Starting phenix.real_space_refine on Sat Jun 14 17:12:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bnm_44730/06_2025/9bnm_44730.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bnm_44730/06_2025/9bnm_44730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bnm_44730/06_2025/9bnm_44730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bnm_44730/06_2025/9bnm_44730.map" model { file = "/net/cci-nas-00/data/ceres_data/9bnm_44730/06_2025/9bnm_44730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bnm_44730/06_2025/9bnm_44730.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 10270 2.51 5 N 2731 2.21 5 O 3334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16450 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3414 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 4 Chain: "B" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3416 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 4 Chain: "C" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3438 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Chain: "H" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1005 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Chain: "X" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "Y" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "Z" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" 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: "Z" 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 Time building chain proxies: 11.62, per 1000 atoms: 0.71 Number of scatterers: 16450 At special positions: 0 Unit cell: (127.82, 122.01, 164.34, 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 3334 8.00 N 2731 7.00 C 10270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS X 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.04 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS Y 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS Z 605 " distance=2.05 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 X 598 " - pdb=" SG CYS X 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 598 " - pdb=" SG CYS Y 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 604 " 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 M 3 " - " MAN M 4 " " BMA S 3 " - " MAN S 4 " " BMA k 3 " - " MAN k 7 " " MAN k 4 " - " MAN k 5 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA k 3 " - " MAN k 4 " " MAN k 4 " - " MAN k 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A 601 " - " ASN A 448 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 88 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 234 " " NAG B 601 " - " ASN B 363 " " NAG B 602 " - " ASN B 355 " " NAG B 603 " - " ASN B 133 " " NAG B 604 " - " ASN B 339 " " NAG B 605 " - " ASN B 234 " " NAG C 601 " - " ASN C 448 " " NAG C 602 " - " ASN C 276 " " NAG C 603 " - " ASN C 355 " " NAG C 604 " - " ASN C 133 " " NAG C 605 " - " ASN C 88 " " NAG C 606 " - " ASN C 339 " " NAG D 1 " - " ASN A 363 " " NAG E 1 " - " ASN A 392 " " NAG F 1 " - " ASN A 386 " " NAG G 1 " - " ASN A 262 " " NAG I 1 " - " ASN A 276 " " NAG J 1 " - " ASN A 355 " " NAG K 1 " - " ASN A 295 " " NAG M 1 " - " ASN A 160 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 332 " " NAG Q 1 " - " ASN B 392 " " NAG R 1 " - " ASN B 386 " " NAG S 1 " - " ASN B 262 " " NAG T 1 " - " ASN B 276 " " NAG U 1 " - " ASN B 295 " " NAG V 1 " - " ASN B 160 " " NAG W 1 " - " ASN B 156 " " NAG Y 701 " - " ASN Y 611 " " NAG Z 701 " - " ASN Z 618 " " NAG a 1 " - " ASN B 197 " " NAG b 1 " - " ASN B 88 " " NAG c 1 " - " ASN B 332 " " NAG d 1 " - " ASN B 301 " " NAG e 1 " - " ASN B 448 " " NAG f 1 " - " ASN C 363 " " NAG g 1 " - " ASN C 392 " " NAG h 1 " - " ASN C 386 " " NAG i 1 " - " ASN C 262 " " NAG j 1 " - " ASN C 295 " " NAG k 1 " - " ASN C 160 " " NAG l 1 " - " ASN C 156 " " NAG m 1 " - " ASN C 197 " " NAG n 1 " - " ASN C 332 " " NAG o 1 " - " ASN C 301 " " NAG p 1 " - " ASN C 234 " Time building additional restraints: 5.33 Conformation dependent library (CDL) restraints added in 1.8 seconds 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3566 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 28 sheets defined 25.6% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.575A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.720A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.574A pdb=" N PHE A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN A 392 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.786A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 117 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.628A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 335 through 354 removed outlier: 3.585A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.923A pdb=" N ARG B 429 " --> pdb=" O MET B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 474 through 484 removed outlier: 4.359A pdb=" N ASN B 478 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 99 through 116 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.810A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 475 through 484 removed outlier: 4.164A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'X' and resid 529 through 534 Processing helix chain 'X' and resid 536 through 544 removed outlier: 4.292A pdb=" N GLN X 540 " --> pdb=" O THR X 536 " (cutoff:3.500A) Processing helix chain 'X' and resid 569 through 595 Processing helix chain 'X' and resid 618 through 623 removed outlier: 3.559A pdb=" N TRP X 623 " --> pdb=" O LEU X 619 " (cutoff:3.500A) Processing helix chain 'X' and resid 627 through 635 Processing helix chain 'X' and resid 638 through 664 removed outlier: 3.507A pdb=" N LEU X 663 " --> pdb=" O ASP X 659 " (cutoff:3.500A) Processing helix chain 'Y' and resid 529 through 535 Processing helix chain 'Y' and resid 536 through 544 removed outlier: 4.185A pdb=" N GLN Y 540 " --> pdb=" O THR Y 536 " (cutoff:3.500A) Processing helix chain 'Y' and resid 569 through 596 removed outlier: 3.710A pdb=" N TRP Y 596 " --> pdb=" O LEU Y 592 " (cutoff:3.500A) Processing helix chain 'Y' and resid 618 through 625 Processing helix chain 'Y' and resid 627 through 636 Processing helix chain 'Y' and resid 638 through 664 removed outlier: 3.556A pdb=" N ILE Y 642 " --> pdb=" O TYR Y 638 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR Y 643 " --> pdb=" O THR Y 639 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY Y 644 " --> pdb=" O GLN Y 640 " (cutoff:3.500A) Processing helix chain 'Z' and resid 523 through 527 removed outlier: 4.537A pdb=" N GLY Z 527 " --> pdb=" O GLY Z 524 " (cutoff:3.500A) Processing helix chain 'Z' and resid 529 through 534 Processing helix chain 'Z' and resid 536 through 544 removed outlier: 4.221A pdb=" N GLN Z 540 " --> pdb=" O THR Z 536 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU Z 544 " --> pdb=" O GLN Z 540 " (cutoff:3.500A) Processing helix chain 'Z' and resid 569 through 596 removed outlier: 3.729A pdb=" N LYS Z 574 " --> pdb=" O VAL Z 570 " (cutoff:3.500A) Processing helix chain 'Z' and resid 618 through 623 removed outlier: 3.916A pdb=" N ILE Z 622 " --> pdb=" O ASN Z 618 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP Z 623 " --> pdb=" O LEU Z 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 618 through 623' Processing helix chain 'Z' and resid 628 through 636 Processing helix chain 'Z' and resid 638 through 664 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.355A pdb=" N VAL A 36 " --> pdb=" O THR X 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.348A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 7.176A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS A 218 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 4.171A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS A 239 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 176 removed outlier: 3.520A pdb=" N MET A 161 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 172 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN A 160 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR A 128 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.031A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 298 removed outlier: 7.127A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 297 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 330 through 334 current: chain 'A' and resid 383 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 413 through 420 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.190A pdb=" N SER A 306 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA A 319 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ARG A 308 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE A 317 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 312 " --> pdb=" O GLN A 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.302A pdb=" N VAL Y 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL B 38 " --> pdb=" O THR Y 606 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR Y 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N TYR B 40 " --> pdb=" O CYS Y 604 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N CYS Y 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.794A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.603A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 169 through 176 removed outlier: 3.529A pdb=" N VAL B 182 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 261 current: chain 'B' and resid 284 through 312 removed outlier: 7.367A pdb=" N ASN B 301 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE B 323 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 315 through 323A current: chain 'B' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 381 through 385 current: chain 'B' and resid 465 through 470 Processing sheet with id=AB6, first strand: chain 'B' and resid 423 through 424 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.238A pdb=" N VAL Z 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL C 38 " --> pdb=" O THR Z 606 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR Z 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR C 40 " --> pdb=" O CYS Z 604 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N CYS Z 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.906A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.156A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 56 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS C 218 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.688A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 170 through 176 removed outlier: 3.535A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 297 removed outlier: 7.261A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 330 through 334 current: chain 'C' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 382 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AC4, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AC5, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.620A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS H 22 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.512A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.989A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL H 37 " --> pdb=" O HIS H 91 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL H 94 " --> pdb=" O VAL H 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.187A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 13 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 469 hydrogen bonds defined for protein. 1308 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: 5.27 Time building geometry restraints manager: 6.16 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: 5102 1.34 - 1.47: 4085 1.47 - 1.59: 7416 1.59 - 1.72: 1 1.72 - 1.84: 152 Bond restraints: 16756 Sorted by residual: bond pdb=" OH TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.679 1.595 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" N VAL H 69 " pdb=" CA VAL H 69 " ideal model delta sigma weight residual 1.456 1.503 -0.047 1.15e-02 7.56e+03 1.71e+01 bond pdb=" N VAL H 100 " pdb=" CA VAL H 100 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.14e-02 7.69e+03 1.10e+01 bond pdb=" N VAL C 120 " pdb=" CA VAL C 120 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.17e-02 7.31e+03 1.09e+01 bond pdb=" N VAL H 32 " pdb=" CA VAL H 32 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.20e-02 6.94e+03 1.02e+01 ... (remaining 16751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 21995 2.40 - 4.81: 675 4.81 - 7.21: 52 7.21 - 9.62: 9 9.62 - 12.02: 1 Bond angle restraints: 22732 Sorted by residual: angle pdb=" CA ASP H 100A" pdb=" CB ASP H 100A" pdb=" CG ASP H 100A" ideal model delta sigma weight residual 112.60 118.55 -5.95 1.00e+00 1.00e+00 3.54e+01 angle pdb=" N ARG H 71 " pdb=" CA ARG H 71 " pdb=" CB ARG H 71 " ideal model delta sigma weight residual 111.05 119.49 -8.44 1.50e+00 4.44e-01 3.16e+01 angle pdb=" CG LYS A 169 " pdb=" CD LYS A 169 " pdb=" CE LYS A 169 " ideal model delta sigma weight residual 111.30 123.32 -12.02 2.30e+00 1.89e-01 2.73e+01 angle pdb=" C ASP H 100A" pdb=" CA ASP H 100A" pdb=" CB ASP H 100A" ideal model delta sigma weight residual 112.09 119.83 -7.74 1.54e+00 4.22e-01 2.53e+01 angle pdb=" C ARG H 71 " pdb=" CA ARG H 71 " pdb=" CB ARG H 71 " ideal model delta sigma weight residual 110.24 100.81 9.43 1.88e+00 2.83e-01 2.52e+01 ... (remaining 22727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 10549 21.67 - 43.34: 632 43.34 - 65.01: 121 65.01 - 86.68: 60 86.68 - 108.35: 28 Dihedral angle restraints: 11390 sinusoidal: 5881 harmonic: 5509 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual 93.00 174.08 -81.08 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS Z 605 " pdb=" CB CYS Z 605 " ideal model delta sinusoidal sigma weight residual -86.00 -6.96 -79.04 1 1.00e+01 1.00e-02 7.77e+01 dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -154.21 68.21 1 1.00e+01 1.00e-02 6.04e+01 ... (remaining 11387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.246: 2837 0.246 - 0.492: 15 0.492 - 0.738: 1 0.738 - 0.984: 1 0.984 - 1.231: 1 Chirality restraints: 2855 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-02 2.50e+03 2.68e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.17e+02 ... (remaining 2852 not shown) Planarity restraints: 2809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.276 2.00e-02 2.50e+03 2.37e-01 7.01e+02 pdb=" C7 NAG M 1 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.414 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " 0.261 2.00e-02 2.50e+03 2.26e-01 6.39e+02 pdb=" C7 NAG M 2 " -0.053 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.007 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " -0.387 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG k 2 " 0.147 2.00e-02 2.50e+03 1.23e-01 1.88e+02 pdb=" C7 NAG k 2 " -0.037 2.00e-02 2.50e+03 pdb=" C8 NAG k 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG k 2 " -0.202 2.00e-02 2.50e+03 pdb=" O7 NAG k 2 " -0.014 2.00e-02 2.50e+03 ... (remaining 2806 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 110 2.55 - 3.14: 13334 3.14 - 3.73: 23585 3.73 - 4.31: 32793 4.31 - 4.90: 54072 Nonbonded interactions: 123894 Sorted by model distance: nonbonded pdb=" O LYS H 75 " pdb=" OD1 ASN H 76 " model vdw 1.963 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 21 " model vdw 2.111 3.040 nonbonded pdb=" OG1 THR C 163 " pdb=" OE1 GLU C 164 " model vdw 2.160 3.040 nonbonded pdb=" OD1 ASN B 276 " pdb=" OG1 THR B 278 " model vdw 2.170 3.040 nonbonded pdb=" O3 NAG K 1 " pdb=" O5 NAG K 2 " model vdw 2.179 3.040 ... (remaining 123889 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' and (resid 33 through 135 or resid 151 through 184 or resid 188 throu \ gh 505 or resid 601 through 605)) selection = (chain 'B' and (resid 33 through 135 or resid 151 through 505 or resid 601 throu \ gh 605)) selection = (chain 'C' and (resid 33 through 135 or resid 151 through 184 or resid 188 throu \ gh 397 or resid 412 through 505 or resid 601 through 605)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'G' selection = chain 'W' selection = chain 'i' selection = chain 'l' } ncs_group { reference = chain 'X' selection = (chain 'Y' and resid 520 through 664) selection = (chain 'Z' and resid 520 through 664) } 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: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.470 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 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 : 0.007 0.312 16895 Z= 0.371 Angle : 1.043 39.083 23111 Z= 0.518 Chirality : 0.065 1.231 2855 Planarity : 0.009 0.237 2756 Dihedral : 15.230 108.349 7710 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 1866 helix: 0.92 (0.27), residues: 421 sheet: -0.91 (0.24), residues: 484 loop : -1.22 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 479 HIS 0.007 0.001 HIS A 352 PHE 0.012 0.001 PHE C 376 TYR 0.065 0.001 TYR L 49 ARG 0.015 0.001 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.04747 ( 53) link_NAG-ASN : angle 4.78232 ( 159) link_ALPHA1-6 : bond 0.03665 ( 3) link_ALPHA1-6 : angle 3.30839 ( 9) link_BETA1-4 : bond 0.03103 ( 41) link_BETA1-4 : angle 4.76560 ( 123) link_ALPHA1-3 : bond 0.04620 ( 4) link_ALPHA1-3 : angle 4.00522 ( 12) hydrogen bonds : bond 0.19815 ( 469) hydrogen bonds : angle 7.82170 ( 1308) SS BOND : bond 0.00458 ( 38) SS BOND : angle 2.24732 ( 76) covalent geometry : bond 0.00597 (16756) covalent geometry : angle 0.89040 (22732) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8033 (ttt) cc_final: 0.7827 (ttt) REVERT: A 271 MET cc_start: 0.7448 (mmt) cc_final: 0.7215 (mmm) REVERT: A 475 MET cc_start: 0.8486 (tpp) cc_final: 0.8151 (tpt) REVERT: B 104 MET cc_start: 0.8815 (tpp) cc_final: 0.8411 (tpt) REVERT: H 82 LEU cc_start: 0.6961 (mm) cc_final: 0.6734 (mm) REVERT: L 82 ASP cc_start: 0.6126 (m-30) cc_final: 0.5620 (t70) REVERT: Z 581 LEU cc_start: 0.9234 (tp) cc_final: 0.8788 (pp) REVERT: Z 586 TYR cc_start: 0.9123 (t80) cc_final: 0.8821 (t80) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.2752 time to fit residues: 129.4370 Evaluate side-chains 219 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 148 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 GLN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 656 ASN ** Z 653 GLN ** 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 = 0.3526 r_free = 0.3526 target = 0.089801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070728 restraints weight = 53512.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.073018 restraints weight = 29769.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.074572 restraints weight = 20399.829| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16895 Z= 0.163 Angle : 0.709 14.513 23111 Z= 0.329 Chirality : 0.047 0.366 2855 Planarity : 0.004 0.050 2756 Dihedral : 10.713 77.735 4128 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.42 % Allowed : 9.29 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.20), residues: 1866 helix: 1.33 (0.27), residues: 414 sheet: -0.51 (0.22), residues: 549 loop : -0.90 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 479 HIS 0.005 0.001 HIS H 58 PHE 0.016 0.002 PHE A 233 TYR 0.024 0.002 TYR L 49 ARG 0.005 0.000 ARG B 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 53) link_NAG-ASN : angle 2.52513 ( 159) link_ALPHA1-6 : bond 0.00926 ( 3) link_ALPHA1-6 : angle 1.80614 ( 9) link_BETA1-4 : bond 0.00563 ( 41) link_BETA1-4 : angle 2.46786 ( 123) link_ALPHA1-3 : bond 0.00944 ( 4) link_ALPHA1-3 : angle 1.93386 ( 12) hydrogen bonds : bond 0.04400 ( 469) hydrogen bonds : angle 5.69265 ( 1308) SS BOND : bond 0.00245 ( 38) SS BOND : angle 0.95893 ( 76) covalent geometry : bond 0.00374 (16756) covalent geometry : angle 0.65354 (22732) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8654 (ppp) cc_final: 0.7926 (ppp) REVERT: A 426 MET cc_start: 0.7642 (tpp) cc_final: 0.7433 (tpp) REVERT: B 279 ASN cc_start: 0.9283 (t0) cc_final: 0.9072 (t0) REVERT: B 475 MET cc_start: 0.8116 (pmm) cc_final: 0.7574 (mmt) REVERT: H 75 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7720 (pttm) REVERT: H 79 TYR cc_start: 0.6992 (m-10) cc_final: 0.6622 (m-80) REVERT: L 87 TYR cc_start: 0.7716 (m-10) cc_final: 0.7017 (m-80) REVERT: X 584 GLU cc_start: 0.8417 (tt0) cc_final: 0.7529 (tm-30) REVERT: X 654 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8576 (mt-10) REVERT: Y 584 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8383 (tm-30) REVERT: Y 654 GLU cc_start: 0.8574 (tt0) cc_final: 0.8327 (pt0) REVERT: Z 586 TYR cc_start: 0.9190 (t80) cc_final: 0.8965 (t80) outliers start: 24 outliers final: 16 residues processed: 244 average time/residue: 0.2746 time to fit residues: 104.1804 Evaluate side-chains 210 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain Y residue 529 THR Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Y residue 593 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Y residue 648 GLU Chi-restraints excluded: chain Z residue 570 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 81 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 130 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 GLN B 348 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 653 GLN ** 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 = 0.3434 r_free = 0.3434 target = 0.084830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.065422 restraints weight = 54129.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.067632 restraints weight = 30187.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.069095 restraints weight = 20771.475| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16895 Z= 0.226 Angle : 0.734 14.168 23111 Z= 0.345 Chirality : 0.048 0.352 2855 Planarity : 0.004 0.066 2756 Dihedral : 9.088 68.656 4128 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.43 % Allowed : 12.49 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.20), residues: 1866 helix: 1.38 (0.27), residues: 407 sheet: -0.45 (0.23), residues: 527 loop : -0.90 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP X 631 HIS 0.004 0.001 HIS B 249 PHE 0.023 0.002 PHE H 29 TYR 0.038 0.002 TYR X 586 ARG 0.005 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 53) link_NAG-ASN : angle 2.62082 ( 159) link_ALPHA1-6 : bond 0.00989 ( 3) link_ALPHA1-6 : angle 2.46377 ( 9) link_BETA1-4 : bond 0.00514 ( 41) link_BETA1-4 : angle 2.34528 ( 123) link_ALPHA1-3 : bond 0.01087 ( 4) link_ALPHA1-3 : angle 2.15829 ( 12) hydrogen bonds : bond 0.04370 ( 469) hydrogen bonds : angle 5.30024 ( 1308) SS BOND : bond 0.00424 ( 38) SS BOND : angle 1.07069 ( 76) covalent geometry : bond 0.00511 (16756) covalent geometry : angle 0.67863 (22732) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8658 (ppp) cc_final: 0.7989 (ppp) REVERT: A 271 MET cc_start: 0.8253 (mmt) cc_final: 0.7843 (mmm) REVERT: A 377 ASN cc_start: 0.7883 (m110) cc_final: 0.7550 (t0) REVERT: A 426 MET cc_start: 0.8241 (tpp) cc_final: 0.7975 (tpp) REVERT: B 449 ILE cc_start: 0.9603 (mt) cc_final: 0.9323 (tp) REVERT: C 95 MET cc_start: 0.8873 (ppp) cc_final: 0.8207 (ppp) REVERT: C 377 ASN cc_start: 0.8825 (t0) cc_final: 0.8557 (t0) REVERT: H 36 TRP cc_start: 0.8390 (m100) cc_final: 0.8117 (m100) REVERT: L 87 TYR cc_start: 0.7797 (m-80) cc_final: 0.7040 (m-80) REVERT: X 584 GLU cc_start: 0.8590 (tt0) cc_final: 0.7745 (tm-30) REVERT: X 654 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8570 (mt-10) REVERT: Z 581 LEU cc_start: 0.9244 (tt) cc_final: 0.8888 (pp) outliers start: 41 outliers final: 29 residues processed: 225 average time/residue: 0.2842 time to fit residues: 99.2562 Evaluate side-chains 208 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain X residue 544 LEU Chi-restraints excluded: chain X residue 589 ASP Chi-restraints excluded: chain Y residue 544 LEU Chi-restraints excluded: chain Y residue 619 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 539 VAL Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 613 SER Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain Z residue 639 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 55 optimal weight: 5.9990 chunk 154 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 653 GLN ** 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 = 0.3440 r_free = 0.3440 target = 0.085184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.065745 restraints weight = 53923.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.067981 restraints weight = 29979.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.069495 restraints weight = 20592.866| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16895 Z= 0.166 Angle : 0.663 14.485 23111 Z= 0.311 Chirality : 0.046 0.358 2855 Planarity : 0.003 0.039 2756 Dihedral : 8.285 61.525 4128 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.66 % Allowed : 15.21 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1866 helix: 1.46 (0.27), residues: 407 sheet: -0.44 (0.22), residues: 559 loop : -0.92 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP X 631 HIS 0.003 0.001 HIS C 249 PHE 0.013 0.001 PHE H 100O TYR 0.035 0.002 TYR X 586 ARG 0.006 0.000 ARG B 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 53) link_NAG-ASN : angle 2.49625 ( 159) link_ALPHA1-6 : bond 0.01055 ( 3) link_ALPHA1-6 : angle 2.28167 ( 9) link_BETA1-4 : bond 0.00474 ( 41) link_BETA1-4 : angle 2.11334 ( 123) link_ALPHA1-3 : bond 0.01073 ( 4) link_ALPHA1-3 : angle 2.27723 ( 12) hydrogen bonds : bond 0.03810 ( 469) hydrogen bonds : angle 5.08932 ( 1308) SS BOND : bond 0.00259 ( 38) SS BOND : angle 0.83630 ( 76) covalent geometry : bond 0.00379 (16756) covalent geometry : angle 0.61041 (22732) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8719 (ppp) cc_final: 0.7832 (ppp) REVERT: A 271 MET cc_start: 0.8244 (mmt) cc_final: 0.7914 (mmm) REVERT: A 426 MET cc_start: 0.8297 (tpp) cc_final: 0.8007 (tpp) REVERT: B 96 TRP cc_start: 0.8817 (m100) cc_final: 0.8500 (m100) REVERT: B 116 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8587 (tt) REVERT: B 279 ASN cc_start: 0.9358 (t0) cc_final: 0.9056 (t0) REVERT: C 95 MET cc_start: 0.8854 (ppp) cc_final: 0.8263 (ppp) REVERT: C 424 ILE cc_start: 0.9428 (pt) cc_final: 0.9098 (mt) REVERT: H 51 ILE cc_start: 0.7419 (tp) cc_final: 0.7130 (tt) REVERT: H 75 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8327 (pttp) REVERT: L 87 TYR cc_start: 0.7967 (m-80) cc_final: 0.7254 (m-80) REVERT: X 584 GLU cc_start: 0.8500 (tt0) cc_final: 0.7674 (tm-30) REVERT: X 654 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8556 (mt-10) REVERT: Z 581 LEU cc_start: 0.9254 (tt) cc_final: 0.8942 (pp) REVERT: Z 586 TYR cc_start: 0.9165 (t80) cc_final: 0.8866 (t80) outliers start: 45 outliers final: 30 residues processed: 223 average time/residue: 0.2695 time to fit residues: 94.0413 Evaluate side-chains 212 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain X residue 544 LEU Chi-restraints excluded: chain X residue 589 ASP Chi-restraints excluded: chain Y residue 544 LEU Chi-restraints excluded: chain Y residue 592 LEU Chi-restraints excluded: chain Y residue 619 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain Z residue 639 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 106 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 179 optimal weight: 0.0870 chunk 7 optimal weight: 2.9990 chunk 85 optimal weight: 0.0270 chunk 0 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 20.0000 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 630 GLN ** Z 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.086060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.066891 restraints weight = 54055.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.069118 restraints weight = 30264.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.070636 restraints weight = 20831.938| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16895 Z= 0.125 Angle : 0.632 14.180 23111 Z= 0.296 Chirality : 0.045 0.332 2855 Planarity : 0.003 0.038 2756 Dihedral : 7.885 59.493 4128 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.54 % Allowed : 16.27 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1866 helix: 1.55 (0.27), residues: 413 sheet: -0.34 (0.22), residues: 558 loop : -0.86 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 631 HIS 0.003 0.001 HIS C 249 PHE 0.012 0.001 PHE C 288 TYR 0.025 0.002 TYR X 586 ARG 0.011 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 53) link_NAG-ASN : angle 2.41212 ( 159) link_ALPHA1-6 : bond 0.01065 ( 3) link_ALPHA1-6 : angle 2.04081 ( 9) link_BETA1-4 : bond 0.00457 ( 41) link_BETA1-4 : angle 1.93936 ( 123) link_ALPHA1-3 : bond 0.00955 ( 4) link_ALPHA1-3 : angle 2.27308 ( 12) hydrogen bonds : bond 0.03586 ( 469) hydrogen bonds : angle 4.92486 ( 1308) SS BOND : bond 0.00195 ( 38) SS BOND : angle 0.72204 ( 76) covalent geometry : bond 0.00284 (16756) covalent geometry : angle 0.58199 (22732) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.8230 (mmt) cc_final: 0.7942 (mmm) REVERT: A 426 MET cc_start: 0.8313 (tpp) cc_final: 0.8039 (tpp) REVERT: A 434 MET cc_start: 0.8790 (tmm) cc_final: 0.8340 (tmm) REVERT: B 96 TRP cc_start: 0.8767 (m100) cc_final: 0.8487 (m100) REVERT: B 107 ASP cc_start: 0.8509 (m-30) cc_final: 0.8275 (m-30) REVERT: B 116 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8453 (tp) REVERT: C 95 MET cc_start: 0.8865 (ppp) cc_final: 0.8211 (ppp) REVERT: C 161 MET cc_start: 0.8321 (mmm) cc_final: 0.8089 (mmt) REVERT: C 424 ILE cc_start: 0.9350 (pt) cc_final: 0.9056 (mt) REVERT: H 51 ILE cc_start: 0.7461 (tp) cc_final: 0.7155 (tt) REVERT: L 42 ARG cc_start: 0.7333 (ptp-170) cc_final: 0.7108 (ptp90) REVERT: L 87 TYR cc_start: 0.7938 (m-80) cc_final: 0.7281 (m-80) REVERT: X 543 ASN cc_start: 0.8715 (t0) cc_final: 0.8475 (t0) REVERT: X 584 GLU cc_start: 0.8521 (tt0) cc_final: 0.7658 (tm-30) REVERT: Y 574 LYS cc_start: 0.8163 (pttt) cc_final: 0.7733 (ptpt) REVERT: Y 586 TYR cc_start: 0.9367 (t80) cc_final: 0.9081 (t80) REVERT: Z 537 LEU cc_start: 0.9104 (mp) cc_final: 0.8846 (mm) REVERT: Z 581 LEU cc_start: 0.9266 (tt) cc_final: 0.8929 (pp) REVERT: Z 586 TYR cc_start: 0.9088 (t80) cc_final: 0.8785 (t80) REVERT: Z 648 GLU cc_start: 0.8904 (tp30) cc_final: 0.8354 (tm-30) outliers start: 43 outliers final: 29 residues processed: 227 average time/residue: 0.2518 time to fit residues: 89.9804 Evaluate side-chains 207 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain X residue 544 LEU Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Y residue 619 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain Z residue 639 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 179 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.086420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.067201 restraints weight = 54035.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.069416 restraints weight = 30447.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.070913 restraints weight = 21105.821| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16895 Z= 0.124 Angle : 0.627 14.201 23111 Z= 0.296 Chirality : 0.044 0.330 2855 Planarity : 0.003 0.038 2756 Dihedral : 7.577 58.320 4128 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.84 % Allowed : 16.75 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1866 helix: 1.52 (0.27), residues: 415 sheet: -0.23 (0.22), residues: 547 loop : -0.85 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP X 631 HIS 0.003 0.001 HIS C 249 PHE 0.023 0.001 PHE H 29 TYR 0.022 0.001 TYR L 49 ARG 0.006 0.000 ARG B 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 53) link_NAG-ASN : angle 2.37307 ( 159) link_ALPHA1-6 : bond 0.01170 ( 3) link_ALPHA1-6 : angle 1.97853 ( 9) link_BETA1-4 : bond 0.00461 ( 41) link_BETA1-4 : angle 1.84031 ( 123) link_ALPHA1-3 : bond 0.01052 ( 4) link_ALPHA1-3 : angle 2.28033 ( 12) hydrogen bonds : bond 0.03490 ( 469) hydrogen bonds : angle 4.84162 ( 1308) SS BOND : bond 0.00243 ( 38) SS BOND : angle 1.03748 ( 76) covalent geometry : bond 0.00286 (16756) covalent geometry : angle 0.57745 (22732) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 193 time to evaluate : 1.676 Fit side-chains revert: symmetry clash REVERT: A 271 MET cc_start: 0.8210 (mmt) cc_final: 0.7852 (mmm) REVERT: A 434 MET cc_start: 0.8820 (tmm) cc_final: 0.8341 (tmm) REVERT: B 96 TRP cc_start: 0.8740 (m100) cc_final: 0.8499 (m100) REVERT: B 107 ASP cc_start: 0.8539 (m-30) cc_final: 0.8236 (m-30) REVERT: B 116 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8472 (tp) REVERT: C 95 MET cc_start: 0.8848 (ppp) cc_final: 0.8202 (ppp) REVERT: C 424 ILE cc_start: 0.9324 (pt) cc_final: 0.9110 (mt) REVERT: H 51 ILE cc_start: 0.7507 (tp) cc_final: 0.7247 (tt) REVERT: H 73 GLU cc_start: 0.7459 (pm20) cc_final: 0.6716 (mp0) REVERT: H 82 MET cc_start: 0.6044 (ptt) cc_final: 0.5333 (ptp) REVERT: L 5 THR cc_start: 0.8702 (p) cc_final: 0.8434 (t) REVERT: L 87 TYR cc_start: 0.7920 (m-80) cc_final: 0.7246 (m-80) REVERT: X 543 ASN cc_start: 0.8694 (t0) cc_final: 0.8422 (t0) REVERT: X 584 GLU cc_start: 0.8513 (tt0) cc_final: 0.7633 (tm-30) REVERT: Y 574 LYS cc_start: 0.8287 (pttt) cc_final: 0.7894 (ptpt) REVERT: Y 586 TYR cc_start: 0.9353 (t80) cc_final: 0.9052 (t80) REVERT: Y 654 GLU cc_start: 0.8817 (tt0) cc_final: 0.8291 (pt0) REVERT: Z 581 LEU cc_start: 0.9260 (tt) cc_final: 0.8932 (pp) REVERT: Z 586 TYR cc_start: 0.9081 (t80) cc_final: 0.8766 (t80) outliers start: 48 outliers final: 33 residues processed: 227 average time/residue: 0.2519 time to fit residues: 89.1022 Evaluate side-chains 211 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Y residue 544 LEU Chi-restraints excluded: chain Y residue 619 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 635 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.0370 chunk 174 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 591 GLN ** Z 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 653 GLN ** 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 = 0.3473 r_free = 0.3473 target = 0.087039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.067853 restraints weight = 53830.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.070094 restraints weight = 30328.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.071602 restraints weight = 20972.253| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16895 Z= 0.115 Angle : 0.615 14.120 23111 Z= 0.290 Chirality : 0.044 0.323 2855 Planarity : 0.003 0.038 2756 Dihedral : 7.292 57.956 4128 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.08 % Allowed : 17.34 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1866 helix: 1.53 (0.27), residues: 418 sheet: -0.06 (0.23), residues: 534 loop : -0.81 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP X 631 HIS 0.003 0.001 HIS B 216 PHE 0.016 0.001 PHE H 29 TYR 0.025 0.002 TYR Z 638 ARG 0.005 0.000 ARG B 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 53) link_NAG-ASN : angle 2.33116 ( 159) link_ALPHA1-6 : bond 0.01095 ( 3) link_ALPHA1-6 : angle 1.84795 ( 9) link_BETA1-4 : bond 0.00453 ( 41) link_BETA1-4 : angle 1.76394 ( 123) link_ALPHA1-3 : bond 0.00960 ( 4) link_ALPHA1-3 : angle 2.26911 ( 12) hydrogen bonds : bond 0.03428 ( 469) hydrogen bonds : angle 4.74748 ( 1308) SS BOND : bond 0.00205 ( 38) SS BOND : angle 0.93443 ( 76) covalent geometry : bond 0.00262 (16756) covalent geometry : angle 0.56834 (22732) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8666 (ppp) cc_final: 0.7606 (ppp) REVERT: A 271 MET cc_start: 0.8187 (mmt) cc_final: 0.7891 (mmm) REVERT: A 434 MET cc_start: 0.8874 (tmm) cc_final: 0.8380 (tmm) REVERT: B 96 TRP cc_start: 0.8698 (m100) cc_final: 0.8494 (m100) REVERT: B 107 ASP cc_start: 0.8447 (m-30) cc_final: 0.8182 (m-30) REVERT: B 116 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8542 (tp) REVERT: C 95 MET cc_start: 0.8849 (ppp) cc_final: 0.8239 (ppp) REVERT: C 320 THR cc_start: 0.9054 (m) cc_final: 0.8844 (m) REVERT: C 424 ILE cc_start: 0.9373 (pt) cc_final: 0.9172 (mt) REVERT: H 51 ILE cc_start: 0.7508 (tp) cc_final: 0.7229 (tt) REVERT: H 73 GLU cc_start: 0.7436 (pm20) cc_final: 0.6808 (mp0) REVERT: L 5 THR cc_start: 0.8626 (p) cc_final: 0.8368 (t) REVERT: L 87 TYR cc_start: 0.7839 (m-80) cc_final: 0.7278 (m-80) REVERT: X 543 ASN cc_start: 0.8563 (t0) cc_final: 0.8256 (t0) REVERT: X 584 GLU cc_start: 0.8467 (tt0) cc_final: 0.7562 (tm-30) REVERT: X 654 GLU cc_start: 0.8629 (tp30) cc_final: 0.8333 (tp30) REVERT: Y 654 GLU cc_start: 0.8701 (tt0) cc_final: 0.8344 (pt0) REVERT: Z 581 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8955 (pp) REVERT: Z 586 TYR cc_start: 0.9110 (t80) cc_final: 0.8869 (t80) REVERT: Z 591 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8163 (tp40) outliers start: 52 outliers final: 36 residues processed: 228 average time/residue: 0.2502 time to fit residues: 89.7277 Evaluate side-chains 218 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain X residue 544 LEU Chi-restraints excluded: chain Y residue 529 THR Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Y residue 544 LEU Chi-restraints excluded: chain Y residue 619 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 581 LEU Chi-restraints excluded: chain Z residue 591 GLN Chi-restraints excluded: chain Z residue 635 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 82 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 158 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 653 GLN ** 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 = 0.3439 r_free = 0.3439 target = 0.085165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.065857 restraints weight = 54047.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.068109 restraints weight = 30053.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.069636 restraints weight = 20569.187| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16895 Z= 0.160 Angle : 0.651 14.290 23111 Z= 0.307 Chirality : 0.045 0.322 2855 Planarity : 0.004 0.055 2756 Dihedral : 7.291 57.720 4128 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.96 % Allowed : 17.46 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1866 helix: 1.52 (0.26), residues: 415 sheet: -0.07 (0.23), residues: 528 loop : -0.84 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 631 HIS 0.003 0.001 HIS C 249 PHE 0.015 0.001 PHE H 29 TYR 0.028 0.002 TYR Z 643 ARG 0.005 0.000 ARG B 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 53) link_NAG-ASN : angle 2.37725 ( 159) link_ALPHA1-6 : bond 0.01011 ( 3) link_ALPHA1-6 : angle 1.87614 ( 9) link_BETA1-4 : bond 0.00431 ( 41) link_BETA1-4 : angle 1.80633 ( 123) link_ALPHA1-3 : bond 0.00882 ( 4) link_ALPHA1-3 : angle 2.30668 ( 12) hydrogen bonds : bond 0.03584 ( 469) hydrogen bonds : angle 4.79345 ( 1308) SS BOND : bond 0.00303 ( 38) SS BOND : angle 0.97954 ( 76) covalent geometry : bond 0.00369 (16756) covalent geometry : angle 0.60537 (22732) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.8248 (mmt) cc_final: 0.7957 (mmm) REVERT: A 434 MET cc_start: 0.8903 (tmm) cc_final: 0.8409 (tmm) REVERT: B 116 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8539 (tp) REVERT: C 95 MET cc_start: 0.8861 (ppp) cc_final: 0.8249 (ppp) REVERT: C 104 MET cc_start: 0.9319 (tpp) cc_final: 0.8702 (tpp) REVERT: C 161 MET cc_start: 0.8441 (mmm) cc_final: 0.8211 (mmm) REVERT: C 320 THR cc_start: 0.9102 (m) cc_final: 0.8883 (m) REVERT: C 377 ASN cc_start: 0.8758 (t0) cc_final: 0.8457 (t0) REVERT: H 51 ILE cc_start: 0.7495 (tp) cc_final: 0.7226 (tt) REVERT: H 73 GLU cc_start: 0.7452 (pm20) cc_final: 0.6785 (mp0) REVERT: L 5 THR cc_start: 0.8588 (p) cc_final: 0.8297 (t) REVERT: L 87 TYR cc_start: 0.7828 (m-80) cc_final: 0.7227 (m-80) REVERT: X 543 ASN cc_start: 0.8698 (t0) cc_final: 0.8314 (t0) REVERT: X 584 GLU cc_start: 0.8525 (tt0) cc_final: 0.7639 (tm-30) REVERT: Y 654 GLU cc_start: 0.8772 (tt0) cc_final: 0.8408 (pt0) REVERT: Z 581 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8957 (pp) REVERT: Z 586 TYR cc_start: 0.9112 (t80) cc_final: 0.8901 (t80) REVERT: Z 591 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8374 (tp40) REVERT: Z 648 GLU cc_start: 0.8827 (tp30) cc_final: 0.8458 (pp20) outliers start: 50 outliers final: 39 residues processed: 219 average time/residue: 0.2525 time to fit residues: 87.7143 Evaluate side-chains 213 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Y residue 544 LEU Chi-restraints excluded: chain Y residue 619 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 581 LEU Chi-restraints excluded: chain Z residue 591 GLN Chi-restraints excluded: chain Z residue 635 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 38 optimal weight: 0.8980 chunk 125 optimal weight: 0.0030 chunk 2 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 186 optimal weight: 7.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.086483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.067227 restraints weight = 53925.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.069514 restraints weight = 29829.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.071076 restraints weight = 20376.718| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16895 Z= 0.116 Angle : 0.620 14.158 23111 Z= 0.293 Chirality : 0.044 0.317 2855 Planarity : 0.003 0.038 2756 Dihedral : 7.104 58.071 4128 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.84 % Allowed : 17.87 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1866 helix: 1.53 (0.26), residues: 415 sheet: -0.01 (0.22), residues: 546 loop : -0.77 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 96 HIS 0.003 0.001 HIS C 249 PHE 0.014 0.001 PHE C 382 TYR 0.029 0.002 TYR C 486 ARG 0.004 0.000 ARG B 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 53) link_NAG-ASN : angle 2.31579 ( 159) link_ALPHA1-6 : bond 0.01088 ( 3) link_ALPHA1-6 : angle 1.73310 ( 9) link_BETA1-4 : bond 0.00451 ( 41) link_BETA1-4 : angle 1.71657 ( 123) link_ALPHA1-3 : bond 0.00938 ( 4) link_ALPHA1-3 : angle 2.30187 ( 12) hydrogen bonds : bond 0.03412 ( 469) hydrogen bonds : angle 4.70780 ( 1308) SS BOND : bond 0.00172 ( 38) SS BOND : angle 0.86351 ( 76) covalent geometry : bond 0.00267 (16756) covalent geometry : angle 0.57539 (22732) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.7723 (m-10) cc_final: 0.7389 (m-10) REVERT: A 271 MET cc_start: 0.8205 (mmt) cc_final: 0.7942 (mmm) REVERT: A 426 MET cc_start: 0.8492 (tpp) cc_final: 0.8289 (tpp) REVERT: A 434 MET cc_start: 0.8914 (tmm) cc_final: 0.8407 (tmm) REVERT: B 116 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8547 (tp) REVERT: C 95 MET cc_start: 0.8920 (ppp) cc_final: 0.8284 (ppp) REVERT: C 161 MET cc_start: 0.8321 (mmm) cc_final: 0.8097 (mmt) REVERT: C 320 THR cc_start: 0.9053 (m) cc_final: 0.8816 (m) REVERT: C 490 LYS cc_start: 0.7600 (ttmt) cc_final: 0.7260 (tmmt) REVERT: H 73 GLU cc_start: 0.7483 (pm20) cc_final: 0.6826 (mp0) REVERT: L 5 THR cc_start: 0.8575 (p) cc_final: 0.8276 (t) REVERT: L 87 TYR cc_start: 0.7918 (m-80) cc_final: 0.7074 (m-80) REVERT: X 543 ASN cc_start: 0.8640 (t0) cc_final: 0.8292 (t0) REVERT: X 584 GLU cc_start: 0.8453 (tt0) cc_final: 0.7563 (tm-30) REVERT: Y 574 LYS cc_start: 0.8255 (pttt) cc_final: 0.7740 (ptpt) REVERT: Y 586 TYR cc_start: 0.9401 (t80) cc_final: 0.9113 (t80) REVERT: Y 654 GLU cc_start: 0.8810 (tt0) cc_final: 0.8441 (pt0) REVERT: Z 581 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8949 (pp) outliers start: 48 outliers final: 38 residues processed: 226 average time/residue: 0.2460 time to fit residues: 87.3656 Evaluate side-chains 223 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain X residue 544 LEU Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Y residue 544 LEU Chi-restraints excluded: chain Y residue 619 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 581 LEU Chi-restraints excluded: chain Z residue 635 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 166 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN C 258 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 653 GLN ** 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 = 0.3446 r_free = 0.3446 target = 0.085608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.066417 restraints weight = 54487.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.068660 restraints weight = 30800.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.070126 restraints weight = 21278.232| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16895 Z= 0.144 Angle : 0.646 14.287 23111 Z= 0.305 Chirality : 0.044 0.319 2855 Planarity : 0.003 0.044 2756 Dihedral : 7.102 57.414 4128 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.54 % Allowed : 18.28 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1866 helix: 1.47 (0.26), residues: 415 sheet: 0.02 (0.23), residues: 529 loop : -0.80 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP X 631 HIS 0.003 0.001 HIS C 249 PHE 0.014 0.001 PHE C 382 TYR 0.028 0.002 TYR Z 638 ARG 0.006 0.000 ARG L 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 53) link_NAG-ASN : angle 2.34694 ( 159) link_ALPHA1-6 : bond 0.01079 ( 3) link_ALPHA1-6 : angle 1.75232 ( 9) link_BETA1-4 : bond 0.00449 ( 41) link_BETA1-4 : angle 1.74326 ( 123) link_ALPHA1-3 : bond 0.00877 ( 4) link_ALPHA1-3 : angle 2.29304 ( 12) hydrogen bonds : bond 0.03522 ( 469) hydrogen bonds : angle 4.75011 ( 1308) SS BOND : bond 0.00244 ( 38) SS BOND : angle 0.97540 ( 76) covalent geometry : bond 0.00332 (16756) covalent geometry : angle 0.60203 (22732) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.8238 (mmt) cc_final: 0.7932 (mmm) REVERT: A 426 MET cc_start: 0.8567 (tpp) cc_final: 0.8316 (tpp) REVERT: A 434 MET cc_start: 0.8917 (tmm) cc_final: 0.8402 (tmm) REVERT: B 116 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8525 (tp) REVERT: C 95 MET cc_start: 0.8943 (ppp) cc_final: 0.8322 (ppp) REVERT: C 104 MET cc_start: 0.9321 (tpp) cc_final: 0.8746 (tpp) REVERT: C 161 MET cc_start: 0.8340 (mmm) cc_final: 0.8087 (mmt) REVERT: C 320 THR cc_start: 0.9076 (m) cc_final: 0.8832 (m) REVERT: C 490 LYS cc_start: 0.7634 (ttmt) cc_final: 0.7271 (tmmt) REVERT: H 73 GLU cc_start: 0.7437 (pm20) cc_final: 0.6727 (mp0) REVERT: L 5 THR cc_start: 0.8590 (p) cc_final: 0.8287 (t) REVERT: L 87 TYR cc_start: 0.7937 (m-80) cc_final: 0.7340 (m-80) REVERT: L 98 PHE cc_start: 0.8216 (m-80) cc_final: 0.7628 (m-80) REVERT: X 543 ASN cc_start: 0.8685 (t0) cc_final: 0.8325 (t0) REVERT: X 584 GLU cc_start: 0.8476 (tt0) cc_final: 0.7568 (tm-30) REVERT: X 631 TRP cc_start: 0.8840 (t-100) cc_final: 0.8570 (t-100) REVERT: Y 574 LYS cc_start: 0.8311 (pttt) cc_final: 0.7857 (ptpt) REVERT: Y 654 GLU cc_start: 0.8898 (tt0) cc_final: 0.8453 (pt0) REVERT: Z 581 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8957 (pp) outliers start: 43 outliers final: 38 residues processed: 219 average time/residue: 0.2527 time to fit residues: 87.3681 Evaluate side-chains 215 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Y residue 544 LEU Chi-restraints excluded: chain Y residue 592 LEU Chi-restraints excluded: chain Y residue 619 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 581 LEU Chi-restraints excluded: chain Z residue 635 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 86 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.085724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.066560 restraints weight = 54383.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.068767 restraints weight = 30694.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.070228 restraints weight = 21287.039| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16895 Z= 0.138 Angle : 0.651 14.230 23111 Z= 0.309 Chirality : 0.044 0.319 2855 Planarity : 0.003 0.045 2756 Dihedral : 7.057 57.940 4128 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.60 % Allowed : 18.46 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1866 helix: 1.50 (0.26), residues: 412 sheet: 0.03 (0.23), residues: 536 loop : -0.77 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP X 631 HIS 0.003 0.001 HIS C 249 PHE 0.012 0.001 PHE H 100O TYR 0.052 0.002 TYR Z 643 ARG 0.005 0.000 ARG L 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 53) link_NAG-ASN : angle 2.32828 ( 159) link_ALPHA1-6 : bond 0.01060 ( 3) link_ALPHA1-6 : angle 1.68582 ( 9) link_BETA1-4 : bond 0.00436 ( 41) link_BETA1-4 : angle 1.72243 ( 123) link_ALPHA1-3 : bond 0.00825 ( 4) link_ALPHA1-3 : angle 2.34017 ( 12) hydrogen bonds : bond 0.03519 ( 469) hydrogen bonds : angle 4.73639 ( 1308) SS BOND : bond 0.00194 ( 38) SS BOND : angle 0.93869 ( 76) covalent geometry : bond 0.00321 (16756) covalent geometry : angle 0.60804 (22732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4752.73 seconds wall clock time: 83 minutes 44.37 seconds (5024.37 seconds total)