Starting phenix.real_space_refine on Sun Aug 24 05:56:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9w_29880/08_2025/8g9w_29880.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9w_29880/08_2025/8g9w_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g9w_29880/08_2025/8g9w_29880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9w_29880/08_2025/8g9w_29880.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9w_29880/08_2025/8g9w_29880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9w_29880/08_2025/8g9w_29880.cif" } 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-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 3 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.08, per 1000 atoms: 0.24 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: 1.63 Conformation dependent library (CDL) restraints added in 562.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.67 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: 2.71 Time building geometry restraints manager: 2.01 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 - 21.92: 10822 21.92 - 43.85: 846 43.85 - 65.77: 154 65.77 - 87.70: 135 87.70 - 109.62: 73 Dihedral angle restraints: 12030 sinusoidal: 6329 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 12027 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.200 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 : 19.421 109.623 8236 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 aren 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 covalent geometry : bond 0.00808 (17451) covalent geometry : angle 1.35617 (23683) SS BOND : bond 0.00589 ( 38) SS BOND : angle 2.62946 ( 76) hydrogen bonds : bond 0.15487 ( 461) hydrogen bonds : angle 8.83581 ( 1227) link_ALPHA1-3 : bond 0.00352 ( 6) link_ALPHA1-3 : angle 1.88665 ( 18) link_ALPHA1-6 : bond 0.00432 ( 3) link_ALPHA1-6 : angle 1.56214 ( 9) link_BETA1-4 : bond 0.00906 ( 57) link_BETA1-4 : angle 2.64136 ( 171) link_NAG-ASN : bond 0.00893 ( 54) link_NAG-ASN : angle 4.28632 ( 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 : 0.467 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: 0.0993 time to fit residues: 11.2067 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 : 0.583 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2761 r_free = 0.2761 target = 0.026110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.018970 restraints weight = 264956.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.019642 restraints weight = 165595.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.020127 restraints weight = 120278.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.020479 restraints weight = 95704.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.020728 restraints weight = 81058.224| |-----------------------------------------------------------------------------| r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17609 Z= 0.164 Angle : 0.794 10.204 24119 Z= 0.381 Chirality : 0.046 0.279 3020 Planarity : 0.005 0.035 2855 Dihedral : 15.315 81.607 4574 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % 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 aren not related in a simple way. whole: -3.76 (0.17), residues: 1949 helix: -2.78 (0.20), residues: 418 sheet: -2.61 (0.19), residues: 549 loop : -2.19 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 298 TYR 0.020 0.001 TYR D 638 PHE 0.014 0.002 PHE P 288 TRP 0.024 0.002 TRP P 479 HIS 0.005 0.001 HIS L 41 Details of bonding type rmsd covalent geometry : bond 0.00320 (17451) covalent geometry : angle 0.73772 (23683) SS BOND : bond 0.00628 ( 38) SS BOND : angle 1.38327 ( 76) hydrogen bonds : bond 0.04166 ( 461) hydrogen bonds : angle 6.56438 ( 1227) link_ALPHA1-3 : bond 0.01090 ( 6) link_ALPHA1-3 : angle 2.59829 ( 18) link_ALPHA1-6 : bond 0.00473 ( 3) link_ALPHA1-6 : angle 1.93493 ( 9) link_BETA1-4 : bond 0.00557 ( 57) link_BETA1-4 : angle 2.14886 ( 171) link_NAG-ASN : bond 0.00352 ( 54) link_NAG-ASN : angle 2.76032 ( 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 : 0.672 Fit side-chains REVERT: B 530 MET cc_start: 0.8818 (mpp) cc_final: 0.8173 (mpp) REVERT: D 530 MET cc_start: 0.9258 (mpp) cc_final: 0.7421 (mpp) REVERT: D 626 MET cc_start: 0.8869 (tmm) cc_final: 0.7843 (ppp) REVERT: E 95 MET cc_start: 0.9706 (ppp) cc_final: 0.8810 (ppp) REVERT: E 285 LEU cc_start: 0.9866 (mp) cc_final: 0.9515 (tt) REVERT: G 45 TRP cc_start: 0.9432 (p90) cc_final: 0.9166 (p90) REVERT: G 161 MET cc_start: 0.9238 (tmm) cc_final: 0.8801 (tmm) REVERT: O 530 MET cc_start: 0.8490 (mmp) cc_final: 0.7974 (mmp) REVERT: P 95 MET cc_start: 0.9455 (pmm) cc_final: 0.9096 (pmm) REVERT: P 100 MET cc_start: 0.9277 (pmm) cc_final: 0.9052 (pmm) REVERT: P 161 MET cc_start: 0.9357 (tpt) cc_final: 0.8709 (tpt) REVERT: P 271 MET cc_start: 0.9724 (mmp) cc_final: 0.9406 (mmm) REVERT: P 426 MET cc_start: 0.9586 (ptt) cc_final: 0.9281 (pmm) REVERT: P 475 MET cc_start: 0.8745 (pmm) cc_final: 0.8266 (pmm) REVERT: P 483 LEU cc_start: 0.9832 (mt) cc_final: 0.9502 (tp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1304 time to fit residues: 13.9890 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 : 0.560 ------------------------------------------------------------------------------- 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: 10.0000 chunk 50 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 182 optimal weight: 0.3980 chunk 123 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** O 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 656 ASN P 103 GLN P 432 GLN P 478 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.028225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.023131 restraints weight = 303890.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.023826 restraints weight = 162123.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.024292 restraints weight = 105910.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.024595 restraints weight = 78147.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.024819 restraints weight = 62923.657| |-----------------------------------------------------------------------------| r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17609 Z= 0.155 Angle : 0.745 9.499 24119 Z= 0.354 Chirality : 0.046 0.260 3020 Planarity : 0.004 0.050 2855 Dihedral : 11.899 71.440 4574 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.12 % Allowed : 4.60 % Favored : 95.28 % 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 aren not related in a simple way. whole: -3.09 (0.17), residues: 1949 helix: -1.76 (0.24), residues: 430 sheet: -2.44 (0.20), residues: 522 loop : -1.87 (0.18), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 298 TYR 0.014 0.001 TYR O 638 PHE 0.012 0.002 PHE P 176 TRP 0.024 0.002 TRP G 427 HIS 0.007 0.001 HIS P 374 Details of bonding type rmsd covalent geometry : bond 0.00310 (17451) covalent geometry : angle 0.69672 (23683) SS BOND : bond 0.00277 ( 38) SS BOND : angle 1.22300 ( 76) hydrogen bonds : bond 0.03427 ( 461) hydrogen bonds : angle 5.99383 ( 1227) link_ALPHA1-3 : bond 0.01185 ( 6) link_ALPHA1-3 : angle 1.87378 ( 18) link_ALPHA1-6 : bond 0.00523 ( 3) link_ALPHA1-6 : angle 1.97603 ( 9) link_BETA1-4 : bond 0.00502 ( 57) link_BETA1-4 : angle 1.93221 ( 171) link_NAG-ASN : bond 0.00396 ( 54) link_NAG-ASN : angle 2.52324 ( 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 67 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 100 MET cc_start: 0.9271 (pmm) cc_final: 0.9037 (pmm) REVERT: E 285 LEU cc_start: 0.9823 (mp) cc_final: 0.9486 (tt) REVERT: G 45 TRP cc_start: 0.9522 (p90) cc_final: 0.8914 (p90) REVERT: L 85 MET cc_start: 0.9566 (tpt) cc_final: 0.9359 (tpp) REVERT: P 95 MET cc_start: 0.9465 (pmm) cc_final: 0.9106 (pmm) REVERT: P 100 MET cc_start: 0.8865 (pmm) cc_final: 0.8626 (pmm) REVERT: P 161 MET cc_start: 0.9092 (tpt) cc_final: 0.8373 (tpt) REVERT: P 271 MET cc_start: 0.9597 (mmp) cc_final: 0.9201 (mmm) REVERT: P 434 MET cc_start: 0.9638 (tpp) cc_final: 0.9344 (tpp) REVERT: P 475 MET cc_start: 0.8630 (pmm) cc_final: 0.8047 (pmm) REVERT: P 483 LEU cc_start: 0.9877 (mt) cc_final: 0.9652 (tp) outliers start: 2 outliers final: 0 residues processed: 67 average time/residue: 0.1279 time to fit residues: 14.0152 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 : 0.767 ------------------------------------------------------------------------------- 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: 5.9990 chunk 93 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 GLN G 432 GLN G 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.026596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.021539 restraints weight = 316084.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.022193 restraints weight = 173698.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.022646 restraints weight = 115237.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.022942 restraints weight = 85666.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.023158 restraints weight = 69444.137| |-----------------------------------------------------------------------------| r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17609 Z= 0.226 Angle : 0.789 9.334 24119 Z= 0.377 Chirality : 0.045 0.266 3020 Planarity : 0.004 0.038 2855 Dihedral : 10.525 64.723 4574 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % 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 aren not related in a simple way. whole: -2.73 (0.18), residues: 1949 helix: -1.35 (0.25), residues: 435 sheet: -2.33 (0.21), residues: 498 loop : -1.67 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 469 TYR 0.017 0.002 TYR D 638 PHE 0.021 0.002 PHE P 176 TRP 0.020 0.002 TRP P 479 HIS 0.006 0.002 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00448 (17451) covalent geometry : angle 0.74220 (23683) SS BOND : bond 0.00815 ( 38) SS BOND : angle 1.40194 ( 76) hydrogen bonds : bond 0.03621 ( 461) hydrogen bonds : angle 5.95056 ( 1227) link_ALPHA1-3 : bond 0.01023 ( 6) link_ALPHA1-3 : angle 2.42719 ( 18) link_ALPHA1-6 : bond 0.00646 ( 3) link_ALPHA1-6 : angle 2.15552 ( 9) link_BETA1-4 : bond 0.00460 ( 57) link_BETA1-4 : angle 1.89630 ( 171) link_NAG-ASN : bond 0.00575 ( 54) link_NAG-ASN : angle 2.57523 ( 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 62 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: B 530 MET cc_start: 0.9141 (mpp) cc_final: 0.8806 (mpp) REVERT: D 530 MET cc_start: 0.9176 (mpp) cc_final: 0.6798 (mpp) REVERT: D 626 MET cc_start: 0.8498 (tmm) cc_final: 0.7295 (ppp) REVERT: L 85 MET cc_start: 0.9558 (tpt) cc_final: 0.9334 (tpp) REVERT: P 95 MET cc_start: 0.9501 (pmm) cc_final: 0.9152 (pmm) REVERT: P 100 MET cc_start: 0.8871 (pmm) cc_final: 0.8628 (pmm) REVERT: P 161 MET cc_start: 0.9018 (tpt) cc_final: 0.8217 (tpt) REVERT: P 271 MET cc_start: 0.9574 (mmp) cc_final: 0.9154 (mmm) REVERT: P 426 MET cc_start: 0.9590 (pmm) cc_final: 0.9358 (pmm) REVERT: P 475 MET cc_start: 0.8809 (pmm) cc_final: 0.8125 (pmm) REVERT: P 483 LEU cc_start: 0.9910 (mt) cc_final: 0.9637 (tp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1152 time to fit residues: 11.6825 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 : 0.581 ------------------------------------------------------------------------------- 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: 10.0000 chunk 147 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 131 optimal weight: 30.0000 chunk 151 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 653 GLN ** 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 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.025402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.020471 restraints weight = 323438.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.021102 restraints weight = 179867.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.021526 restraints weight = 120564.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.021825 restraints weight = 90860.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.022011 restraints weight = 73773.574| |-----------------------------------------------------------------------------| r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17609 Z= 0.268 Angle : 0.848 10.061 24119 Z= 0.406 Chirality : 0.047 0.274 3020 Planarity : 0.005 0.047 2855 Dihedral : 10.180 59.843 4574 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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 aren not related in a simple way. whole: -2.72 (0.18), residues: 1949 helix: -1.51 (0.23), residues: 450 sheet: -2.37 (0.21), residues: 486 loop : -1.56 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 192 TYR 0.023 0.002 TYR D 638 PHE 0.026 0.003 PHE P 176 TRP 0.021 0.003 TRP O 596 HIS 0.008 0.002 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00529 (17451) covalent geometry : angle 0.80592 (23683) SS BOND : bond 0.00597 ( 38) SS BOND : angle 1.24393 ( 76) hydrogen bonds : bond 0.03881 ( 461) hydrogen bonds : angle 6.16550 ( 1227) link_ALPHA1-3 : bond 0.01163 ( 6) link_ALPHA1-3 : angle 2.23921 ( 18) link_ALPHA1-6 : bond 0.00723 ( 3) link_ALPHA1-6 : angle 1.98079 ( 9) link_BETA1-4 : bond 0.00444 ( 57) link_BETA1-4 : angle 1.82379 ( 171) link_NAG-ASN : bond 0.00680 ( 54) link_NAG-ASN : angle 2.66197 ( 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 : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9073 (mpp) cc_final: 0.8467 (mpp) REVERT: B 626 MET cc_start: 0.9354 (pmm) cc_final: 0.8957 (pmm) REVERT: D 530 MET cc_start: 0.9100 (mpp) cc_final: 0.8178 (mmt) REVERT: G 475 MET cc_start: 0.9170 (pmm) cc_final: 0.8966 (pmm) REVERT: L 85 MET cc_start: 0.9548 (tpt) cc_final: 0.9313 (tpp) REVERT: O 530 MET cc_start: 0.8464 (mmp) cc_final: 0.8201 (mmp) REVERT: P 95 MET cc_start: 0.9556 (pmm) cc_final: 0.9238 (pmm) REVERT: P 161 MET cc_start: 0.9053 (tpt) cc_final: 0.8536 (tpp) REVERT: P 271 MET cc_start: 0.9486 (mmp) cc_final: 0.8992 (mmm) REVERT: P 426 MET cc_start: 0.9604 (pmm) cc_final: 0.9347 (pmm) REVERT: P 475 MET cc_start: 0.8914 (pmm) cc_final: 0.8591 (pmm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1198 time to fit residues: 11.1148 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 : 0.663 ------------------------------------------------------------------------------- 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: 2.9990 chunk 144 optimal weight: 0.1980 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 40.0000 chunk 88 optimal weight: 6.9990 chunk 160 optimal weight: 0.4980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 ASN D 653 GLN D 658 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 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 = 0.2693 r_free = 0.2693 target = 0.023533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.017353 restraints weight = 280776.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.017961 restraints weight = 177471.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.018401 restraints weight = 129052.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.018706 restraints weight = 102518.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.018939 restraints weight = 86765.205| |-----------------------------------------------------------------------------| r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3118 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= 0.120 Angle : 0.706 9.576 24119 Z= 0.333 Chirality : 0.046 0.268 3020 Planarity : 0.004 0.035 2855 Dihedral : 9.644 59.952 4574 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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 aren not related in a simple way. whole: -2.48 (0.18), residues: 1949 helix: -1.10 (0.24), residues: 448 sheet: -2.12 (0.21), residues: 498 loop : -1.57 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 192 TYR 0.020 0.001 TYR D 638 PHE 0.020 0.001 PHE H 67 TRP 0.015 0.001 TRP P 96 HIS 0.007 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00250 (17451) covalent geometry : angle 0.66247 (23683) SS BOND : bond 0.00355 ( 38) SS BOND : angle 1.32904 ( 76) hydrogen bonds : bond 0.03019 ( 461) hydrogen bonds : angle 5.73942 ( 1227) link_ALPHA1-3 : bond 0.01113 ( 6) link_ALPHA1-3 : angle 1.80807 ( 18) link_ALPHA1-6 : bond 0.00876 ( 3) link_ALPHA1-6 : angle 1.92855 ( 9) link_BETA1-4 : bond 0.00472 ( 57) link_BETA1-4 : angle 1.63293 ( 171) link_NAG-ASN : bond 0.00386 ( 54) link_NAG-ASN : angle 2.41276 ( 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 62 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8990 (mpp) cc_final: 0.8335 (mpp) REVERT: B 626 MET cc_start: 0.9347 (pmm) cc_final: 0.9046 (pmm) REVERT: E 100 MET cc_start: 0.9480 (pmm) cc_final: 0.9227 (pmm) REVERT: L 85 MET cc_start: 0.9568 (tpt) cc_final: 0.9362 (tpp) REVERT: P 95 MET cc_start: 0.9514 (pmm) cc_final: 0.9156 (pmm) REVERT: P 161 MET cc_start: 0.9054 (tpt) cc_final: 0.8748 (tpp) REVERT: P 271 MET cc_start: 0.9414 (mmp) cc_final: 0.8954 (mmm) REVERT: P 426 MET cc_start: 0.9605 (pmm) cc_final: 0.9356 (pmm) REVERT: P 475 MET cc_start: 0.8621 (pmm) cc_final: 0.8196 (pmm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1198 time to fit residues: 11.9785 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 : 0.635 ------------------------------------------------------------------------------- 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: 0.0060 chunk 158 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 147 optimal weight: 0.0270 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN P 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.023928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.017635 restraints weight = 276731.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.018227 restraints weight = 178572.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.018657 restraints weight = 131803.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.018972 restraints weight = 105863.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.019182 restraints weight = 89940.434| |-----------------------------------------------------------------------------| r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17609 Z= 0.110 Angle : 0.658 9.529 24119 Z= 0.308 Chirality : 0.044 0.265 3020 Planarity : 0.004 0.039 2855 Dihedral : 8.931 59.775 4574 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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 aren not related in a simple way. whole: -2.29 (0.18), residues: 1949 helix: -0.85 (0.25), residues: 447 sheet: -1.73 (0.23), residues: 468 loop : -1.68 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 192 TYR 0.013 0.001 TYR D 638 PHE 0.012 0.001 PHE G 288 TRP 0.015 0.001 TRP P 96 HIS 0.005 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00228 (17451) covalent geometry : angle 0.62108 (23683) SS BOND : bond 0.00282 ( 38) SS BOND : angle 1.09335 ( 76) hydrogen bonds : bond 0.02758 ( 461) hydrogen bonds : angle 5.36079 ( 1227) link_ALPHA1-3 : bond 0.01130 ( 6) link_ALPHA1-3 : angle 1.57018 ( 18) link_ALPHA1-6 : bond 0.00862 ( 3) link_ALPHA1-6 : angle 1.88122 ( 9) link_BETA1-4 : bond 0.00484 ( 57) link_BETA1-4 : angle 1.49613 ( 171) link_NAG-ASN : bond 0.00294 ( 54) link_NAG-ASN : angle 2.17706 ( 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 65 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9055 (mpp) cc_final: 0.8276 (mpp) REVERT: B 626 MET cc_start: 0.9506 (pmm) cc_final: 0.9111 (pmm) REVERT: D 530 MET cc_start: 0.8985 (mpp) cc_final: 0.8476 (mpp) REVERT: H 82 MET cc_start: 0.5919 (ptp) cc_final: 0.5698 (ptp) REVERT: P 95 MET cc_start: 0.9499 (pmm) cc_final: 0.9161 (pmm) REVERT: P 161 MET cc_start: 0.9134 (tpt) cc_final: 0.8824 (tpp) REVERT: P 271 MET cc_start: 0.9356 (mmp) cc_final: 0.8955 (mmm) REVERT: P 426 MET cc_start: 0.9599 (pmm) cc_final: 0.9355 (pmm) REVERT: P 475 MET cc_start: 0.8631 (pmm) cc_final: 0.8401 (pmm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1256 time to fit residues: 12.8981 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 : 0.621 ------------------------------------------------------------------------------- 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: 10.0000 chunk 136 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** 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 = 0.2801 r_free = 0.2801 target = 0.026781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.021776 restraints weight = 314030.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.022439 restraints weight = 170387.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.022896 restraints weight = 112748.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.023190 restraints weight = 83740.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.023403 restraints weight = 67642.426| |-----------------------------------------------------------------------------| r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3482 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= 0.146 Angle : 0.684 9.814 24119 Z= 0.322 Chirality : 0.044 0.265 3020 Planarity : 0.004 0.119 2855 Dihedral : 8.795 59.862 4574 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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 aren not related in a simple way. whole: -2.22 (0.18), residues: 1949 helix: -0.77 (0.25), residues: 447 sheet: -1.69 (0.23), residues: 471 loop : -1.64 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 585 TYR 0.011 0.001 TYR D 638 PHE 0.011 0.001 PHE G 288 TRP 0.013 0.001 TRP P 96 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00298 (17451) covalent geometry : angle 0.64722 (23683) SS BOND : bond 0.00303 ( 38) SS BOND : angle 1.01781 ( 76) hydrogen bonds : bond 0.02881 ( 461) hydrogen bonds : angle 5.39124 ( 1227) link_ALPHA1-3 : bond 0.01022 ( 6) link_ALPHA1-3 : angle 1.63923 ( 18) link_ALPHA1-6 : bond 0.00774 ( 3) link_ALPHA1-6 : angle 1.84556 ( 9) link_BETA1-4 : bond 0.00438 ( 57) link_BETA1-4 : angle 1.54608 ( 171) link_NAG-ASN : bond 0.00357 ( 54) link_NAG-ASN : angle 2.22505 ( 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 60 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9068 (mpp) cc_final: 0.8251 (mpp) REVERT: B 626 MET cc_start: 0.9486 (pmm) cc_final: 0.9119 (pmm) REVERT: E 150 MET cc_start: -0.1456 (tmm) cc_final: -0.2246 (ptt) REVERT: O 530 MET cc_start: 0.8524 (mmp) cc_final: 0.8303 (mmm) REVERT: P 95 MET cc_start: 0.9511 (pmm) cc_final: 0.9220 (pmm) REVERT: P 161 MET cc_start: 0.9095 (tpt) cc_final: 0.8292 (tpt) REVERT: P 271 MET cc_start: 0.9350 (mmp) cc_final: 0.8945 (mmm) REVERT: P 426 MET cc_start: 0.9584 (pmm) cc_final: 0.9287 (pmm) REVERT: P 475 MET cc_start: 0.8686 (pmm) cc_final: 0.8206 (pmm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1315 time to fit residues: 12.6715 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 : 0.521 ------------------------------------------------------------------------------- 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: 1.9990 chunk 194 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2743 r_free = 0.2743 target = 0.025267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.020318 restraints weight = 325387.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.020947 restraints weight = 181406.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.021377 restraints weight = 121625.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.021653 restraints weight = 91558.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.021857 restraints weight = 74744.946| |-----------------------------------------------------------------------------| r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17609 Z= 0.242 Angle : 0.811 11.088 24119 Z= 0.387 Chirality : 0.045 0.273 3020 Planarity : 0.005 0.104 2855 Dihedral : 9.058 59.927 4574 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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 aren not related in a simple way. whole: -2.34 (0.18), residues: 1949 helix: -0.98 (0.24), residues: 431 sheet: -1.66 (0.23), residues: 462 loop : -1.72 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 166 TYR 0.026 0.002 TYR D 638 PHE 0.024 0.003 PHE P 176 TRP 0.034 0.002 TRP P 69 HIS 0.008 0.002 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00480 (17451) covalent geometry : angle 0.77326 (23683) SS BOND : bond 0.00488 ( 38) SS BOND : angle 1.26802 ( 76) hydrogen bonds : bond 0.03536 ( 461) hydrogen bonds : angle 5.95374 ( 1227) link_ALPHA1-3 : bond 0.00920 ( 6) link_ALPHA1-3 : angle 1.83247 ( 18) link_ALPHA1-6 : bond 0.00697 ( 3) link_ALPHA1-6 : angle 1.72243 ( 9) link_BETA1-4 : bond 0.00444 ( 57) link_BETA1-4 : angle 1.74559 ( 171) link_NAG-ASN : bond 0.00609 ( 54) link_NAG-ASN : angle 2.43780 ( 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 58 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8989 (mpp) cc_final: 0.8238 (mpp) REVERT: B 626 MET cc_start: 0.9453 (pmm) cc_final: 0.8989 (pmm) REVERT: D 530 MET cc_start: 0.9079 (mpp) cc_final: 0.8519 (mpp) REVERT: E 100 MET cc_start: 0.9467 (pmm) cc_final: 0.9233 (pmm) REVERT: E 150 MET cc_start: -0.0402 (tmm) cc_final: -0.0683 (ptm) REVERT: G 104 MET cc_start: 0.9366 (ppp) cc_final: 0.9155 (ppp) REVERT: G 475 MET cc_start: 0.9106 (pmm) cc_final: 0.8842 (pmm) REVERT: H 82 MET cc_start: 0.5946 (ptp) cc_final: 0.5689 (ptp) REVERT: L 85 MET cc_start: 0.9499 (tpt) cc_final: 0.9296 (tpp) REVERT: O 530 MET cc_start: 0.8536 (mmp) cc_final: 0.8264 (mmp) REVERT: P 95 MET cc_start: 0.9522 (pmm) cc_final: 0.9237 (pmm) REVERT: P 161 MET cc_start: 0.9099 (tpt) cc_final: 0.8230 (tpt) REVERT: P 271 MET cc_start: 0.9255 (mmp) cc_final: 0.8845 (mmm) REVERT: P 426 MET cc_start: 0.9562 (pmm) cc_final: 0.9256 (pmm) REVERT: P 475 MET cc_start: 0.8919 (pmm) cc_final: 0.8301 (pmm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1188 time to fit residues: 10.9011 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 : 0.521 ------------------------------------------------------------------------------- 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: 10.0000 chunk 140 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2765 r_free = 0.2765 target = 0.025790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.020792 restraints weight = 318804.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.021449 restraints weight = 178182.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.021887 restraints weight = 118307.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.022166 restraints weight = 88308.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.022377 restraints weight = 71733.496| |-----------------------------------------------------------------------------| r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17609 Z= 0.178 Angle : 0.727 10.794 24119 Z= 0.345 Chirality : 0.045 0.285 3020 Planarity : 0.004 0.091 2855 Dihedral : 8.964 60.000 4574 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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 aren not related in a simple way. whole: -2.14 (0.18), residues: 1949 helix: -0.66 (0.26), residues: 413 sheet: -1.56 (0.24), residues: 432 loop : -1.66 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 166 TYR 0.023 0.002 TYR D 638 PHE 0.017 0.002 PHE G 288 TRP 0.017 0.002 TRP P 69 HIS 0.010 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00359 (17451) covalent geometry : angle 0.68965 (23683) SS BOND : bond 0.00318 ( 38) SS BOND : angle 1.33301 ( 76) hydrogen bonds : bond 0.03154 ( 461) hydrogen bonds : angle 5.79049 ( 1227) link_ALPHA1-3 : bond 0.00927 ( 6) link_ALPHA1-3 : angle 1.56832 ( 18) link_ALPHA1-6 : bond 0.00667 ( 3) link_ALPHA1-6 : angle 1.74196 ( 9) link_BETA1-4 : bond 0.00434 ( 57) link_BETA1-4 : angle 1.58330 ( 171) link_NAG-ASN : bond 0.00417 ( 54) link_NAG-ASN : angle 2.26707 ( 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 57 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8983 (mpp) cc_final: 0.8246 (mpp) REVERT: B 626 MET cc_start: 0.9470 (pmm) cc_final: 0.9085 (pmm) REVERT: E 100 MET cc_start: 0.9455 (pmm) cc_final: 0.9233 (pmm) REVERT: G 475 MET cc_start: 0.9072 (pmm) cc_final: 0.8851 (pmm) REVERT: H 82 MET cc_start: 0.5907 (ptp) cc_final: 0.5655 (ptp) REVERT: L 85 MET cc_start: 0.9470 (tpt) cc_final: 0.9258 (tpp) REVERT: O 530 MET cc_start: 0.8539 (mmp) cc_final: 0.8268 (mmm) REVERT: P 95 MET cc_start: 0.9501 (pmm) cc_final: 0.9206 (pmm) REVERT: P 161 MET cc_start: 0.9107 (tpt) cc_final: 0.8229 (tpt) REVERT: P 271 MET cc_start: 0.9202 (mmp) cc_final: 0.8793 (mmm) REVERT: P 426 MET cc_start: 0.9581 (pmm) cc_final: 0.9300 (pmm) REVERT: P 475 MET cc_start: 0.8841 (pmm) cc_final: 0.8253 (pmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1273 time to fit residues: 11.5129 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 : 0.397 ------------------------------------------------------------------------------- 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: 7.9990 chunk 62 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 155 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** 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 = 0.2744 r_free = 0.2744 target = 0.025197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.020250 restraints weight = 324794.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.020888 restraints weight = 183710.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.021322 restraints weight = 122846.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.021615 restraints weight = 91929.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.021816 restraints weight = 74793.137| |-----------------------------------------------------------------------------| r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17609 Z= 0.208 Angle : 0.773 10.568 24119 Z= 0.367 Chirality : 0.045 0.298 3020 Planarity : 0.005 0.078 2855 Dihedral : 8.994 59.599 4574 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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 aren not related in a simple way. whole: -2.15 (0.18), residues: 1949 helix: -0.71 (0.26), residues: 395 sheet: -1.60 (0.24), residues: 432 loop : -1.62 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 166 TYR 0.024 0.002 TYR D 638 PHE 0.020 0.002 PHE P 176 TRP 0.018 0.002 TRP P 96 HIS 0.008 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00418 (17451) covalent geometry : angle 0.73546 (23683) SS BOND : bond 0.00548 ( 38) SS BOND : angle 1.37780 ( 76) hydrogen bonds : bond 0.03342 ( 461) hydrogen bonds : angle 5.96590 ( 1227) link_ALPHA1-3 : bond 0.00853 ( 6) link_ALPHA1-3 : angle 1.63077 ( 18) link_ALPHA1-6 : bond 0.00625 ( 3) link_ALPHA1-6 : angle 1.63898 ( 9) link_BETA1-4 : bond 0.00426 ( 57) link_BETA1-4 : angle 1.67585 ( 171) link_NAG-ASN : bond 0.00528 ( 54) link_NAG-ASN : angle 2.36159 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1994.36 seconds wall clock time: 36 minutes 4.69 seconds (2164.69 seconds total)