Starting phenix.real_space_refine on Sun Aug 24 13:45:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gpi_34193/08_2025/8gpi_34193.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gpi_34193/08_2025/8gpi_34193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gpi_34193/08_2025/8gpi_34193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gpi_34193/08_2025/8gpi_34193.map" model { file = "/net/cci-nas-00/data/ceres_data/8gpi_34193/08_2025/8gpi_34193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gpi_34193/08_2025/8gpi_34193.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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 117 5.16 5 C 12666 2.51 5 N 3297 2.21 5 O 4185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20265 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "C" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "R" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 966 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "S" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 966 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "T" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 966 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "X" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3408 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 3 Chain: "Y" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3408 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 3 Chain: "Z" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3408 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 3 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: "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: "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: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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: 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: "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: "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: 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: 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: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "l" 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: "m" 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: "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: "R" 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: "S" 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: "T" 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: "X" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "Y" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "Z" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.33, per 1000 atoms: 0.26 Number of scatterers: 20265 At special positions: 0 Unit cell: (150.52, 155.82, 126.14, 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 117 16.00 O 4185 8.00 N 3297 7.00 C 12666 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 598 " - pdb=" SG CYS R 604 " distance=2.03 Simple disulfide: pdb=" SG CYS R 605 " - pdb=" SG CYS X 501 " distance=2.03 Simple disulfide: pdb=" SG CYS S 598 " - pdb=" SG CYS S 604 " distance=2.03 Simple disulfide: pdb=" SG CYS S 605 " - pdb=" SG CYS Y 501 " distance=2.03 Simple disulfide: pdb=" SG CYS T 598 " - pdb=" SG CYS T 604 " distance=2.03 Simple disulfide: pdb=" SG CYS T 605 " - pdb=" SG CYS Z 501 " distance=2.03 Simple disulfide: pdb=" SG CYS X 54 " - pdb=" SG CYS X 74 " distance=2.03 Simple disulfide: pdb=" SG CYS X 119 " - pdb=" SG CYS X 205 " distance=2.03 Simple disulfide: pdb=" SG CYS X 126 " - pdb=" SG CYS X 196 " distance=2.03 Simple disulfide: pdb=" SG CYS X 131 " - pdb=" SG CYS X 157 " distance=2.03 Simple disulfide: pdb=" SG CYS X 218 " - pdb=" SG CYS X 247 " distance=2.05 Simple disulfide: pdb=" SG CYS X 228 " - pdb=" SG CYS X 239 " distance=2.03 Simple disulfide: pdb=" SG CYS X 296 " - pdb=" SG CYS X 331 " distance=2.03 Simple disulfide: pdb=" SG CYS X 378 " - pdb=" SG CYS X 445 " distance=2.03 Simple disulfide: pdb=" SG CYS X 385 " - pdb=" SG CYS X 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 54 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 119 " - pdb=" SG CYS Y 205 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 126 " - pdb=" SG CYS Y 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 131 " - pdb=" SG CYS Y 157 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 218 " - pdb=" SG CYS Y 247 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 228 " - pdb=" SG CYS Y 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 296 " - pdb=" SG CYS Y 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 378 " - pdb=" SG CYS Y 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 385 " - pdb=" SG CYS Y 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 54 " - pdb=" SG CYS Z 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 126 " - pdb=" SG CYS Z 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 131 " - pdb=" SG CYS Z 157 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 218 " - pdb=" SG CYS Z 247 " distance=2.05 Simple disulfide: pdb=" SG CYS Z 228 " - pdb=" SG CYS Z 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 296 " - pdb=" SG CYS Z 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 378 " - pdb=" SG CYS Z 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 385 " - pdb=" SG CYS Z 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " " MAN K 8 " - " MAN K 9 " " MAN K 10 " - " MAN K 11 " " MAN b 4 " - " MAN b 5 " " MAN b 5 " - " MAN b 6 " " MAN b 8 " - " MAN b 9 " " MAN b 10 " - " MAN b 11 " " MAN k 4 " - " MAN k 5 " " MAN k 5 " - " MAN k 6 " " MAN k 8 " - " MAN k 9 " " MAN k 10 " - " MAN k 11 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 8 " " BMA M 3 " - " MAN M 4 " " BMA b 3 " - " MAN b 4 " " MAN b 7 " - " MAN b 8 " " BMA c 3 " - " MAN c 4 " " BMA k 3 " - " MAN k 4 " " MAN k 7 " - " MAN k 8 " " BMA l 3 " - " MAN l 4 " ALPHA1-6 " BMA K 3 " - " MAN K 7 " " MAN K 7 " - " MAN K 10 " " BMA M 3 " - " MAN M 5 " " BMA b 3 " - " MAN b 7 " " MAN b 7 " - " MAN b 10 " " BMA c 3 " - " MAN c 5 " " BMA k 3 " - " MAN k 7 " " MAN k 7 " - " MAN k 10 " " BMA l 3 " - " MAN l 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG 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-ASN " NAG B 1 " - " ASN R 637 " " NAG F 1 " - " ASN S 637 " " NAG G 1 " - " ASN T 637 " " NAG I 1 " - " ASN X 156 " " NAG J 1 " - " ASN X 197 " " NAG K 1 " - " ASN X 234 " " NAG M 1 " - " ASN X 262 " " NAG N 1 " - " ASN X 444 " " NAG O 1 " - " ASN X 386 " " NAG P 1 " - " ASN X 276 " " NAG Q 1 " - " ASN X 289 " " NAG R 701 " - " ASN R 611 " " NAG S 701 " - " ASN S 611 " " NAG T 701 " - " ASN T 611 " " NAG U 1 " - " ASN X 339 " " NAG V 1 " - " ASN X 130 " " NAG W 1 " - " ASN Y 156 " " NAG X 701 " - " ASN X 88 " " NAG X 702 " - " ASN X 135 " " NAG X 703 " - " ASN X 149 " " NAG X 704 " - " ASN X 160 " " NAG X 705 " - " ASN X 241 " " NAG X 706 " - " ASN X 448 " " NAG X 707 " - " ASN X 301 " " NAG X 708 " - " ASN X 334 " " NAG Y 701 " - " ASN Y 88 " " NAG Y 702 " - " ASN Y 135 " " NAG Y 703 " - " ASN Y 149 " " NAG Y 704 " - " ASN Y 160 " " NAG Y 705 " - " ASN Y 241 " " NAG Y 706 " - " ASN Y 301 " " NAG Y 707 " - " ASN Y 334 " " NAG Y 708 " - " ASN Y 339 " " NAG Y 709 " - " ASN Y 448 " " NAG Z 701 " - " ASN Z 88 " " NAG Z 702 " - " ASN Z 135 " " NAG Z 703 " - " ASN Z 149 " " NAG Z 704 " - " ASN Z 160 " " NAG Z 705 " - " ASN Z 241 " " NAG Z 706 " - " ASN Z 448 " " NAG Z 707 " - " ASN Z 301 " " NAG Z 708 " - " ASN Z 334 " " NAG Z 709 " - " ASN Z 356 " " NAG a 1 " - " ASN Y 197 " " NAG b 1 " - " ASN Y 234 " " NAG c 1 " - " ASN Y 262 " " NAG d 1 " - " ASN Y 276 " " NAG e 1 " - " ASN Y 289 " " NAG f 1 " - " ASN Y 386 " " NAG g 1 " - " ASN Y 444 " " NAG h 1 " - " ASN Y 130 " " NAG i 1 " - " ASN Z 156 " " NAG j 1 " - " ASN Z 197 " " NAG k 1 " - " ASN Z 234 " " NAG l 1 " - " ASN Z 262 " " NAG m 1 " - " ASN Z 276 " " NAG n 1 " - " ASN Z 289 " " NAG o 1 " - " ASN Z 339 " " NAG p 1 " - " ASN Z 386 " " NAG q 1 " - " ASN Z 444 " " NAG r 1 " - " ASN Z 130 " Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 970.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4362 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 38 sheets defined 19.1% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 60 through 63 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.978A pdb=" N THR A 93 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.599A pdb=" N PHE C 83 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 63 removed outlier: 3.563A pdb=" N ARG D 63 " --> pdb=" O HIS D 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing helix chain 'D' and resid 89 through 93 removed outlier: 4.029A pdb=" N THR D 93 " --> pdb=" O SER D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.584A pdb=" N PHE E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 63 Processing helix chain 'H' and resid 89 through 93 removed outlier: 4.079A pdb=" N THR H 93 " --> pdb=" O SER H 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 529 through 534 Processing helix chain 'R' and resid 536 through 544 removed outlier: 4.308A pdb=" N GLN R 540 " --> pdb=" O THR R 536 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN R 543 " --> pdb=" O VAL R 539 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU R 544 " --> pdb=" O GLN R 540 " (cutoff:3.500A) Processing helix chain 'R' and resid 572 through 596 removed outlier: 3.701A pdb=" N TRP R 596 " --> pdb=" O PHE R 592 " (cutoff:3.500A) Processing helix chain 'R' and resid 618 through 625 Processing helix chain 'R' and resid 627 through 635 Processing helix chain 'R' and resid 638 through 663 Processing helix chain 'S' and resid 529 through 534 Processing helix chain 'S' and resid 537 through 544 removed outlier: 3.562A pdb=" N ALA S 541 " --> pdb=" O LEU S 537 " (cutoff:3.500A) Processing helix chain 'S' and resid 572 through 596 removed outlier: 3.662A pdb=" N TRP S 596 " --> pdb=" O PHE S 592 " (cutoff:3.500A) Processing helix chain 'S' and resid 618 through 625 Processing helix chain 'S' and resid 627 through 635 Processing helix chain 'S' and resid 638 through 663 Processing helix chain 'T' and resid 529 through 534 Processing helix chain 'T' and resid 538 through 544 Processing helix chain 'T' and resid 572 through 596 removed outlier: 3.600A pdb=" N TRP T 596 " --> pdb=" O PHE T 592 " (cutoff:3.500A) Processing helix chain 'T' and resid 618 through 625 Processing helix chain 'T' and resid 627 through 635 Processing helix chain 'T' and resid 638 through 663 removed outlier: 3.588A pdb=" N ASP T 644 " --> pdb=" O ASN T 640 " (cutoff:3.500A) Processing helix chain 'X' and resid 98 through 117 removed outlier: 4.287A pdb=" N GLU X 102 " --> pdb=" O ASN X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 126 removed outlier: 3.667A pdb=" N CYS X 126 " --> pdb=" O THR X 123 " (cutoff:3.500A) Processing helix chain 'X' and resid 195 through 198 Processing helix chain 'X' and resid 335 through 350 Processing helix chain 'X' and resid 476 through 481 removed outlier: 3.748A pdb=" N SER X 481 " --> pdb=" O ASP X 477 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 116 removed outlier: 4.471A pdb=" N GLU Y 102 " --> pdb=" O ASN Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 122 through 126 removed outlier: 3.662A pdb=" N CYS Y 126 " --> pdb=" O THR Y 123 " (cutoff:3.500A) Processing helix chain 'Y' and resid 335 through 350 Processing helix chain 'Y' and resid 368 through 373 removed outlier: 3.567A pdb=" N THR Y 372 " --> pdb=" O ASP Y 368 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET Y 373 " --> pdb=" O LEU Y 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 368 through 373' Processing helix chain 'Y' and resid 476 through 484 removed outlier: 3.639A pdb=" N SER Y 481 " --> pdb=" O ASP Y 477 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU Y 482 " --> pdb=" O ASN Y 478 " (cutoff:3.500A) Processing helix chain 'Z' and resid 98 through 116 removed outlier: 4.378A pdb=" N GLU Z 102 " --> pdb=" O ASN Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 123 through 126 removed outlier: 3.615A pdb=" N CYS Z 126 " --> pdb=" O THR Z 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 123 through 126' Processing helix chain 'Z' and resid 149 through 152 removed outlier: 4.367A pdb=" N ASP Z 152 " --> pdb=" O ASN Z 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 149 through 152' Processing helix chain 'Z' and resid 195 through 198 Processing helix chain 'Z' and resid 335 through 350 Processing helix chain 'Z' and resid 368 through 373 removed outlier: 3.609A pdb=" N THR Z 372 " --> pdb=" O ASP Z 368 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET Z 373 " --> pdb=" O LEU Z 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 368 through 373' Processing helix chain 'Z' and resid 475 through 484 removed outlier: 3.685A pdb=" N TRP Z 479 " --> pdb=" O ILE Z 475 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU Z 482 " --> pdb=" O ASN Z 478 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR Z 484 " --> pdb=" O ARG Z 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 9 through 10 current: chain 'A' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 55 through 58 current: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 112 Processing sheet with id=AA4, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA5, first strand: chain 'C' and resid 9 through 10 removed outlier: 6.639A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 2 through 5 Processing sheet with id=AA7, first strand: chain 'D' and resid 9 through 10 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 9 through 10 current: chain 'D' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 55 through 58 current: chain 'D' and resid 120 through 121 Processing sheet with id=AA8, first strand: chain 'D' and resid 111 through 112 Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 10 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 9 through 10 current: chain 'E' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 53 through 54 current: chain 'E' and resid 97 through 98 Processing sheet with id=AB2, first strand: chain 'H' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'H' and resid 9 through 10 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 9 through 10 current: chain 'H' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 55 through 58 current: chain 'H' and resid 120 through 121 Processing sheet with id=AB4, first strand: chain 'H' and resid 111 through 112 Processing sheet with id=AB5, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AB6, first strand: chain 'L' and resid 33 through 38 removed outlier: 6.364A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 97 through 98 Processing sheet with id=AB7, first strand: chain 'R' and resid 603 through 609 removed outlier: 5.111A pdb=" N VAL X 36 " --> pdb=" O THR R 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 603 through 609 removed outlier: 5.426A pdb=" N VAL Y 36 " --> pdb=" O THR S 606 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'T' and resid 603 through 609 removed outlier: 4.940A pdb=" N VAL Z 36 " --> pdb=" O THR T 606 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 45 through 47 removed outlier: 4.409A pdb=" N VAL X 242 " --> pdb=" O LEU X 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'X' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'X' and resid 169 through 177 Processing sheet with id=AC5, first strand: chain 'X' and resid 201 through 203 removed outlier: 6.544A pdb=" N LYS X 202 " --> pdb=" O TYR X 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 259 through 261 current: chain 'X' and resid 284 through 298 removed outlier: 7.446A pdb=" N SER X 293 " --> pdb=" O ASN X 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASN X 334 " --> pdb=" O SER X 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 330 through 334 current: chain 'X' and resid 381 through 385 removed outlier: 4.035A pdb=" N PHE X 382 " --> pdb=" O LYS X 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 413 through 421 current: chain 'X' and resid 465 through 470 Processing sheet with id=AC7, first strand: chain 'X' and resid 302 through 312 removed outlier: 6.887A pdb=" N THR X 303 " --> pdb=" O GLY X 320A" (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN X 315 " --> pdb=" O ILE X 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 45 through 47 removed outlier: 4.609A pdb=" N VAL Y 242 " --> pdb=" O LEU Y 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Y' and resid 53 through 55 Processing sheet with id=AD1, first strand: chain 'Y' and resid 91 through 94 Processing sheet with id=AD2, first strand: chain 'Y' and resid 169 through 177 Processing sheet with id=AD3, first strand: chain 'Y' and resid 202 through 203 removed outlier: 6.474A pdb=" N LYS Y 202 " --> pdb=" O TYR Y 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Y' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 259 through 261 current: chain 'Y' and resid 284 through 298 removed outlier: 7.370A pdb=" N SER Y 293 " --> pdb=" O ASN Y 334 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN Y 334 " --> pdb=" O SER Y 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 329 through 334 current: chain 'Y' and resid 381 through 385 removed outlier: 4.274A pdb=" N PHE Y 382 " --> pdb=" O LYS Y 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 413 through 421 current: chain 'Y' and resid 465 through 470 Processing sheet with id=AD5, first strand: chain 'Y' and resid 304 through 308 Processing sheet with id=AD6, first strand: chain 'Z' and resid 45 through 47 removed outlier: 4.575A pdb=" N VAL Z 242 " --> pdb=" O LEU Z 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 53 through 55 Processing sheet with id=AD8, first strand: chain 'Z' and resid 91 through 94 Processing sheet with id=AD9, first strand: chain 'Z' and resid 120 through 121 removed outlier: 3.927A pdb=" N VAL Z 120 " --> pdb=" O GLN Z 203 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS Z 202 " --> pdb=" O TYR Z 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'Z' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 259 through 261 current: chain 'Z' and resid 284 through 312 removed outlier: 6.362A pdb=" N GLY Z 324 " --> pdb=" O PRO Z 299 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN Z 301 " --> pdb=" O ILE Z 322 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE Z 322 " --> pdb=" O ASN Z 301 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR Z 303 " --> pdb=" O GLY Z 320A" (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLN Z 315 " --> pdb=" O ILE Z 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 315 through 324 current: chain 'Z' and resid 381 through 385 removed outlier: 4.248A pdb=" N PHE Z 382 " --> pdb=" O LYS Z 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 413 through 421 current: chain 'Z' and resid 465 through 470 570 hydrogen bonds defined for protein. 1533 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6234 1.35 - 1.48: 5542 1.48 - 1.61: 8732 1.61 - 1.74: 0 1.74 - 1.86: 156 Bond restraints: 20664 Sorted by residual: bond pdb=" C1 MAN b 5 " pdb=" C2 MAN b 5 " ideal model delta sigma weight residual 1.526 1.568 -0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" C1 MAN c 4 " pdb=" C2 MAN c 4 " ideal model delta sigma weight residual 1.526 1.567 -0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" C1 MAN K 5 " pdb=" C2 MAN K 5 " ideal model delta sigma weight residual 1.526 1.566 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C1 MAN k 5 " pdb=" C2 MAN k 5 " ideal model delta sigma weight residual 1.526 1.565 -0.039 2.00e-02 2.50e+03 3.74e+00 bond pdb=" C2 BMA K 3 " pdb=" C3 BMA K 3 " ideal model delta sigma weight residual 1.544 1.506 0.038 2.00e-02 2.50e+03 3.55e+00 ... (remaining 20659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 27075 1.88 - 3.76: 790 3.76 - 5.65: 130 5.65 - 7.53: 56 7.53 - 9.41: 5 Bond angle restraints: 28056 Sorted by residual: angle pdb=" C GLN Z 432 " pdb=" CA GLN Z 432 " pdb=" CB GLN Z 432 " ideal model delta sigma weight residual 117.23 110.56 6.67 1.36e+00 5.41e-01 2.40e+01 angle pdb=" CA CYS X 247 " pdb=" CB CYS X 247 " pdb=" SG CYS X 247 " ideal model delta sigma weight residual 114.40 123.81 -9.41 2.30e+00 1.89e-01 1.67e+01 angle pdb=" CA CYS Z 247 " pdb=" CB CYS Z 247 " pdb=" SG CYS Z 247 " ideal model delta sigma weight residual 114.40 123.23 -8.83 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CA GLN Z 432 " pdb=" C GLN Z 432 " pdb=" N ALA Z 433 " ideal model delta sigma weight residual 119.98 116.89 3.09 8.50e-01 1.38e+00 1.32e+01 angle pdb=" CA PRO X 206 " pdb=" N PRO X 206 " pdb=" CD PRO X 206 " ideal model delta sigma weight residual 112.00 107.35 4.65 1.40e+00 5.10e-01 1.10e+01 ... (remaining 28051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.83: 13215 21.83 - 43.66: 572 43.66 - 65.49: 118 65.49 - 87.32: 84 87.32 - 109.15: 39 Dihedral angle restraints: 14028 sinusoidal: 7248 harmonic: 6780 Sorted by residual: dihedral pdb=" CB CYS X 54 " pdb=" SG CYS X 54 " pdb=" SG CYS X 74 " pdb=" CB CYS X 74 " ideal model delta sinusoidal sigma weight residual 93.00 20.15 72.85 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CB CYS Z 378 " pdb=" SG CYS Z 378 " pdb=" SG CYS Z 445 " pdb=" CB CYS Z 445 " ideal model delta sinusoidal sigma weight residual -86.00 -157.87 71.87 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CB CYS Y 378 " pdb=" SG CYS Y 378 " pdb=" SG CYS Y 445 " pdb=" CB CYS Y 445 " ideal model delta sinusoidal sigma weight residual -86.00 -155.58 69.58 1 1.00e+01 1.00e-02 6.25e+01 ... (remaining 14025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2839 0.058 - 0.116: 596 0.116 - 0.174: 101 0.174 - 0.231: 0 0.231 - 0.289: 10 Chirality restraints: 3546 Sorted by residual: chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C1 NAG q 1 " pdb=" ND2 ASN Z 444 " pdb=" C2 NAG q 1 " pdb=" O5 NAG q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C5 BMA k 3 " pdb=" C4 BMA k 3 " pdb=" C6 BMA k 3 " pdb=" O5 BMA k 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 3543 not shown) Planarity restraints: 3436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS X 205 " 0.068 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO X 206 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO X 206 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO X 206 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL Y 75 " 0.054 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO Y 76 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO Y 76 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO Y 76 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 32 " 0.016 2.00e-02 2.50e+03 1.45e-02 5.26e+00 pdb=" CG TRP L 32 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP L 32 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP L 32 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 32 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP L 32 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 32 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 32 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP L 32 " 0.004 2.00e-02 2.50e+03 ... (remaining 3433 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1026 2.73 - 3.27: 18705 3.27 - 3.82: 32183 3.82 - 4.36: 37999 4.36 - 4.90: 67032 Nonbonded interactions: 156945 Sorted by model distance: nonbonded pdb=" OG SER A 69 " pdb=" OG SER A 82 " model vdw 2.188 3.040 nonbonded pdb=" OG1 THR X 37 " pdb=" OG1 THR X 499 " model vdw 2.208 3.040 nonbonded pdb=" OG SER H 69 " pdb=" OG SER H 82 " model vdw 2.216 3.040 nonbonded pdb=" OG1 THR A 74 " pdb=" OG SER A 77 " model vdw 2.249 3.040 nonbonded pdb=" OE1 GLU D 84 " pdb=" O4 MAN K 6 " model vdw 2.263 3.040 ... (remaining 156940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'b' selection = chain 'k' } ncs_group { reference = chain 'M' selection = chain 'c' selection = chain 'l' } ncs_group { reference = chain 'P' selection = chain 'd' selection = chain 'm' } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'X' selection = (chain 'Y' and resid 33 through 708) selection = (chain 'Z' and resid 33 through 708) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.470 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.090 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 20834 Z= 0.248 Angle : 0.795 9.409 28528 Z= 0.356 Chirality : 0.050 0.289 3546 Planarity : 0.005 0.100 3375 Dihedral : 14.805 109.151 9552 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.17), residues: 2316 helix: 1.41 (0.28), residues: 384 sheet: 0.96 (0.20), residues: 666 loop : -0.33 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG X 166 TYR 0.022 0.001 TYR L 91 PHE 0.024 0.002 PHE R 522 TRP 0.038 0.002 TRP L 32 HIS 0.007 0.001 HIS Y 374 Details of bonding type rmsd covalent geometry : bond 0.00532 (20664) covalent geometry : angle 0.76121 (28056) SS BOND : bond 0.00470 ( 38) SS BOND : angle 1.62326 ( 76) hydrogen bonds : bond 0.12412 ( 570) hydrogen bonds : angle 5.68932 ( 1533) link_ALPHA1-2 : bond 0.00270 ( 12) link_ALPHA1-2 : angle 1.76673 ( 36) link_ALPHA1-3 : bond 0.00384 ( 9) link_ALPHA1-3 : angle 1.61489 ( 27) link_ALPHA1-6 : bond 0.00191 ( 9) link_ALPHA1-6 : angle 2.09288 ( 27) link_BETA1-4 : bond 0.00584 ( 41) link_BETA1-4 : angle 1.86249 ( 123) link_NAG-ASN : bond 0.00293 ( 61) link_NAG-ASN : angle 2.15374 ( 183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.763 Fit side-chains REVERT: D 116 MET cc_start: 0.8146 (mtp) cc_final: 0.7941 (mtm) REVERT: H 110 LEU cc_start: 0.8619 (mt) cc_final: 0.8403 (mt) REVERT: X 211 ASP cc_start: 0.7264 (t0) cc_final: 0.7059 (t0) REVERT: X 326 ILE cc_start: 0.8364 (mm) cc_final: 0.8109 (mp) REVERT: X 457 ASP cc_start: 0.7378 (t0) cc_final: 0.7158 (t0) REVERT: X 466 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7139 (tp30) REVERT: Y 111 LEU cc_start: 0.8044 (tt) cc_final: 0.7829 (tp) REVERT: Y 207 LYS cc_start: 0.7464 (mtmm) cc_final: 0.7260 (mtmm) REVERT: Y 231 LYS cc_start: 0.7675 (mtpp) cc_final: 0.7472 (mtpp) REVERT: Y 347 GLU cc_start: 0.7255 (tp30) cc_final: 0.6985 (tp30) REVERT: Y 443 ILE cc_start: 0.8399 (mm) cc_final: 0.8172 (mp) REVERT: Y 477 ASP cc_start: 0.7908 (m-30) cc_final: 0.7678 (m-30) REVERT: Z 123 THR cc_start: 0.8421 (t) cc_final: 0.8182 (p) REVERT: Z 168 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7916 (mmmm) REVERT: Z 211 ASP cc_start: 0.7379 (t0) cc_final: 0.7179 (t0) REVERT: Z 240 LYS cc_start: 0.7675 (mppt) cc_final: 0.7416 (mtmm) outliers start: 0 outliers final: 1 residues processed: 403 average time/residue: 0.7384 time to fit residues: 332.1793 Evaluate side-chains 375 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 208 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN ** S 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 ASN X 114 GLN X 425 ASN Y 105 GLN Y 375 HIS Z 98 ASN Z 169 GLN Z 315 GLN Z 343 ASN Z 474 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.101929 restraints weight = 29952.894| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.51 r_work: 0.3164 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20834 Z= 0.209 Angle : 0.644 8.878 28528 Z= 0.309 Chirality : 0.045 0.201 3546 Planarity : 0.005 0.083 3375 Dihedral : 11.038 84.510 5210 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.94 % Allowed : 7.85 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.17), residues: 2316 helix: 1.80 (0.27), residues: 387 sheet: 0.85 (0.19), residues: 711 loop : -0.28 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Y 327 TYR 0.021 0.002 TYR E 91 PHE 0.016 0.002 PHE Y 176 TRP 0.015 0.002 TRP C 32 HIS 0.008 0.001 HIS Y 374 Details of bonding type rmsd covalent geometry : bond 0.00498 (20664) covalent geometry : angle 0.60170 (28056) SS BOND : bond 0.00408 ( 38) SS BOND : angle 1.50292 ( 76) hydrogen bonds : bond 0.05213 ( 570) hydrogen bonds : angle 4.74004 ( 1533) link_ALPHA1-2 : bond 0.00381 ( 12) link_ALPHA1-2 : angle 1.73566 ( 36) link_ALPHA1-3 : bond 0.00875 ( 9) link_ALPHA1-3 : angle 1.83467 ( 27) link_ALPHA1-6 : bond 0.00180 ( 9) link_ALPHA1-6 : angle 2.07094 ( 27) link_BETA1-4 : bond 0.00445 ( 41) link_BETA1-4 : angle 1.79804 ( 123) link_NAG-ASN : bond 0.00369 ( 61) link_NAG-ASN : angle 2.09157 ( 183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 391 time to evaluate : 0.792 Fit side-chains REVERT: A 125 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8213 (p) REVERT: H 110 LEU cc_start: 0.8839 (mt) cc_final: 0.8631 (mt) REVERT: L 58 VAL cc_start: 0.7769 (t) cc_final: 0.7474 (p) REVERT: R 624 ASN cc_start: 0.8218 (m110) cc_final: 0.7997 (m-40) REVERT: S 606 THR cc_start: 0.8609 (t) cc_final: 0.8362 (p) REVERT: T 610 TRP cc_start: 0.8386 (t-100) cc_final: 0.8169 (t-100) REVERT: X 211 ASP cc_start: 0.7803 (t0) cc_final: 0.7521 (t0) REVERT: X 232 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8368 (mtmm) REVERT: X 457 ASP cc_start: 0.8065 (t0) cc_final: 0.7742 (t0) REVERT: X 466 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7610 (tp30) REVERT: Y 166 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.8047 (mtm110) REVERT: Y 207 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7585 (mtmm) REVERT: Y 231 LYS cc_start: 0.8037 (mtpp) cc_final: 0.7782 (mtpp) REVERT: Y 347 GLU cc_start: 0.8130 (tp30) cc_final: 0.7736 (tp30) REVERT: Y 477 ASP cc_start: 0.8415 (m-30) cc_final: 0.8213 (m-30) REVERT: Z 103 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: Z 105 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7686 (tp40) REVERT: Z 168 LYS cc_start: 0.8453 (mmmm) cc_final: 0.8238 (mmmm) REVERT: Z 211 ASP cc_start: 0.7864 (t0) cc_final: 0.7629 (t0) REVERT: Z 240 LYS cc_start: 0.8088 (mppt) cc_final: 0.7793 (mtmm) REVERT: Z 333 LEU cc_start: 0.8135 (tt) cc_final: 0.7844 (tt) REVERT: Z 426 MET cc_start: 0.6371 (mtt) cc_final: 0.5672 (mtt) outliers start: 40 outliers final: 19 residues processed: 401 average time/residue: 0.6908 time to fit residues: 311.3569 Evaluate side-chains 398 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 376 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 208 ILE Chi-restraints excluded: chain Y residue 443 ILE Chi-restraints excluded: chain Z residue 103 GLN Chi-restraints excluded: chain Z residue 105 GLN Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 303 THR Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 23 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 209 optimal weight: 0.0570 chunk 81 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** S 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 315 GLN X 425 ASN Y 375 HIS Z 169 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101079 restraints weight = 30097.854| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.50 r_work: 0.3154 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20834 Z= 0.209 Angle : 0.635 8.561 28528 Z= 0.307 Chirality : 0.046 0.220 3546 Planarity : 0.005 0.088 3375 Dihedral : 9.637 74.563 5208 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.66 % Allowed : 9.74 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.17), residues: 2316 helix: 1.92 (0.27), residues: 387 sheet: 0.74 (0.19), residues: 714 loop : -0.27 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Z 166 TYR 0.019 0.002 TYR E 91 PHE 0.016 0.002 PHE Y 176 TRP 0.016 0.002 TRP C 32 HIS 0.009 0.001 HIS Y 375 Details of bonding type rmsd covalent geometry : bond 0.00494 (20664) covalent geometry : angle 0.59269 (28056) SS BOND : bond 0.00417 ( 38) SS BOND : angle 1.60107 ( 76) hydrogen bonds : bond 0.05107 ( 570) hydrogen bonds : angle 4.64400 ( 1533) link_ALPHA1-2 : bond 0.00361 ( 12) link_ALPHA1-2 : angle 1.66103 ( 36) link_ALPHA1-3 : bond 0.00884 ( 9) link_ALPHA1-3 : angle 1.76678 ( 27) link_ALPHA1-6 : bond 0.00143 ( 9) link_ALPHA1-6 : angle 1.91589 ( 27) link_BETA1-4 : bond 0.00448 ( 41) link_BETA1-4 : angle 1.78574 ( 123) link_NAG-ASN : bond 0.00365 ( 61) link_NAG-ASN : angle 2.06812 ( 183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 381 time to evaluate : 0.596 Fit side-chains REVERT: A 100 THR cc_start: 0.8806 (m) cc_final: 0.8478 (t) REVERT: A 125 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8274 (p) REVERT: H 67 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7944 (tp) REVERT: L 58 VAL cc_start: 0.7774 (t) cc_final: 0.7472 (p) REVERT: R 624 ASN cc_start: 0.8264 (m110) cc_final: 0.7958 (m-40) REVERT: S 606 THR cc_start: 0.8624 (t) cc_final: 0.8391 (p) REVERT: S 626 MET cc_start: 0.8390 (mtp) cc_final: 0.8138 (mtm) REVERT: T 610 TRP cc_start: 0.8399 (t-100) cc_final: 0.8198 (t-100) REVERT: X 211 ASP cc_start: 0.7792 (t0) cc_final: 0.7521 (t0) REVERT: X 232 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8404 (mtmm) REVERT: X 457 ASP cc_start: 0.8061 (t0) cc_final: 0.7741 (t0) REVERT: X 466 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7640 (tp30) REVERT: Y 207 LYS cc_start: 0.7913 (mtmm) cc_final: 0.7624 (mtmm) REVERT: Y 231 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7730 (mtpp) REVERT: Y 347 GLU cc_start: 0.8194 (tp30) cc_final: 0.7802 (tp30) REVERT: Y 443 ILE cc_start: 0.8589 (mm) cc_final: 0.8388 (mp) REVERT: Y 456 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.7495 (ttm170) REVERT: Y 503 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7645 (mtm-85) REVERT: Z 107 ASP cc_start: 0.8123 (m-30) cc_final: 0.7922 (m-30) REVERT: Z 211 ASP cc_start: 0.7866 (t0) cc_final: 0.7624 (t0) REVERT: Z 240 LYS cc_start: 0.8128 (mppt) cc_final: 0.7841 (mtmm) REVERT: Z 321 ASP cc_start: 0.8050 (t0) cc_final: 0.7792 (t70) REVERT: Z 381 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7925 (mm-30) REVERT: Z 426 MET cc_start: 0.6590 (mtt) cc_final: 0.5881 (mtt) outliers start: 55 outliers final: 30 residues processed: 398 average time/residue: 0.6710 time to fit residues: 299.3547 Evaluate side-chains 411 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 377 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 377 ASN Chi-restraints excluded: chain Z residue 464 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 140 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN ** S 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 GLN X 203 GLN X 315 GLN X 425 ASN Y 375 HIS Z 169 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.101049 restraints weight = 30326.567| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.47 r_work: 0.3150 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20834 Z= 0.204 Angle : 0.629 8.558 28528 Z= 0.303 Chirality : 0.045 0.198 3546 Planarity : 0.005 0.085 3375 Dihedral : 8.966 71.337 5208 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.59 % Favored : 97.37 % Rotamer: Outliers : 3.10 % Allowed : 11.43 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.18), residues: 2316 helix: 1.97 (0.28), residues: 387 sheet: 0.74 (0.19), residues: 738 loop : -0.25 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 166 TYR 0.018 0.001 TYR E 91 PHE 0.013 0.002 PHE Y 176 TRP 0.015 0.001 TRP C 32 HIS 0.008 0.001 HIS Y 375 Details of bonding type rmsd covalent geometry : bond 0.00485 (20664) covalent geometry : angle 0.58694 (28056) SS BOND : bond 0.00411 ( 38) SS BOND : angle 1.55803 ( 76) hydrogen bonds : bond 0.05005 ( 570) hydrogen bonds : angle 4.62858 ( 1533) link_ALPHA1-2 : bond 0.00353 ( 12) link_ALPHA1-2 : angle 1.66828 ( 36) link_ALPHA1-3 : bond 0.00878 ( 9) link_ALPHA1-3 : angle 1.84071 ( 27) link_ALPHA1-6 : bond 0.00134 ( 9) link_ALPHA1-6 : angle 1.91134 ( 27) link_BETA1-4 : bond 0.00439 ( 41) link_BETA1-4 : angle 1.77722 ( 123) link_NAG-ASN : bond 0.00358 ( 61) link_NAG-ASN : angle 2.05434 ( 183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 382 time to evaluate : 0.725 Fit side-chains REVERT: A 74 THR cc_start: 0.8276 (t) cc_final: 0.8046 (t) REVERT: A 100 THR cc_start: 0.8762 (m) cc_final: 0.8445 (t) REVERT: A 125 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8273 (p) REVERT: D 67 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7963 (tp) REVERT: H 67 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7972 (tp) REVERT: R 624 ASN cc_start: 0.8316 (m110) cc_final: 0.7994 (m-40) REVERT: S 606 THR cc_start: 0.8644 (t) cc_final: 0.8414 (p) REVERT: X 199 SER cc_start: 0.8460 (p) cc_final: 0.8197 (t) REVERT: X 211 ASP cc_start: 0.7815 (t0) cc_final: 0.7541 (t0) REVERT: X 232 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8401 (mtmm) REVERT: X 457 ASP cc_start: 0.8051 (t0) cc_final: 0.7725 (t0) REVERT: X 466 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7548 (tp30) REVERT: Y 205 CYS cc_start: 0.7590 (t) cc_final: 0.7281 (m) REVERT: Y 207 LYS cc_start: 0.7923 (mtmm) cc_final: 0.7691 (mtmm) REVERT: Y 347 GLU cc_start: 0.8117 (tp30) cc_final: 0.7704 (tp30) REVERT: Y 426 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.5762 (mtp) REVERT: Y 456 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7510 (ttm170) REVERT: Y 503 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7732 (mtm-85) REVERT: Z 91 GLU cc_start: 0.8241 (tp30) cc_final: 0.8010 (tp30) REVERT: Z 211 ASP cc_start: 0.7907 (t0) cc_final: 0.7655 (t0) REVERT: Z 240 LYS cc_start: 0.8134 (mppt) cc_final: 0.7883 (mtmm) REVERT: Z 381 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7874 (mm-30) REVERT: Z 426 MET cc_start: 0.6569 (mtt) cc_final: 0.5926 (mtt) outliers start: 64 outliers final: 36 residues processed: 404 average time/residue: 0.7124 time to fit residues: 322.4591 Evaluate side-chains 416 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 374 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain X residue 246 GLN Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 434 MET Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 303 THR Chi-restraints excluded: chain Z residue 377 ASN Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 190 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 43 GLN L 38 GLN ** S 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 315 GLN X 425 ASN ** Y 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 375 HIS Z 169 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.101765 restraints weight = 30191.261| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.45 r_work: 0.3160 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20834 Z= 0.142 Angle : 0.579 7.764 28528 Z= 0.279 Chirality : 0.044 0.226 3546 Planarity : 0.004 0.086 3375 Dihedral : 8.449 70.324 5208 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.20 % Favored : 97.75 % Rotamer: Outliers : 2.71 % Allowed : 13.08 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.18), residues: 2316 helix: 2.33 (0.28), residues: 369 sheet: 0.76 (0.19), residues: 738 loop : -0.17 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Z 166 TYR 0.014 0.001 TYR E 91 PHE 0.011 0.001 PHE X 53 TRP 0.017 0.001 TRP C 32 HIS 0.007 0.001 HIS Y 375 Details of bonding type rmsd covalent geometry : bond 0.00334 (20664) covalent geometry : angle 0.54100 (28056) SS BOND : bond 0.00353 ( 38) SS BOND : angle 1.33862 ( 76) hydrogen bonds : bond 0.04377 ( 570) hydrogen bonds : angle 4.49959 ( 1533) link_ALPHA1-2 : bond 0.00404 ( 12) link_ALPHA1-2 : angle 1.55537 ( 36) link_ALPHA1-3 : bond 0.00952 ( 9) link_ALPHA1-3 : angle 1.78605 ( 27) link_ALPHA1-6 : bond 0.00271 ( 9) link_ALPHA1-6 : angle 1.85382 ( 27) link_BETA1-4 : bond 0.00446 ( 41) link_BETA1-4 : angle 1.63629 ( 123) link_NAG-ASN : bond 0.00217 ( 61) link_NAG-ASN : angle 1.85933 ( 183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 379 time to evaluate : 0.745 Fit side-chains REVERT: A 74 THR cc_start: 0.8274 (t) cc_final: 0.8049 (t) REVERT: A 100 THR cc_start: 0.8704 (m) cc_final: 0.8369 (t) REVERT: A 125 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8306 (p) REVERT: D 55 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7896 (mmtt) REVERT: D 67 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7964 (tp) REVERT: E 100 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6629 (pm20) REVERT: H 67 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7957 (tp) REVERT: L 104 VAL cc_start: 0.7890 (OUTLIER) cc_final: 0.7642 (p) REVERT: R 624 ASN cc_start: 0.8323 (m110) cc_final: 0.7984 (m-40) REVERT: S 606 THR cc_start: 0.8603 (t) cc_final: 0.8393 (p) REVERT: T 601 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8542 (mtpp) REVERT: X 208 ILE cc_start: 0.8276 (mm) cc_final: 0.8071 (OUTLIER) REVERT: X 211 ASP cc_start: 0.7799 (t0) cc_final: 0.7527 (t0) REVERT: X 232 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8416 (mtmm) REVERT: X 389 LYS cc_start: 0.8776 (ttmt) cc_final: 0.8527 (ttmm) REVERT: X 457 ASP cc_start: 0.8036 (t0) cc_final: 0.7735 (t0) REVERT: Y 207 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7566 (mtmm) REVERT: Y 347 GLU cc_start: 0.8112 (tp30) cc_final: 0.7712 (tp30) REVERT: Y 426 MET cc_start: 0.6501 (OUTLIER) cc_final: 0.5769 (mtp) REVERT: Y 456 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7475 (ttm170) REVERT: Y 503 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7715 (mtm-85) REVERT: Z 211 ASP cc_start: 0.7894 (t0) cc_final: 0.7640 (t0) REVERT: Z 326 ILE cc_start: 0.8492 (pt) cc_final: 0.8000 (mm) REVERT: Z 381 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7901 (mm-30) REVERT: Z 426 MET cc_start: 0.6534 (mtt) cc_final: 0.5978 (mtt) outliers start: 56 outliers final: 33 residues processed: 394 average time/residue: 0.6525 time to fit residues: 288.5055 Evaluate side-chains 408 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 367 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain S residue 636 SER Chi-restraints excluded: chain T residue 589 ASP Chi-restraints excluded: chain T residue 592 PHE Chi-restraints excluded: chain T residue 601 LYS Chi-restraints excluded: chain X residue 246 GLN Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 443 ILE Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 208 ILE Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 0.0670 chunk 216 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN L 38 GLN ** S 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 169 GLN ** Y 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 169 GLN Z 315 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.102514 restraints weight = 30141.467| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.45 r_work: 0.3172 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20834 Z= 0.121 Angle : 0.561 7.269 28528 Z= 0.271 Chirality : 0.044 0.235 3546 Planarity : 0.004 0.082 3375 Dihedral : 8.048 69.466 5208 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.67 % Rotamer: Outliers : 2.96 % Allowed : 13.86 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.18), residues: 2316 helix: 2.44 (0.28), residues: 369 sheet: 0.77 (0.19), residues: 744 loop : -0.11 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Z 166 TYR 0.013 0.001 TYR E 91 PHE 0.011 0.001 PHE X 53 TRP 0.019 0.001 TRP C 32 HIS 0.003 0.001 HIS Z 72 Details of bonding type rmsd covalent geometry : bond 0.00280 (20664) covalent geometry : angle 0.52415 (28056) SS BOND : bond 0.00345 ( 38) SS BOND : angle 1.24810 ( 76) hydrogen bonds : bond 0.04038 ( 570) hydrogen bonds : angle 4.39640 ( 1533) link_ALPHA1-2 : bond 0.00410 ( 12) link_ALPHA1-2 : angle 1.53059 ( 36) link_ALPHA1-3 : bond 0.00969 ( 9) link_ALPHA1-3 : angle 1.79043 ( 27) link_ALPHA1-6 : bond 0.00335 ( 9) link_ALPHA1-6 : angle 1.80887 ( 27) link_BETA1-4 : bond 0.00442 ( 41) link_BETA1-4 : angle 1.57251 ( 123) link_NAG-ASN : bond 0.00198 ( 61) link_NAG-ASN : angle 1.80277 ( 183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 377 time to evaluate : 0.745 Fit side-chains REVERT: A 43 GLN cc_start: 0.7197 (mp10) cc_final: 0.5725 (mp10) REVERT: A 74 THR cc_start: 0.8268 (t) cc_final: 0.8061 (t) REVERT: A 100 THR cc_start: 0.8668 (m) cc_final: 0.8324 (t) REVERT: A 125 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8356 (p) REVERT: D 55 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7895 (mmtt) REVERT: D 67 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7971 (tp) REVERT: E 100 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6632 (pm20) REVERT: H 67 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7966 (tp) REVERT: R 624 ASN cc_start: 0.8330 (m110) cc_final: 0.7980 (m-40) REVERT: R 661 LEU cc_start: 0.8300 (mt) cc_final: 0.8059 (mp) REVERT: T 601 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8515 (mtpp) REVERT: X 203 GLN cc_start: 0.8610 (tt0) cc_final: 0.8392 (tt0) REVERT: X 208 ILE cc_start: 0.8238 (mm) cc_final: 0.8027 (OUTLIER) REVERT: X 211 ASP cc_start: 0.7802 (t0) cc_final: 0.7526 (t0) REVERT: X 232 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8407 (mtmm) REVERT: X 373 MET cc_start: 0.8627 (mmm) cc_final: 0.8351 (mtt) REVERT: X 389 LYS cc_start: 0.8767 (ttmt) cc_final: 0.8521 (ttmm) REVERT: X 457 ASP cc_start: 0.8024 (t0) cc_final: 0.7745 (t0) REVERT: Y 207 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7421 (mtmm) REVERT: Y 347 GLU cc_start: 0.8124 (tp30) cc_final: 0.7715 (tp30) REVERT: Y 422 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8186 (mt0) REVERT: Y 426 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.5775 (mtp) REVERT: Y 456 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7466 (ttm170) REVERT: Y 503 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7716 (mtm-85) REVERT: Z 105 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7712 (tp40) REVERT: Z 107 ASP cc_start: 0.8251 (m-30) cc_final: 0.8015 (t0) REVERT: Z 161 MET cc_start: 0.8369 (mmm) cc_final: 0.8122 (mmm) REVERT: Z 164 GLU cc_start: 0.7676 (pm20) cc_final: 0.7437 (pm20) REVERT: Z 211 ASP cc_start: 0.7911 (t0) cc_final: 0.7659 (t0) REVERT: Z 325 ASP cc_start: 0.7994 (m-30) cc_final: 0.7762 (t0) REVERT: Z 326 ILE cc_start: 0.8504 (pt) cc_final: 0.8057 (mm) REVERT: Z 347 GLU cc_start: 0.7632 (pp20) cc_final: 0.7405 (pp20) REVERT: Z 381 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7864 (mm-30) REVERT: Z 426 MET cc_start: 0.6521 (mtt) cc_final: 0.5933 (mtt) outliers start: 61 outliers final: 35 residues processed: 397 average time/residue: 0.6879 time to fit residues: 305.4331 Evaluate side-chains 409 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 365 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain S residue 636 SER Chi-restraints excluded: chain T residue 592 PHE Chi-restraints excluded: chain T residue 601 LYS Chi-restraints excluded: chain X residue 246 GLN Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 290 LYS Chi-restraints excluded: chain Y residue 316 MET Chi-restraints excluded: chain Y residue 422 GLN Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 443 ILE Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 105 GLN Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 208 ILE Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 96 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 222 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 GLN Y 169 GLN ** Y 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 169 GLN Z 315 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101419 restraints weight = 30191.022| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.46 r_work: 0.3152 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20834 Z= 0.186 Angle : 0.610 7.881 28528 Z= 0.293 Chirality : 0.045 0.196 3546 Planarity : 0.005 0.082 3375 Dihedral : 8.075 70.661 5208 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.59 % Favored : 97.37 % Rotamer: Outliers : 3.29 % Allowed : 13.95 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.18), residues: 2316 helix: 2.36 (0.28), residues: 369 sheet: 0.76 (0.19), residues: 738 loop : -0.19 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Z 166 TYR 0.017 0.001 TYR E 91 PHE 0.014 0.002 PHE X 53 TRP 0.018 0.001 TRP L 32 HIS 0.005 0.001 HIS Y 374 Details of bonding type rmsd covalent geometry : bond 0.00442 (20664) covalent geometry : angle 0.56888 (28056) SS BOND : bond 0.00418 ( 38) SS BOND : angle 1.49315 ( 76) hydrogen bonds : bond 0.04605 ( 570) hydrogen bonds : angle 4.46243 ( 1533) link_ALPHA1-2 : bond 0.00374 ( 12) link_ALPHA1-2 : angle 1.62785 ( 36) link_ALPHA1-3 : bond 0.00903 ( 9) link_ALPHA1-3 : angle 1.80965 ( 27) link_ALPHA1-6 : bond 0.00216 ( 9) link_ALPHA1-6 : angle 1.86108 ( 27) link_BETA1-4 : bond 0.00439 ( 41) link_BETA1-4 : angle 1.70453 ( 123) link_NAG-ASN : bond 0.00321 ( 61) link_NAG-ASN : angle 1.98863 ( 183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 373 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 74 THR cc_start: 0.8275 (t) cc_final: 0.8062 (t) REVERT: A 100 THR cc_start: 0.8715 (m) cc_final: 0.8391 (t) REVERT: A 125 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8344 (p) REVERT: D 55 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7903 (mmtt) REVERT: D 67 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7967 (tp) REVERT: D 116 MET cc_start: 0.8578 (mtp) cc_final: 0.8354 (mtp) REVERT: E 100 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6665 (pm20) REVERT: H 67 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7965 (tp) REVERT: R 610 TRP cc_start: 0.8548 (t-100) cc_final: 0.8154 (t-100) REVERT: R 624 ASN cc_start: 0.8351 (m110) cc_final: 0.7974 (m-40) REVERT: T 601 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8536 (mtpp) REVERT: X 211 ASP cc_start: 0.7843 (t0) cc_final: 0.7554 (t0) REVERT: X 389 LYS cc_start: 0.8735 (ttmt) cc_final: 0.8493 (ttmm) REVERT: X 457 ASP cc_start: 0.8020 (t0) cc_final: 0.7737 (t0) REVERT: Y 207 LYS cc_start: 0.7746 (mtmm) cc_final: 0.7493 (mtmm) REVERT: Y 347 GLU cc_start: 0.8127 (tp30) cc_final: 0.7722 (tp30) REVERT: Y 419 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.8091 (mtm-85) REVERT: Y 422 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8201 (mt0) REVERT: Y 426 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.5807 (mtp) REVERT: Y 456 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7519 (ttm170) REVERT: Y 492 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8292 (mt-10) REVERT: Y 503 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7742 (mtm-85) REVERT: Z 105 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7737 (tp40) REVERT: Z 107 ASP cc_start: 0.8271 (m-30) cc_final: 0.7981 (t0) REVERT: Z 211 ASP cc_start: 0.7904 (t0) cc_final: 0.7655 (t0) REVERT: Z 240 LYS cc_start: 0.8080 (mppt) cc_final: 0.7823 (mtmm) REVERT: Z 321 ASP cc_start: 0.8044 (t0) cc_final: 0.7803 (t0) REVERT: Z 326 ILE cc_start: 0.8481 (pt) cc_final: 0.8022 (mm) REVERT: Z 327 ARG cc_start: 0.8571 (mtm-85) cc_final: 0.8205 (mtm110) REVERT: Z 381 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7858 (mm-30) REVERT: Z 426 MET cc_start: 0.6636 (mtt) cc_final: 0.6048 (mtt) outliers start: 68 outliers final: 43 residues processed: 395 average time/residue: 0.6489 time to fit residues: 287.2941 Evaluate side-chains 422 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 369 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain S residue 636 SER Chi-restraints excluded: chain T residue 601 LYS Chi-restraints excluded: chain X residue 201 ILE Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain X residue 246 GLN Chi-restraints excluded: chain X residue 247 CYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain X residue 443 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 290 LYS Chi-restraints excluded: chain Y residue 390 LEU Chi-restraints excluded: chain Y residue 422 GLN Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Y residue 501 CYS Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 105 GLN Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 215 ILE Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 85 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 196 optimal weight: 0.0470 chunk 162 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 315 GLN Y 169 GLN ** Y 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 169 GLN Z 315 GLN Z 343 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.102404 restraints weight = 30071.527| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.45 r_work: 0.3177 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20834 Z= 0.115 Angle : 0.563 7.582 28528 Z= 0.271 Chirality : 0.043 0.194 3546 Planarity : 0.004 0.081 3375 Dihedral : 7.786 69.136 5208 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.16 % Favored : 97.80 % Rotamer: Outliers : 2.86 % Allowed : 14.58 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.18), residues: 2316 helix: 2.44 (0.28), residues: 369 sheet: 0.66 (0.19), residues: 765 loop : -0.12 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Z 166 TYR 0.013 0.001 TYR E 91 PHE 0.013 0.001 PHE X 53 TRP 0.025 0.001 TRP L 32 HIS 0.003 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00267 (20664) covalent geometry : angle 0.52717 (28056) SS BOND : bond 0.00344 ( 38) SS BOND : angle 1.26991 ( 76) hydrogen bonds : bond 0.03969 ( 570) hydrogen bonds : angle 4.34874 ( 1533) link_ALPHA1-2 : bond 0.00429 ( 12) link_ALPHA1-2 : angle 1.51128 ( 36) link_ALPHA1-3 : bond 0.00972 ( 9) link_ALPHA1-3 : angle 1.76698 ( 27) link_ALPHA1-6 : bond 0.00384 ( 9) link_ALPHA1-6 : angle 1.79027 ( 27) link_BETA1-4 : bond 0.00442 ( 41) link_BETA1-4 : angle 1.55813 ( 123) link_NAG-ASN : bond 0.00180 ( 61) link_NAG-ASN : angle 1.75641 ( 183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 372 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 74 THR cc_start: 0.8265 (t) cc_final: 0.8052 (t) REVERT: A 100 THR cc_start: 0.8641 (m) cc_final: 0.8312 (t) REVERT: D 55 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7883 (mmtt) REVERT: D 67 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7958 (tp) REVERT: D 115 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8628 (t) REVERT: D 116 MET cc_start: 0.8552 (mtp) cc_final: 0.8324 (mtp) REVERT: E 100 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: H 67 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7955 (tp) REVERT: L 48 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7655 (mp) REVERT: R 624 ASN cc_start: 0.8327 (m110) cc_final: 0.7944 (m-40) REVERT: R 661 LEU cc_start: 0.8279 (mt) cc_final: 0.8049 (mp) REVERT: T 601 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8506 (mtpp) REVERT: X 211 ASP cc_start: 0.7828 (t0) cc_final: 0.7530 (t0) REVERT: X 389 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8497 (ttmm) REVERT: X 457 ASP cc_start: 0.8005 (t0) cc_final: 0.7730 (t0) REVERT: Y 111 LEU cc_start: 0.8338 (tt) cc_final: 0.8092 (tp) REVERT: Y 207 LYS cc_start: 0.7720 (mtmm) cc_final: 0.7463 (mtmm) REVERT: Y 347 GLU cc_start: 0.8153 (tp30) cc_final: 0.7743 (tp30) REVERT: Y 419 ARG cc_start: 0.8236 (mtm-85) cc_final: 0.8032 (mtm-85) REVERT: Y 422 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8152 (mt0) REVERT: Y 426 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.5766 (mtp) REVERT: Y 456 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7473 (ttm170) REVERT: Z 107 ASP cc_start: 0.8275 (m-30) cc_final: 0.7973 (t0) REVERT: Z 161 MET cc_start: 0.8293 (mmm) cc_final: 0.8041 (mmm) REVERT: Z 164 GLU cc_start: 0.7694 (pm20) cc_final: 0.7386 (pm20) REVERT: Z 211 ASP cc_start: 0.7893 (t0) cc_final: 0.7642 (t0) REVERT: Z 321 ASP cc_start: 0.8015 (t0) cc_final: 0.7759 (t0) REVERT: Z 326 ILE cc_start: 0.8531 (pt) cc_final: 0.8056 (mm) REVERT: Z 327 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8251 (mtm-85) REVERT: Z 347 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7367 (pp20) REVERT: Z 381 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7818 (mm-30) REVERT: Z 426 MET cc_start: 0.6504 (mtt) cc_final: 0.5947 (mtt) outliers start: 59 outliers final: 33 residues processed: 391 average time/residue: 0.7040 time to fit residues: 307.8147 Evaluate side-chains 402 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 359 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain S residue 636 SER Chi-restraints excluded: chain T residue 601 LYS Chi-restraints excluded: chain T residue 660 LEU Chi-restraints excluded: chain X residue 246 GLN Chi-restraints excluded: chain X residue 247 CYS Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 443 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 390 LEU Chi-restraints excluded: chain Y residue 422 GLN Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 443 ILE Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 208 ILE Chi-restraints excluded: chain Z residue 215 ILE Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 347 GLU Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 154 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 182 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN ** Y 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 169 GLN Z 315 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.116166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.100190 restraints weight = 30125.823| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.44 r_work: 0.3142 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20834 Z= 0.270 Angle : 0.691 8.779 28528 Z= 0.331 Chirality : 0.047 0.205 3546 Planarity : 0.005 0.083 3375 Dihedral : 8.195 71.087 5208 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.94 % Favored : 97.02 % Rotamer: Outliers : 3.34 % Allowed : 14.44 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.18), residues: 2316 helix: 2.19 (0.28), residues: 369 sheet: 0.68 (0.19), residues: 732 loop : -0.29 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG X 166 TYR 0.022 0.002 TYR E 91 PHE 0.015 0.002 PHE X 53 TRP 0.029 0.002 TRP L 32 HIS 0.008 0.001 HIS Y 374 Details of bonding type rmsd covalent geometry : bond 0.00642 (20664) covalent geometry : angle 0.64459 (28056) SS BOND : bond 0.00475 ( 38) SS BOND : angle 1.97311 ( 76) hydrogen bonds : bond 0.05304 ( 570) hydrogen bonds : angle 4.63384 ( 1533) link_ALPHA1-2 : bond 0.00360 ( 12) link_ALPHA1-2 : angle 1.79037 ( 36) link_ALPHA1-3 : bond 0.00822 ( 9) link_ALPHA1-3 : angle 1.86597 ( 27) link_ALPHA1-6 : bond 0.00178 ( 9) link_ALPHA1-6 : angle 1.92119 ( 27) link_BETA1-4 : bond 0.00451 ( 41) link_BETA1-4 : angle 1.90010 ( 123) link_NAG-ASN : bond 0.00513 ( 61) link_NAG-ASN : angle 2.24906 ( 183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 379 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 74 THR cc_start: 0.8271 (t) cc_final: 0.8058 (t) REVERT: A 100 THR cc_start: 0.8723 (m) cc_final: 0.8418 (t) REVERT: D 55 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7884 (mmtt) REVERT: D 115 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8754 (t) REVERT: D 116 MET cc_start: 0.8563 (mtp) cc_final: 0.8343 (mtp) REVERT: E 100 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6725 (pm20) REVERT: H 67 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8035 (tp) REVERT: H 121 TRP cc_start: 0.8934 (m100) cc_final: 0.8633 (m100) REVERT: R 610 TRP cc_start: 0.8542 (t-100) cc_final: 0.8140 (t-100) REVERT: R 624 ASN cc_start: 0.8384 (m110) cc_final: 0.7959 (m-40) REVERT: T 601 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8630 (mtpp) REVERT: X 161 MET cc_start: 0.8206 (ttp) cc_final: 0.7914 (ttm) REVERT: X 199 SER cc_start: 0.8401 (p) cc_final: 0.8166 (t) REVERT: X 211 ASP cc_start: 0.7880 (t0) cc_final: 0.7598 (t0) REVERT: X 389 LYS cc_start: 0.8710 (ttmt) cc_final: 0.8469 (ttmm) REVERT: X 457 ASP cc_start: 0.8059 (t0) cc_final: 0.7772 (t0) REVERT: Y 111 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8120 (tp) REVERT: Y 207 LYS cc_start: 0.7856 (mtmm) cc_final: 0.7613 (mtmm) REVERT: Y 347 GLU cc_start: 0.8143 (tp30) cc_final: 0.7747 (tp30) REVERT: Y 422 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8219 (mt0) REVERT: Y 456 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7524 (ttm170) REVERT: Z 105 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7740 (tp40) REVERT: Z 107 ASP cc_start: 0.8262 (m-30) cc_final: 0.7959 (t0) REVERT: Z 164 GLU cc_start: 0.7769 (pm20) cc_final: 0.7454 (pm20) REVERT: Z 240 LYS cc_start: 0.8119 (mppt) cc_final: 0.7846 (mtmm) REVERT: Z 321 ASP cc_start: 0.8048 (t0) cc_final: 0.7814 (t0) REVERT: Z 326 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8103 (mm) REVERT: Z 327 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.8109 (mtm-85) REVERT: Z 347 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7400 (pp20) REVERT: Z 349 LEU cc_start: 0.8484 (mt) cc_final: 0.8231 (mp) REVERT: Z 381 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7828 (mm-30) REVERT: Z 426 MET cc_start: 0.6691 (mtt) cc_final: 0.6137 (mtt) outliers start: 69 outliers final: 40 residues processed: 404 average time/residue: 0.6606 time to fit residues: 299.9123 Evaluate side-chains 428 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 378 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain S residue 636 SER Chi-restraints excluded: chain T residue 601 LYS Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 201 ILE Chi-restraints excluded: chain X residue 244 THR Chi-restraints excluded: chain X residue 246 GLN Chi-restraints excluded: chain X residue 247 CYS Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain X residue 443 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 390 LEU Chi-restraints excluded: chain Y residue 422 GLN Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 427 TRP Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Y residue 501 CYS Chi-restraints excluded: chain Z residue 105 GLN Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 326 ILE Chi-restraints excluded: chain Z residue 347 GLU Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 191 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 224 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 131 optimal weight: 0.0270 chunk 63 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.4640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 169 GLN ** Y 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 169 GLN Z 315 GLN Z 343 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.102483 restraints weight = 29945.277| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.45 r_work: 0.3176 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20834 Z= 0.110 Angle : 0.576 8.297 28528 Z= 0.278 Chirality : 0.043 0.195 3546 Planarity : 0.004 0.081 3375 Dihedral : 7.671 68.858 5208 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.81 % Favored : 98.14 % Rotamer: Outliers : 2.03 % Allowed : 16.67 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.18), residues: 2316 helix: 2.38 (0.28), residues: 369 sheet: 0.58 (0.19), residues: 768 loop : -0.14 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG X 166 TYR 0.014 0.001 TYR E 91 PHE 0.017 0.001 PHE X 53 TRP 0.033 0.001 TRP L 32 HIS 0.003 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00253 (20664) covalent geometry : angle 0.54133 (28056) SS BOND : bond 0.00356 ( 38) SS BOND : angle 1.54320 ( 76) hydrogen bonds : bond 0.03871 ( 570) hydrogen bonds : angle 4.36199 ( 1533) link_ALPHA1-2 : bond 0.00446 ( 12) link_ALPHA1-2 : angle 1.46649 ( 36) link_ALPHA1-3 : bond 0.00978 ( 9) link_ALPHA1-3 : angle 1.76432 ( 27) link_ALPHA1-6 : bond 0.00447 ( 9) link_ALPHA1-6 : angle 1.76898 ( 27) link_BETA1-4 : bond 0.00449 ( 41) link_BETA1-4 : angle 1.52666 ( 123) link_NAG-ASN : bond 0.00158 ( 61) link_NAG-ASN : angle 1.71417 ( 183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 388 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 74 THR cc_start: 0.8257 (t) cc_final: 0.8039 (t) REVERT: A 100 THR cc_start: 0.8611 (m) cc_final: 0.8266 (t) REVERT: D 55 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7845 (mmtt) REVERT: D 115 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8624 (t) REVERT: E 100 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6668 (pm20) REVERT: H 67 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7956 (tp) REVERT: L 87 TYR cc_start: 0.8414 (m-80) cc_final: 0.7901 (m-80) REVERT: R 610 TRP cc_start: 0.8538 (t-100) cc_final: 0.8052 (t-100) REVERT: R 624 ASN cc_start: 0.8332 (m110) cc_final: 0.7920 (m-40) REVERT: T 601 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8525 (mtpp) REVERT: X 161 MET cc_start: 0.8154 (ttp) cc_final: 0.7899 (ttm) REVERT: X 203 GLN cc_start: 0.8620 (tt0) cc_final: 0.8404 (tt0) REVERT: X 211 ASP cc_start: 0.7805 (t0) cc_final: 0.7492 (t0) REVERT: X 231 LYS cc_start: 0.8344 (mtpp) cc_final: 0.8045 (mmmm) REVERT: X 373 MET cc_start: 0.8629 (mmm) cc_final: 0.8369 (mtt) REVERT: X 389 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8479 (ttmm) REVERT: X 457 ASP cc_start: 0.7992 (t0) cc_final: 0.7729 (t0) REVERT: Y 111 LEU cc_start: 0.8356 (tt) cc_final: 0.8089 (tp) REVERT: Y 207 LYS cc_start: 0.7742 (mtmm) cc_final: 0.7482 (mtmm) REVERT: Y 264 SER cc_start: 0.8556 (m) cc_final: 0.8312 (p) REVERT: Y 308 ARG cc_start: 0.8532 (ttm110) cc_final: 0.8317 (ttp80) REVERT: Y 347 GLU cc_start: 0.8150 (tp30) cc_final: 0.7739 (tp30) REVERT: Y 426 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.5782 (mtp) REVERT: Y 456 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7473 (ttm170) REVERT: Z 107 ASP cc_start: 0.8273 (m-30) cc_final: 0.7961 (t0) REVERT: Z 161 MET cc_start: 0.8222 (mmm) cc_final: 0.7936 (mmm) REVERT: Z 164 GLU cc_start: 0.7707 (pm20) cc_final: 0.7387 (pm20) REVERT: Z 242 VAL cc_start: 0.8920 (m) cc_final: 0.8716 (t) REVERT: Z 321 ASP cc_start: 0.8047 (t0) cc_final: 0.7787 (t0) REVERT: Z 326 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8079 (mm) REVERT: Z 327 ARG cc_start: 0.8480 (mtm-85) cc_final: 0.8065 (mtm-85) REVERT: Z 347 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7365 (pp20) REVERT: Z 381 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7811 (mm-30) REVERT: Z 426 MET cc_start: 0.6388 (mtt) cc_final: 0.5922 (mtt) outliers start: 42 outliers final: 26 residues processed: 402 average time/residue: 0.6619 time to fit residues: 298.3957 Evaluate side-chains 410 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 376 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain S residue 636 SER Chi-restraints excluded: chain T residue 601 LYS Chi-restraints excluded: chain X residue 246 GLN Chi-restraints excluded: chain X residue 247 CYS Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Z residue 208 ILE Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 326 ILE Chi-restraints excluded: chain Z residue 347 GLU Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 475 ILE Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 93 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 189 optimal weight: 0.0980 chunk 198 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 146 optimal weight: 0.0980 chunk 73 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 HIS ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN L 38 GLN S 540 GLN T 577 GLN X 105 GLN X 283 ASN Y 169 GLN ** Y 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 169 GLN Z 315 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.103341 restraints weight = 30034.505| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.46 r_work: 0.3185 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20834 Z= 0.109 Angle : 0.566 8.767 28528 Z= 0.272 Chirality : 0.043 0.196 3546 Planarity : 0.004 0.077 3375 Dihedral : 7.415 68.458 5208 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.33 % Favored : 97.63 % Rotamer: Outliers : 1.65 % Allowed : 17.30 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.18), residues: 2316 helix: 2.49 (0.28), residues: 369 sheet: 0.70 (0.19), residues: 759 loop : -0.11 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Z 166 TYR 0.013 0.001 TYR E 91 PHE 0.014 0.001 PHE X 53 TRP 0.034 0.001 TRP L 32 HIS 0.003 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00254 (20664) covalent geometry : angle 0.53118 (28056) SS BOND : bond 0.00342 ( 38) SS BOND : angle 1.46538 ( 76) hydrogen bonds : bond 0.03735 ( 570) hydrogen bonds : angle 4.24791 ( 1533) link_ALPHA1-2 : bond 0.00421 ( 12) link_ALPHA1-2 : angle 1.50745 ( 36) link_ALPHA1-3 : bond 0.00941 ( 9) link_ALPHA1-3 : angle 1.77348 ( 27) link_ALPHA1-6 : bond 0.00465 ( 9) link_ALPHA1-6 : angle 1.72725 ( 27) link_BETA1-4 : bond 0.00447 ( 41) link_BETA1-4 : angle 1.53152 ( 123) link_NAG-ASN : bond 0.00170 ( 61) link_NAG-ASN : angle 1.70314 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7219.50 seconds wall clock time: 123 minutes 55.71 seconds (7435.71 seconds total)