed outlier: 3.515A pdb=" N LYS O 633 " --> pdb=" O LEU O 629 " (cutoff:3.500A) Processing helix chain 'O' and resid 641 through 664 removed outlier: 3.682A pdb=" N GLU O 647 " --> pdb=" O TYR O 643 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU O 648 " --> pdb=" O GLY O 644 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN O 653 " --> pdb=" O SER O 649 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU O 663 " --> pdb=" O ASP O 659 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP O 664 " --> pdb=" O LEU O 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.658A pdb=" N GLU P 62 " --> pdb=" O LYS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 115 removed outlier: 3.645A pdb=" N MET P 104 " --> pdb=" O MET P 100 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS P 105 " --> pdb=" O VAL P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 126 removed outlier: 3.924A pdb=" N LEU P 125 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 354 removed outlier: 3.577A pdb=" N LYS P 347 " --> pdb=" O GLY P 343 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG P 350 " --> pdb=" O VAL P 346 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS P 351 " --> pdb=" O LYS P 347 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS P 352 " --> pdb=" O GLN P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 425 through 429 removed outlier: 4.315A pdb=" N ARG P 429 " --> pdb=" O MET P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 475 through 480 removed outlier: 3.871A pdb=" N TRP P 479 " --> pdb=" O MET P 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 604 removed outlier: 4.225A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL G 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 603 through 604 removed outlier: 3.760A pdb=" N CYS D 604 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL P 38 " --> pdb=" O CYS D 604 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 495 through 499 removed outlier: 3.678A pdb=" N VAL E 38 " --> pdb=" O CYS O 604 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS O 604 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.817A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU E 86 " --> pdb=" O VAL E 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.832A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'E' and resid 159 through 162 Processing sheet with id=AA8, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.801A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.033A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.864A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.495A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.801A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 297 through 298 Processing sheet with id=AB3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.592A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 330 through 334 Processing sheet with id=AB5, first strand: chain 'E' and resid 375 through 378 Processing sheet with id=AB6, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.793A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 91 through 92 Processing sheet with id=AB8, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AB9, first strand: chain 'G' and resid 159 through 162 Processing sheet with id=AC1, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AC2, first strand: chain 'G' and resid 260 through 261 removed outlier: 7.091A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 11.106A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 12.062A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.695A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 260 through 261 removed outlier: 7.091A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 297 through 298 Processing sheet with id=AC5, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.643A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 330 through 334 Processing sheet with id=AC7, first strand: chain 'G' and resid 375 through 378 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.796A pdb=" N LEU H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.795A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG H 94 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.937A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.246A pdb=" N LEU L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LYS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.975A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 45 through 47 removed outlier: 4.660A pdb=" N VAL P 242 " --> pdb=" O LEU P 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 91 through 92 Processing sheet with id=AD7, first strand: chain 'P' and resid 154 through 155 Processing sheet with id=AD8, first strand: chain 'P' and resid 159 through 162 Processing sheet with id=AD9, first strand: chain 'P' and resid 181 through 183 Processing sheet with id=AE1, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.806A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY P 451 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N THR P 290 " --> pdb=" O GLY P 451 " (cutoff:3.500A) removed outlier: 11.337A pdb=" N ILE P 453 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 11.899A pdb=" N PHE P 288 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N THR P 455 " --> pdb=" O VAL P 286 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N VAL P 286 " --> pdb=" O THR P 455 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG P 273 " --> pdb=" O LEU P 285 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.806A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG P 360 " --> pdb=" O PHE P 468 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER P 393 " --> pdb=" O PHE P 361 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 297 through 298 Processing sheet with id=AE4, first strand: chain 'P' and resid 304 through 312 removed outlier: 6.745A pdb=" N GLN P 315 " --> pdb=" O ILE P 309 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 330 through 334 Processing sheet with id=AE6, first strand: chain 'P' and resid 375 through 378 475 hydrogen bonds defined for protein. 1227 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: 2.61 Time building geometry restraints manager: 1.87 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: 5281 1.34 - 1.47: 4494 1.47 - 1.59: 7522 1.59 - 1.72: 0 1.72 - 1.84: 154 Bond restraints: 17451 Sorted by residual: bond pdb=" C1 BMA R 3 " pdb=" C2 BMA R 3 " ideal model delta sigma weight residual 1.519 1.573 -0.054 2.00e-02 2.50e+03 7.38e+00 bond pdb=" CG GLU D 584 " pdb=" CD GLU D 584 " ideal model delta sigma weight residual 1.516 1.455 0.061 2.50e-02 1.60e+03 5.99e+00 bond pdb=" CB GLN D 658 " pdb=" CG GLN D 658 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.85e+00 bond pdb=" CB ASN E 276 " pdb=" CG ASN E 276 " ideal model delta sigma weight residual 1.516 1.462 0.054 2.50e-02 1.60e+03 4.63e+00 bond pdb=" C1 MAN f 4 " pdb=" O5 MAN f 4 " ideal model delta sigma weight residual 1.399 1.440 -0.041 2.00e-02 2.50e+03 4.14e+00 ... (remaining 17446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 23139 3.85 - 7.70: 495 7.70 - 11.56: 43 11.56 - 15.41: 4 15.41 - 19.26: 2 Bond angle restraints: 23683 Sorted by residual: angle pdb=" CB MET P 100 " pdb=" CG MET P 100 " pdb=" SD MET P 100 " ideal model delta sigma weight residual 112.70 131.96 -19.26 3.00e+00 1.11e-01 4.12e+01 angle pdb=" N GLU D 657 " pdb=" CA GLU D 657 " pdb=" CB GLU D 657 " ideal model delta sigma weight residual 110.28 120.07 -9.79 1.55e+00 4.16e-01 3.99e+01 angle pdb=" CB MET E 100 " pdb=" CG MET E 100 " pdb=" SD MET E 100 " ideal model delta sigma weight residual 112.70 131.37 -18.67 3.00e+00 1.11e-01 3.87e+01 angle pdb=" N GLY P 152 " pdb=" CA GLY P 152 " pdb=" C GLY P 152 " ideal model delta sigma weight residual 113.18 99.03 14.15 2.37e+00 1.78e-01 3.56e+01 angle pdb=" CA MET E 100 " pdb=" CB MET E 100 " pdb=" CG MET E 100 " ideal model delta sigma weight residual 114.10 124.85 -10.75 2.00e+00 2.50e-01 2.89e+01 ... (remaining 23678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 8385 16.25 - 32.49: 935 32.49 - 48.74: 190 48.74 - 64.98: 26 64.98 - 81.23: 28 Dihedral angle restraints: 9564 sinusoidal: 3863 harmonic: 5701 Sorted by residual: dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -156.84 70.84 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS P 126 " pdb=" SG CYS P 126 " pdb=" SG CYS P 196 " pdb=" CB CYS P 196 " ideal model delta sinusoidal sigma weight residual 93.00 161.21 -68.21 1 1.00e+01 1.00e-02 6.04e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -154.11 68.11 1 1.00e+01 1.00e-02 6.02e+01 ... (remaining 9561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2688 0.108 - 0.216: 285 0.216 - 0.324: 42 0.324 - 0.432: 3 0.432 - 0.540: 2 Chirality restraints: 3020 Sorted by residual: chirality pdb=" CB ILE G 284 " pdb=" CA ILE G 284 " pdb=" CG1 ILE G 284 " pdb=" CG2 ILE G 284 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.54 2.00e-01 2.50e+01 7.29e+00 chirality pdb=" C1 NAG t 1 " pdb=" ND2 ASN P 392 " pdb=" C2 NAG t 1 " pdb=" O5 NAG t 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 5.98e+00 ... (remaining 3017 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 581 " 0.022 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C LEU D 581 " -0.078 2.00e-02 2.50e+03 pdb=" O LEU D 581 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA D 582 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 574 " 0.022 2.00e-02 2.50e+03 4.42e-02 1.96e+01 pdb=" C LYS D 574 " -0.077 2.00e-02 2.50e+03 pdb=" O LYS D 574 " 0.029 2.00e-02 2.50e+03 pdb=" N GLN D 575 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN P 99 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C ASN P 99 " 0.073 2.00e-02 2.50e+03 pdb=" O ASN P 99 " -0.028 2.00e-02 2.50e+03 pdb=" N MET P 100 " -0.024 2.00e-02 2.50e+03 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1840 2.73 - 3.27: 17135 3.27 - 3.81: 28522 3.81 - 4.36: 32828 4.36 - 4.90: 55521 Nonbonded interactions: 135846 Sorted by model distance: nonbonded pdb=" O SER D 649 " pdb=" NE2 GLN D 653 " model vdw 2.186 3.120 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR P 61 " pdb=" O CYS P 74 " model vdw 2.215 3.040 nonbonded pdb=" OG SER L 12 " pdb=" OE2 GLU L 105 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASN E 302 " pdb=" OG1 THR E 320 " model vdw 2.223 3.040 ... (remaining 135841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'u' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'j' selection = chain 'q' selection = chain 'r' selection = chain 't' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'a' selection = chain 'n' } ncs_group { reference = chain 'S' selection = chain 'f' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.420 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.008 0.068 17609 Z= 0.403 Angle : 1.416 19.262 24119 Z= 0.713 Chirality : 0.073 0.540 3020 Planarity : 0.008 0.057 2855 Dihedral : 14.176 81.228 5770 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.83 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -4.89 (0.15), residues: 1949 helix: -4.60 (0.10), residues: 432 sheet: -2.91 (0.19), residues: 547 loop : -2.69 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG G 327 TYR 0.027 0.003 TYR D 638 PHE 0.033 0.004 PHE P 176 TRP 0.050 0.005 TRP E 427 HIS 0.012 0.003 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00808 / 0.40 (17451) covalent geometry : angle 1.35617 / 0.70 (23683) SS BOND : bond 0.00589 / 0.40 ( 38) SS BOND : angle 2.62946 / 1.79 ( 76) hydrogen bonds : bond 0.15487 / 10.15 ( 461) hydrogen bonds : angle 8.83581 / 6.04 ( 1227) link_ALPHA1-3 : bond 0.00352 / 0.20 ( 6) link_ALPHA1-3 : angle 1.88665 / 1.23 ( 18) link_ALPHA1-6 : bond 0.00432 / 0.22 ( 3) link_ALPHA1-6 : angle 1.56214 / 0.90 ( 9) link_BETA1-4 : bond 0.00906 / 0.67 ( 57) link_BETA1-4 : angle 2.64136 / 1.76 ( 171) link_NAG-ASN : bond 0.00893 / 0.63 ( 54) link_NAG-ASN : angle 4.28632 / 2.87 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: B 530 MET cc_start: 0.9138 (mpp) cc_final: 0.8395 (mpp) REVERT: G 45 TRP cc_start: 0.9545 (p90) cc_final: 0.9181 (p90) REVERT: P 95 MET cc_start: 0.9482 (pmm) cc_final: 0.9226 (pmm) REVERT: P 161 MET cc_start: 0.9255 (tpt) cc_final: 0.8548 (tpt) REVERT: P 475 MET cc_start: 0.8644 (pmm) cc_final: 0.8245 (pmm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0979 time to fit residues: 10.7524 Evaluate side-chains 55 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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: 7.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0060 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 607 ASN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN ** O 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 658 GLN P 103 GLN P 289 ASN ** P 374 HIS ** 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 = 0.2869 r_free = 0.2869 target = 0.028750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.023670 restraints weight = 299671.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.024372 restraints weight = 159614.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.024841 restraints weight = 103875.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.025160 restraints weight = 76199.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.025384 restraints weight = 60751.641| |-----------------------------------------------------------------------------| r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17609 Z= 0.160 Angle : 0.757 9.713 24119 Z= 0.372 Chirality : 0.044 0.274 3020 Planarity : 0.005 0.035 2855 Dihedral : 6.209 29.497 2108 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.17), residues: 1949 helix: -2.80 (0.19), residues: 418 sheet: -2.62 (0.19), residues: 549 loop : -2.19 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 298 TYR 0.019 0.001 TYR D 638 PHE 0.015 0.002 PHE P 288 TRP 0.025 0.002 TRP E 427 HIS 0.005 0.001 HIS P 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (17451) covalent geometry : angle 0.70983 / 0.36 (23683) SS BOND : bond 0.00638 / 0.48 ( 38) SS BOND : angle 1.36813 / 0.99 ( 76) hydrogen bonds : bond 0.04122 / 2.68 ( 461) hydrogen bonds : angle 6.57447 / 4.44 ( 1227) link_ALPHA1-3 : bond 0.00651 / 0.38 ( 6) link_ALPHA1-3 : angle 1.75270 / 1.16 ( 18) link_ALPHA1-6 : bond 0.00462 / 0.24 ( 3) link_ALPHA1-6 : angle 1.40733 / 0.84 ( 9) link_BETA1-4 : bond 0.00545 / 0.40 ( 57) link_BETA1-4 : angle 1.75986 / 1.20 ( 171) link_NAG-ASN : bond 0.00357 / 0.25 ( 54) link_NAG-ASN : angle 2.66502 / 1.80 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.551 Fit side-chains REVERT: B 530 MET cc_start: 0.8838 (mpp) cc_final: 0.8274 (mpp) REVERT: D 530 MET cc_start: 0.9335 (mpp) cc_final: 0.7413 (mpp) REVERT: D 626 MET cc_start: 0.8181 (tmm) cc_final: 0.7121 (ppp) REVERT: E 95 MET cc_start: 0.9721 (ppp) cc_final: 0.8743 (ppp) REVERT: E 285 LEU cc_start: 0.9829 (mp) cc_final: 0.9506 (tt) REVERT: G 45 TRP cc_start: 0.9469 (p90) cc_final: 0.9008 (p90) REVERT: G 161 MET cc_start: 0.9155 (tmm) cc_final: 0.8765 (tmm) REVERT: L 85 MET cc_start: 0.9514 (tpt) cc_final: 0.9312 (tpp) REVERT: P 95 MET cc_start: 0.9446 (pmm) cc_final: 0.9079 (pmm) REVERT: P 100 MET cc_start: 0.9004 (pmm) cc_final: 0.8709 (pmm) REVERT: P 161 MET cc_start: 0.9094 (tpt) cc_final: 0.8388 (tpt) REVERT: P 271 MET cc_start: 0.9657 (mmp) cc_final: 0.9333 (mmm) REVERT: P 475 MET cc_start: 0.8543 (pmm) cc_final: 0.8032 (pmm) REVERT: P 483 LEU cc_start: 0.9854 (mt) cc_final: 0.9561 (tp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1191 time to fit residues: 12.7471 Evaluate side-chains 53 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 145 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 123 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 656 ASN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 GLN P 432 GLN P 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.023557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.017399 restraints weight = 281896.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.017979 restraints weight = 180138.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.018400 restraints weight = 132184.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.018703 restraints weight = 105731.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.018922 restraints weight = 89717.412| |-----------------------------------------------------------------------------| r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17609 Z= 0.219 Angle : 0.783 9.328 24119 Z= 0.381 Chirality : 0.043 0.273 3020 Planarity : 0.004 0.065 2855 Dihedral : 5.888 31.349 2108 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % 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: -3.06 (0.18), residues: 1949 helix: -1.58 (0.24), residues: 427 sheet: -2.51 (0.20), residues: 522 loop : -1.88 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 469 TYR 0.016 0.002 TYR O 638 PHE 0.021 0.002 PHE P 176 TRP 0.024 0.002 TRP P 479 HIS 0.007 0.002 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.22 (17451) covalent geometry : angle 0.74137 / 0.37 (23683) SS BOND : bond 0.01057 / 0.79 ( 38) SS BOND : angle 1.18209 / 0.80 ( 76) hydrogen bonds : bond 0.03762 / 2.47 ( 461) hydrogen bonds : angle 6.17536 / 4.15 ( 1227) link_ALPHA1-3 : bond 0.00629 / 0.38 ( 6) link_ALPHA1-3 : angle 1.53006 / 1.02 ( 18) link_ALPHA1-6 : bond 0.00396 / 0.20 ( 3) link_ALPHA1-6 : angle 1.51175 / 0.88 ( 9) link_BETA1-4 : bond 0.00457 / 0.34 ( 57) link_BETA1-4 : angle 1.73410 / 1.18 ( 171) link_NAG-ASN : bond 0.00591 / 0.42 ( 54) link_NAG-ASN : angle 2.59929 / 1.77 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.664 Fit side-chains REVERT: D 530 MET cc_start: 0.9115 (mpp) cc_final: 0.8590 (mmt) REVERT: E 100 MET cc_start: 0.9369 (pmm) cc_final: 0.9089 (pmm) REVERT: L 85 MET cc_start: 0.9528 (tpt) cc_final: 0.9305 (tpp) REVERT: P 95 MET cc_start: 0.9476 (pmm) cc_final: 0.9140 (pmm) REVERT: P 100 MET cc_start: 0.8988 (pmm) cc_final: 0.8725 (pmm) REVERT: P 161 MET cc_start: 0.9003 (tpt) cc_final: 0.8277 (tpt) REVERT: P 271 MET cc_start: 0.9607 (mmp) cc_final: 0.9166 (mmm) REVERT: P 426 MET cc_start: 0.9622 (pmm) cc_final: 0.9389 (pmm) REVERT: P 434 MET cc_start: 0.9729 (tpp) cc_final: 0.9492 (tpp) REVERT: P 475 MET cc_start: 0.8772 (pmm) cc_final: 0.8148 (pmm) REVERT: P 483 LEU cc_start: 0.9885 (mt) cc_final: 0.9643 (tp) outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.0985 time to fit residues: 11.1632 Evaluate side-chains 52 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 154 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 GLN ** P 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.023185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.017189 restraints weight = 288944.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.017756 restraints weight = 186449.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.018170 restraints weight = 137186.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.018466 restraints weight = 109887.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.018680 restraints weight = 93354.745| |-----------------------------------------------------------------------------| r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17609 Z= 0.218 Angle : 0.768 9.394 24119 Z= 0.372 Chirality : 0.044 0.269 3020 Planarity : 0.004 0.038 2855 Dihedral : 5.789 29.684 2108 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.18), residues: 1949 helix: -1.43 (0.24), residues: 435 sheet: -2.37 (0.21), residues: 492 loop : -1.65 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 585 TYR 0.018 0.002 TYR D 638 PHE 0.019 0.002 PHE P 176 TRP 0.020 0.002 TRP P 479 HIS 0.007 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.22 (17451) covalent geometry : angle 0.72825 / 0.36 (23683) SS BOND : bond 0.00518 / 0.36 ( 38) SS BOND : angle 1.32505 / 0.90 ( 76) hydrogen bonds : bond 0.03615 / 2.37 ( 461) hydrogen bonds : angle 6.08476 / 4.07 ( 1227) link_ALPHA1-3 : bond 0.00537 / 0.35 ( 6) link_ALPHA1-3 : angle 1.59436 / 1.07 ( 18) link_ALPHA1-6 : bond 0.00387 / 0.20 ( 3) link_ALPHA1-6 : angle 1.46801 / 0.86 ( 9) link_BETA1-4 : bond 0.00444 / 0.33 ( 57) link_BETA1-4 : angle 1.65583 / 1.13 ( 171) link_NAG-ASN : bond 0.00556 / 0.38 ( 54) link_NAG-ASN : angle 2.49784 / 1.71 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: D 530 MET cc_start: 0.9115 (mpp) cc_final: 0.8569 (mmt) REVERT: L 85 MET cc_start: 0.9515 (tpt) cc_final: 0.9287 (tpp) REVERT: O 530 MET cc_start: 0.8489 (mmp) cc_final: 0.8240 (mmp) REVERT: P 95 MET cc_start: 0.9522 (pmm) cc_final: 0.9167 (pmm) REVERT: P 100 MET cc_start: 0.8939 (pmm) cc_final: 0.8676 (pmm) REVERT: P 161 MET cc_start: 0.8942 (tpt) cc_final: 0.8192 (tpt) REVERT: P 271 MET cc_start: 0.9554 (mmp) cc_final: 0.9059 (mmm) REVERT: P 426 MET cc_start: 0.9660 (pmm) cc_final: 0.9393 (pmm) REVERT: P 475 MET cc_start: 0.8848 (pmm) cc_final: 0.8570 (pmm) REVERT: P 483 LEU cc_start: 0.9908 (mt) cc_final: 0.9641 (tp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1059 time to fit residues: 10.5217 Evaluate side-chains 49 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 178 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 131 optimal weight: 30.0000 chunk 151 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 160 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 GLN G 114 GLN G 315 GLN G 478 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.025714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.020835 restraints weight = 318837.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.021463 restraints weight = 177725.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.021899 restraints weight = 117882.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.022193 restraints weight = 87802.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.022394 restraints weight = 71159.128| |-----------------------------------------------------------------------------| r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17609 Z= 0.229 Angle : 0.794 11.758 24119 Z= 0.382 Chirality : 0.044 0.269 3020 Planarity : 0.004 0.037 2855 Dihedral : 5.854 31.944 2108 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % 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: -2.72 (0.18), residues: 1949 helix: -1.39 (0.23), residues: 450 sheet: -2.41 (0.21), residues: 486 loop : -1.60 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 419 TYR 0.023 0.002 TYR D 638 PHE 0.021 0.002 PHE P 176 TRP 0.019 0.002 TRP O 596 HIS 0.008 0.002 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.23 (17451) covalent geometry : angle 0.75504 / 0.37 (23683) SS BOND : bond 0.00511 / 0.35 ( 38) SS BOND : angle 1.28450 / 0.88 ( 76) hydrogen bonds : bond 0.03656 / 2.43 ( 461) hydrogen bonds : angle 6.10195 / 4.08 ( 1227) link_ALPHA1-3 : bond 0.00572 / 0.35 ( 6) link_ALPHA1-3 : angle 1.57868 / 1.05 ( 18) link_ALPHA1-6 : bond 0.00382 / 0.19 ( 3) link_ALPHA1-6 : angle 1.44498 / 0.85 ( 9) link_BETA1-4 : bond 0.00412 / 0.31 ( 57) link_BETA1-4 : angle 1.67647 / 1.15 ( 171) link_NAG-ASN : bond 0.00594 / 0.42 ( 54) link_NAG-ASN : angle 2.54954 / 1.74 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9056 (mpp) cc_final: 0.8358 (mpp) REVERT: B 626 MET cc_start: 0.9358 (pmm) cc_final: 0.9083 (pmm) REVERT: D 530 MET cc_start: 0.9103 (mpp) cc_final: 0.8586 (mmt) REVERT: G 475 MET cc_start: 0.9071 (pmm) cc_final: 0.8865 (pmm) REVERT: L 85 MET cc_start: 0.9523 (tpt) cc_final: 0.9286 (tpp) REVERT: O 530 MET cc_start: 0.8480 (mmp) cc_final: 0.8259 (mmp) REVERT: P 95 MET cc_start: 0.9517 (pmm) cc_final: 0.9190 (pmm) REVERT: P 161 MET cc_start: 0.9036 (tpt) cc_final: 0.8547 (tpp) REVERT: P 271 MET cc_start: 0.9472 (mmp) cc_final: 0.8987 (mmm) REVERT: P 426 MET cc_start: 0.9684 (pmm) cc_final: 0.9386 (pmm) REVERT: P 475 MET cc_start: 0.8800 (pmm) cc_final: 0.8315 (pmm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1115 time to fit residues: 10.6413 Evaluate side-chains 50 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 3 optimal weight: 10.0000 chunk 144 optimal weight: 0.0030 chunk 98 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 125 optimal weight: 40.0000 chunk 88 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 overall best weight: 2.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 543 ASN D 658 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN O 656 ASN P 315 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.026420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.021482 restraints weight = 313322.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.022137 restraints weight = 171058.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.022581 restraints weight = 112752.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.022880 restraints weight = 83425.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.023071 restraints weight = 67131.782| |-----------------------------------------------------------------------------| r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17609 Z= 0.152 Angle : 0.703 9.713 24119 Z= 0.336 Chirality : 0.044 0.268 3020 Planarity : 0.004 0.034 2855 Dihedral : 5.627 33.493 2108 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.51 (0.18), residues: 1949 helix: -1.13 (0.24), residues: 450 sheet: -2.25 (0.21), residues: 486 loop : -1.53 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 585 TYR 0.022 0.001 TYR D 638 PHE 0.020 0.001 PHE H 67 TRP 0.015 0.002 TRP P 96 HIS 0.006 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (17451) covalent geometry : angle 0.66512 / 0.33 (23683) SS BOND : bond 0.00483 / 0.36 ( 38) SS BOND : angle 1.16485 / 0.81 ( 76) hydrogen bonds : bond 0.03149 / 2.08 ( 461) hydrogen bonds : angle 5.79604 / 3.87 ( 1227) link_ALPHA1-3 : bond 0.00586 / 0.36 ( 6) link_ALPHA1-3 : angle 1.46729 / 0.98 ( 18) link_ALPHA1-6 : bond 0.00388 / 0.20 ( 3) link_ALPHA1-6 : angle 1.41694 / 0.84 ( 9) link_BETA1-4 : bond 0.00434 / 0.33 ( 57) link_BETA1-4 : angle 1.52094 / 1.04 ( 171) link_NAG-ASN : bond 0.00368 / 0.26 ( 54) link_NAG-ASN : angle 2.33273 / 1.59 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9047 (mpp) cc_final: 0.8366 (mpp) REVERT: B 626 MET cc_start: 0.9427 (pmm) cc_final: 0.9068 (pmm) REVERT: E 100 MET cc_start: 0.9496 (pmm) cc_final: 0.9256 (pmm) REVERT: G 475 MET cc_start: 0.9045 (pmm) cc_final: 0.8843 (pmm) REVERT: L 85 MET cc_start: 0.9546 (tpt) cc_final: 0.9314 (tpp) REVERT: P 95 MET cc_start: 0.9468 (pmm) cc_final: 0.9169 (pmm) REVERT: P 161 MET cc_start: 0.9023 (tpt) cc_final: 0.8730 (tpp) REVERT: P 271 MET cc_start: 0.9404 (mmp) cc_final: 0.8954 (mmm) REVERT: P 426 MET cc_start: 0.9678 (pmm) cc_final: 0.9376 (pmm) REVERT: P 475 MET cc_start: 0.8833 (pmm) cc_final: 0.8311 (pmm) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1249 time to fit residues: 12.3589 Evaluate side-chains 51 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 113 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.026242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.021327 restraints weight = 313575.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.021974 restraints weight = 171221.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.022404 restraints weight = 113213.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.022704 restraints weight = 84340.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.022896 restraints weight = 68108.850| |-----------------------------------------------------------------------------| r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17609 Z= 0.149 Angle : 0.688 9.471 24119 Z= 0.327 Chirality : 0.043 0.264 3020 Planarity : 0.004 0.035 2855 Dihedral : 5.408 31.934 2108 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.39 (0.18), residues: 1949 helix: -1.02 (0.24), residues: 452 sheet: -1.95 (0.23), residues: 456 loop : -1.62 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 585 TYR 0.022 0.001 TYR D 638 PHE 0.013 0.001 PHE H 67 TRP 0.016 0.002 TRP P 96 HIS 0.007 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (17451) covalent geometry : angle 0.65191 / 0.32 (23683) SS BOND : bond 0.00302 / 0.21 ( 38) SS BOND : angle 1.15371 / 0.81 ( 76) hydrogen bonds : bond 0.02981 / 1.97 ( 461) hydrogen bonds : angle 5.66085 / 3.77 ( 1227) link_ALPHA1-3 : bond 0.00587 / 0.36 ( 6) link_ALPHA1-3 : angle 1.45167 / 0.97 ( 18) link_ALPHA1-6 : bond 0.00408 / 0.20 ( 3) link_ALPHA1-6 : angle 1.41957 / 0.85 ( 9) link_BETA1-4 : bond 0.00419 / 0.31 ( 57) link_BETA1-4 : angle 1.50385 / 1.02 ( 171) link_NAG-ASN : bond 0.00372 / 0.26 ( 54) link_NAG-ASN : angle 2.24439 / 1.53 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9007 (mpp) cc_final: 0.8279 (mpp) REVERT: B 626 MET cc_start: 0.9458 (pmm) cc_final: 0.9058 (pmm) REVERT: D 530 MET cc_start: 0.8991 (mpp) cc_final: 0.8435 (mpp) REVERT: E 150 MET cc_start: -0.1816 (tmm) cc_final: -0.2061 (ptt) REVERT: G 475 MET cc_start: 0.9038 (pmm) cc_final: 0.8837 (pmm) REVERT: H 82 MET cc_start: 0.5691 (ptp) cc_final: 0.5465 (ptp) REVERT: L 85 MET cc_start: 0.9553 (tpt) cc_final: 0.9335 (tpp) REVERT: P 95 MET cc_start: 0.9466 (pmm) cc_final: 0.9167 (pmm) REVERT: P 161 MET cc_start: 0.9069 (tpt) cc_final: 0.8724 (tpp) REVERT: P 271 MET cc_start: 0.9324 (mmp) cc_final: 0.8885 (mmm) REVERT: P 426 MET cc_start: 0.9664 (pmm) cc_final: 0.9359 (pmm) REVERT: P 475 MET cc_start: 0.8773 (pmm) cc_final: 0.8246 (pmm) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1069 time to fit residues: 10.6853 Evaluate side-chains 50 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 24 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 1 optimal weight: 0.0030 chunk 124 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 overall best weight: 5.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS O 577 GLN ** P 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.025269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.020420 restraints weight = 323792.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.021049 restraints weight = 180498.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.021473 restraints weight = 120606.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.021772 restraints weight = 90573.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.021960 restraints weight = 73027.320| |-----------------------------------------------------------------------------| r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17609 Z= 0.225 Angle : 0.766 9.997 24119 Z= 0.366 Chirality : 0.044 0.266 3020 Planarity : 0.004 0.048 2855 Dihedral : 5.558 31.255 2108 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.42 (0.18), residues: 1949 helix: -1.05 (0.24), residues: 434 sheet: -1.85 (0.23), residues: 444 loop : -1.70 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 585 TYR 0.024 0.002 TYR D 638 PHE 0.019 0.002 PHE P 176 TRP 0.015 0.002 TRP O 596 HIS 0.008 0.002 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.22 (17451) covalent geometry : angle 0.73033 / 0.36 (23683) SS BOND : bond 0.00378 / 0.27 ( 38) SS BOND : angle 1.22346 / 0.84 ( 76) hydrogen bonds : bond 0.03352 / 2.21 ( 461) hydrogen bonds : angle 5.89760 / 3.93 ( 1227) link_ALPHA1-3 : bond 0.00525 / 0.32 ( 6) link_ALPHA1-3 : angle 1.54808 / 1.03 ( 18) link_ALPHA1-6 : bond 0.00376 / 0.19 ( 3) link_ALPHA1-6 : angle 1.41703 / 0.84 ( 9) link_BETA1-4 : bond 0.00413 / 0.30 ( 57) link_BETA1-4 : angle 1.61356 / 1.10 ( 171) link_NAG-ASN : bond 0.00568 / 0.40 ( 54) link_NAG-ASN : angle 2.36220 / 1.62 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9139 (mpp) cc_final: 0.8385 (mpp) REVERT: B 626 MET cc_start: 0.9451 (pmm) cc_final: 0.9076 (pmm) REVERT: D 530 MET cc_start: 0.9062 (mpp) cc_final: 0.8745 (mpp) REVERT: G 475 MET cc_start: 0.9101 (pmm) cc_final: 0.8865 (pmm) REVERT: O 530 MET cc_start: 0.8627 (mmp) cc_final: 0.8098 (mmp) REVERT: P 95 MET cc_start: 0.9513 (pmm) cc_final: 0.9241 (pmm) REVERT: P 161 MET cc_start: 0.9336 (tpt) cc_final: 0.9098 (tpp) REVERT: P 271 MET cc_start: 0.9355 (mmp) cc_final: 0.8927 (mmm) REVERT: P 475 MET cc_start: 0.9030 (pmm) cc_final: 0.8452 (pmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1303 time to fit residues: 12.1205 Evaluate side-chains 49 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 0 optimal weight: 40.0000 chunk 67 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 19 optimal weight: 0.0870 chunk 105 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 658 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 577 GLN ** P 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.026009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.021085 restraints weight = 314630.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.021734 restraints weight = 172597.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.022175 restraints weight = 114505.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.022455 restraints weight = 85202.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.022663 restraints weight = 69267.057| |-----------------------------------------------------------------------------| r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17609 Z= 0.148 Angle : 0.703 11.631 24119 Z= 0.334 Chirality : 0.044 0.267 3020 Planarity : 0.004 0.040 2855 Dihedral : 5.426 31.162 2108 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.35 (0.18), residues: 1949 helix: -0.85 (0.25), residues: 431 sheet: -1.79 (0.23), residues: 468 loop : -1.72 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 585 TYR 0.020 0.001 TYR D 638 PHE 0.015 0.001 PHE H 67 TRP 0.030 0.002 TRP P 69 HIS 0.006 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (17451) covalent geometry : angle 0.66930 / 0.33 (23683) SS BOND : bond 0.00319 / 0.22 ( 38) SS BOND : angle 1.22666 / 0.84 ( 76) hydrogen bonds : bond 0.02979 / 1.99 ( 461) hydrogen bonds : angle 5.77330 / 3.85 ( 1227) link_ALPHA1-3 : bond 0.00587 / 0.36 ( 6) link_ALPHA1-3 : angle 1.43017 / 0.95 ( 18) link_ALPHA1-6 : bond 0.00398 / 0.20 ( 3) link_ALPHA1-6 : angle 1.41434 / 0.84 ( 9) link_BETA1-4 : bond 0.00424 / 0.32 ( 57) link_BETA1-4 : angle 1.48782 / 1.01 ( 171) link_NAG-ASN : bond 0.00364 / 0.26 ( 54) link_NAG-ASN : angle 2.19345 / 1.50 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8984 (mpp) cc_final: 0.8286 (mpp) REVERT: B 626 MET cc_start: 0.9473 (pmm) cc_final: 0.9043 (pmm) REVERT: E 100 MET cc_start: 0.9454 (pmm) cc_final: 0.9233 (pmm) REVERT: G 475 MET cc_start: 0.8995 (pmm) cc_final: 0.8779 (pmm) REVERT: H 82 MET cc_start: 0.5821 (ptp) cc_final: 0.5575 (ptp) REVERT: L 85 MET cc_start: 0.9518 (tpt) cc_final: 0.9288 (tpp) REVERT: O 530 MET cc_start: 0.8479 (mmp) cc_final: 0.8243 (mmm) REVERT: P 95 MET cc_start: 0.9464 (pmm) cc_final: 0.9152 (pmm) REVERT: P 161 MET cc_start: 0.9036 (tpt) cc_final: 0.8697 (tpp) REVERT: P 271 MET cc_start: 0.9227 (mmp) cc_final: 0.8805 (mmm) REVERT: P 475 MET cc_start: 0.8794 (pmm) cc_final: 0.8196 (pmm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1118 time to fit residues: 10.0614 Evaluate side-chains 51 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 188 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 182 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 30 optimal weight: 40.0000 chunk 110 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 543 ASN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 577 GLN ** P 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.021883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2327 r_free = 0.2327 target = 0.015642 restraints weight = 304389.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.016281 restraints weight = 184076.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.016740 restraints weight = 130430.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.017066 restraints weight = 101758.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.017312 restraints weight = 85011.499| |-----------------------------------------------------------------------------| r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17609 Z= 0.222 Angle : 0.786 11.634 24119 Z= 0.375 Chirality : 0.044 0.267 3020 Planarity : 0.004 0.070 2855 Dihedral : 5.617 30.934 2108 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.32 (0.18), residues: 1949 helix: -1.04 (0.24), residues: 431 sheet: -1.71 (0.24), residues: 438 loop : -1.65 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 444 TYR 0.027 0.002 TYR D 638 PHE 0.021 0.002 PHE P 176 TRP 0.027 0.002 TRP D 571 HIS 0.008 0.002 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.22 (17451) covalent geometry : angle 0.75068 / 0.37 (23683) SS BOND : bond 0.00352 / 0.23 ( 38) SS BOND : angle 1.41690 / 0.93 ( 76) hydrogen bonds : bond 0.03412 / 2.27 ( 461) hydrogen bonds : angle 6.05412 / 4.05 ( 1227) link_ALPHA1-3 : bond 0.00562 / 0.34 ( 6) link_ALPHA1-3 : angle 1.57643 / 1.05 ( 18) link_ALPHA1-6 : bond 0.00374 / 0.19 ( 3) link_ALPHA1-6 : angle 1.40088 / 0.83 ( 9) link_BETA1-4 : bond 0.00409 / 0.30 ( 57) link_BETA1-4 : angle 1.63505 / 1.11 ( 171) link_NAG-ASN : bond 0.00562 / 0.39 ( 54) link_NAG-ASN : angle 2.33165 / 1.59 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: B 530 MET cc_start: 0.9067 (mpp) cc_final: 0.8347 (mpp) REVERT: B 626 MET cc_start: 0.9250 (pmm) cc_final: 0.8927 (pmm) REVERT: G 475 MET cc_start: 0.9066 (pmm) cc_final: 0.8834 (pmm) REVERT: H 82 MET cc_start: 0.6638 (ptp) cc_final: 0.6430 (ptp) REVERT: O 530 MET cc_start: 0.8072 (mmp) cc_final: 0.7658 (mmm) REVERT: P 95 MET cc_start: 0.9435 (pmm) cc_final: 0.9150 (pmm) REVERT: P 150 MET cc_start: 0.1019 (tmm) cc_final: 0.0741 (tmm) REVERT: P 271 MET cc_start: 0.9206 (mmp) cc_final: 0.8813 (mmm) REVERT: P 475 MET cc_start: 0.8973 (pmm) cc_final: 0.8433 (pmm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1202 time to fit residues: 10.8250 Evaluate side-chains 48 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 114 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 142 optimal weight: 0.1980 chunk 73 optimal weight: 20.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 577 GLN ** P 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.025466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.020623 restraints weight = 319271.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.021248 restraints weight = 176910.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.021690 restraints weight = 118015.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.021977 restraints weight = 88039.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.022166 restraints weight = 71091.035| |-----------------------------------------------------------------------------| r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17609 Z= 0.167 Angle : 0.722 11.929 24119 Z= 0.343 Chirality : 0.044 0.266 3020 Planarity : 0.004 0.057 2855 Dihedral : 5.512 30.410 2108 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.28 (0.18), residues: 1949 helix: -0.88 (0.25), residues: 420 sheet: -1.92 (0.23), residues: 444 loop : -1.56 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 585 TYR 0.023 0.002 TYR D 638 PHE 0.015 0.002 PHE G 288 TRP 0.024 0.002 TRP D 571 HIS 0.007 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (17451) covalent geometry : angle 0.68818 / 0.34 (23683) SS BOND : bond 0.00382 / 0.23 ( 38) SS BOND : angle 1.36903 / 0.92 ( 76) hydrogen bonds : bond 0.03095 / 2.07 ( 461) hydrogen bonds : angle 5.87925 / 3.94 ( 1227) link_ALPHA1-3 : bond 0.00569 / 0.35 ( 6) link_ALPHA1-3 : angle 1.42122 / 0.95 ( 18) link_ALPHA1-6 : bond 0.00373 / 0.19 ( 3) link_ALPHA1-6 : angle 1.40086 / 0.83 ( 9) link_BETA1-4 : bond 0.00413 / 0.30 ( 57) link_BETA1-4 : angle 1.50132 / 1.02 ( 171) link_NAG-ASN : bond 0.00403 / 0.29 ( 54) link_NAG-ASN : angle 2.18752 / 1.49 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2072.24 seconds wall clock time: 37 minutes 26.74 seconds (2246.74 seconds total)