Starting phenix.real_space_refine on Tue Jun 17 19:33:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gpi_34193/06_2025/8gpi_34193.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gpi_34193/06_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_34193/06_2025/8gpi_34193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gpi_34193/06_2025/8gpi_34193.map" model { file = "/net/cci-nas-00/data/ceres_data/8gpi_34193/06_2025/8gpi_34193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gpi_34193/06_2025/8gpi_34193.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.79, per 1000 atoms: 0.73 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: 7.20 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.55 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: 7.09 Time building geometry restraints manager: 8.10 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 504 or resid 701 through 708)) selection = (chain 'Z' and (resid 33 through 504 or resid 701 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: 1.230 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: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 50.820 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.700 ------------------------------------------------------------------------------- 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 : 5.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (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 TRP 0.038 0.002 TRP L 32 HIS 0.007 0.001 HIS Y 374 PHE 0.024 0.002 PHE R 522 TYR 0.022 0.001 TYR L 91 ARG 0.014 0.001 ARG X 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 61) link_NAG-ASN : angle 2.15374 ( 183) 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_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) hydrogen bonds : bond 0.12412 ( 570) hydrogen bonds : angle 5.68932 ( 1533) SS BOND : bond 0.00470 ( 38) SS BOND : angle 1.62326 ( 76) covalent geometry : bond 0.00532 (20664) covalent geometry : angle 0.76121 (28056) *********************** 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 : 2.250 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: 1.3885 time to fit residues: 627.0049 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 : 2.299 ------------------------------------------------------------------------------- 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 195 optimal weight: 0.0980 chunk 175 optimal weight: 0.0980 chunk 97 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 181 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 209 optimal weight: 4.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.119870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103529 restraints weight = 29932.035| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.52 r_work: 0.3199 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20834 Z= 0.120 Angle : 0.579 7.902 28528 Z= 0.276 Chirality : 0.044 0.210 3546 Planarity : 0.004 0.079 3375 Dihedral : 10.587 80.876 5210 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.65 % Allowed : 8.04 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.17), residues: 2316 helix: 2.18 (0.27), residues: 369 sheet: 1.01 (0.20), residues: 699 loop : -0.15 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 32 HIS 0.007 0.001 HIS Y 375 PHE 0.012 0.001 PHE X 53 TYR 0.017 0.001 TYR L 91 ARG 0.006 0.000 ARG X 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 61) link_NAG-ASN : angle 1.77893 ( 183) link_ALPHA1-6 : bond 0.00305 ( 9) link_ALPHA1-6 : angle 1.86293 ( 27) link_BETA1-4 : bond 0.00495 ( 41) link_BETA1-4 : angle 1.72018 ( 123) link_ALPHA1-2 : bond 0.00434 ( 12) link_ALPHA1-2 : angle 1.61890 ( 36) link_ALPHA1-3 : bond 0.01045 ( 9) link_ALPHA1-3 : angle 2.03116 ( 27) hydrogen bonds : bond 0.04300 ( 570) hydrogen bonds : angle 4.55732 ( 1533) SS BOND : bond 0.00324 ( 38) SS BOND : angle 1.23225 ( 76) covalent geometry : bond 0.00277 (20664) covalent geometry : angle 0.54050 (28056) *********************** 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 412 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 378 time to evaluate : 2.350 Fit side-chains REVERT: A 125 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8180 (p) REVERT: R 624 ASN cc_start: 0.8204 (m110) cc_final: 0.7995 (m-40) REVERT: S 606 THR cc_start: 0.8569 (t) cc_final: 0.8332 (p) REVERT: X 211 ASP cc_start: 0.7771 (t0) cc_final: 0.7474 (t0) REVERT: X 389 LYS cc_start: 0.8824 (ttmt) cc_final: 0.8594 (ttmm) REVERT: X 457 ASP cc_start: 0.8072 (t0) cc_final: 0.7760 (t0) REVERT: X 466 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7624 (tp30) REVERT: Y 111 LEU cc_start: 0.8343 (tt) cc_final: 0.8140 (tp) REVERT: Y 207 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7491 (mtmm) REVERT: Y 231 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7787 (mtpp) REVERT: Y 347 GLU cc_start: 0.8124 (tp30) cc_final: 0.7722 (tp30) REVERT: Y 443 ILE cc_start: 0.8535 (mm) cc_final: 0.8332 (mp) REVERT: Y 477 ASP cc_start: 0.8383 (m-30) cc_final: 0.8178 (m-30) REVERT: Z 103 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: Z 105 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7696 (tp40) REVERT: Z 107 ASP cc_start: 0.8049 (m-30) cc_final: 0.7849 (m-30) REVERT: Z 168 LYS cc_start: 0.8441 (mmmm) cc_final: 0.8230 (mmmm) REVERT: Z 211 ASP cc_start: 0.7869 (t0) cc_final: 0.7625 (t0) REVERT: Z 230 ASP cc_start: 0.8036 (t0) cc_final: 0.7519 (t0) REVERT: Z 231 LYS cc_start: 0.7473 (mtmm) cc_final: 0.7019 (mtmm) REVERT: Z 426 MET cc_start: 0.6076 (mtt) cc_final: 0.5432 (mtt) outliers start: 34 outliers final: 11 residues processed: 385 average time/residue: 1.3364 time to fit residues: 581.2698 Evaluate side-chains 384 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 370 time to evaluate : 2.094 ------------------------------------------------------------------------------- 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 48 ILE Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain H residue 93 THR 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 Z residue 103 GLN Chi-restraints excluded: chain Z residue 105 GLN Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 303 THR Chi-restraints excluded: chain Z residue 464 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 2 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 190 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 60 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 72 HIS X 98 ASN Y 375 HIS Z 169 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 = 0.3566 r_free = 0.3566 target = 0.119806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103387 restraints weight = 29855.634| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.52 r_work: 0.3194 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20834 Z= 0.121 Angle : 0.549 6.896 28528 Z= 0.266 Chirality : 0.043 0.189 3546 Planarity : 0.004 0.082 3375 Dihedral : 9.281 72.851 5208 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.99 % Allowed : 10.17 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 2316 helix: 2.44 (0.28), residues: 369 sheet: 0.83 (0.19), residues: 729 loop : -0.09 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 32 HIS 0.008 0.001 HIS Y 375 PHE 0.010 0.001 PHE Y 176 TYR 0.014 0.001 TYR L 91 ARG 0.009 0.000 ARG Y 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 61) link_NAG-ASN : angle 1.72279 ( 183) link_ALPHA1-6 : bond 0.00347 ( 9) link_ALPHA1-6 : angle 1.78626 ( 27) link_BETA1-4 : bond 0.00460 ( 41) link_BETA1-4 : angle 1.55601 ( 123) link_ALPHA1-2 : bond 0.00445 ( 12) link_ALPHA1-2 : angle 1.55663 ( 36) link_ALPHA1-3 : bond 0.00964 ( 9) link_ALPHA1-3 : angle 1.66605 ( 27) hydrogen bonds : bond 0.04107 ( 570) hydrogen bonds : angle 4.37932 ( 1533) SS BOND : bond 0.00297 ( 38) SS BOND : angle 1.29000 ( 76) covalent geometry : bond 0.00280 (20664) covalent geometry : angle 0.51319 (28056) *********************** 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 423 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 382 time to evaluate : 2.017 Fit side-chains REVERT: A 125 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8242 (p) REVERT: H 110 LEU cc_start: 0.8824 (mt) cc_final: 0.8597 (mt) REVERT: R 624 ASN cc_start: 0.8278 (m110) cc_final: 0.7983 (m-40) REVERT: X 211 ASP cc_start: 0.7771 (t0) cc_final: 0.7473 (t0) REVERT: X 389 LYS cc_start: 0.8814 (ttmt) cc_final: 0.8591 (ttmm) REVERT: X 457 ASP cc_start: 0.8035 (t0) cc_final: 0.7730 (t0) REVERT: Y 207 LYS cc_start: 0.7893 (mtmm) cc_final: 0.7593 (mtmm) REVERT: Y 231 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7733 (mtpp) REVERT: Y 443 ILE cc_start: 0.8537 (mm) cc_final: 0.8325 (mp) REVERT: Y 456 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7408 (ttm170) REVERT: Y 503 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7667 (mtm-85) REVERT: Z 191 TYR cc_start: 0.8574 (m-80) cc_final: 0.8319 (m-80) REVERT: Z 211 ASP cc_start: 0.7866 (t0) cc_final: 0.7624 (t0) REVERT: Z 230 ASP cc_start: 0.8011 (t0) cc_final: 0.7530 (t0) REVERT: Z 231 LYS cc_start: 0.7454 (mtmm) cc_final: 0.6994 (mtmm) REVERT: Z 321 ASP cc_start: 0.8080 (t0) cc_final: 0.7828 (t70) REVERT: Z 381 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7975 (mm-30) REVERT: Z 426 MET cc_start: 0.6296 (mtt) cc_final: 0.5634 (mtt) REVERT: Z 502 LYS cc_start: 0.8322 (tttp) cc_final: 0.7953 (mtpp) outliers start: 41 outliers final: 19 residues processed: 394 average time/residue: 1.3816 time to fit residues: 612.1581 Evaluate side-chains 396 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 374 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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 E residue 3 MET 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 H residue 125 THR Chi-restraints excluded: chain L residue 33 VAL 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 X residue 111 LEU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 78 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 156 optimal weight: 0.0970 chunk 61 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 0.0670 chunk 174 optimal weight: 2.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN H 43 GLN X 98 ASN Y 375 HIS Z 169 GLN Z 315 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102619 restraints weight = 30227.102| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.47 r_work: 0.3182 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20834 Z= 0.138 Angle : 0.566 6.874 28528 Z= 0.272 Chirality : 0.044 0.210 3546 Planarity : 0.004 0.080 3375 Dihedral : 8.686 70.997 5208 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.76 % Allowed : 11.34 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.18), residues: 2316 helix: 2.52 (0.28), residues: 369 sheet: 0.80 (0.19), residues: 759 loop : -0.05 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 32 HIS 0.008 0.001 HIS Y 375 PHE 0.012 0.001 PHE X 53 TYR 0.015 0.001 TYR E 91 ARG 0.009 0.000 ARG Z 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 61) link_NAG-ASN : angle 1.79009 ( 183) link_ALPHA1-6 : bond 0.00276 ( 9) link_ALPHA1-6 : angle 1.85498 ( 27) link_BETA1-4 : bond 0.00436 ( 41) link_BETA1-4 : angle 1.58768 ( 123) link_ALPHA1-2 : bond 0.00371 ( 12) link_ALPHA1-2 : angle 1.56328 ( 36) link_ALPHA1-3 : bond 0.00956 ( 9) link_ALPHA1-3 : angle 1.79785 ( 27) hydrogen bonds : bond 0.04183 ( 570) hydrogen bonds : angle 4.34465 ( 1533) SS BOND : bond 0.00327 ( 38) SS BOND : angle 1.35680 ( 76) covalent geometry : bond 0.00324 (20664) covalent geometry : angle 0.52795 (28056) *********************** 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 431 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 374 time to evaluate : 2.347 Fit side-chains REVERT: A 43 GLN cc_start: 0.7033 (mp10) cc_final: 0.5733 (mp10) REVERT: A 125 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8252 (p) REVERT: E 48 ILE cc_start: 0.8019 (mm) cc_final: 0.7779 (mp) REVERT: H 67 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7929 (tp) REVERT: L 105 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6736 (mt-10) REVERT: R 624 ASN cc_start: 0.8346 (m110) cc_final: 0.8030 (m-40) REVERT: X 211 ASP cc_start: 0.7791 (t0) cc_final: 0.7497 (t0) REVERT: X 232 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8400 (mttm) REVERT: X 322 ILE cc_start: 0.8270 (mm) cc_final: 0.8069 (mm) REVERT: X 389 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8585 (ttmm) REVERT: X 457 ASP cc_start: 0.8001 (t0) cc_final: 0.7729 (t0) REVERT: Y 207 LYS cc_start: 0.7890 (mtmm) cc_final: 0.7642 (mtmm) REVERT: Y 443 ILE cc_start: 0.8587 (mm) cc_final: 0.8387 (mp) REVERT: Y 456 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7447 (ttm170) REVERT: Y 503 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7785 (mtm-85) REVERT: Z 107 ASP cc_start: 0.8234 (m-30) cc_final: 0.8005 (t0) REVERT: Z 211 ASP cc_start: 0.7899 (t0) cc_final: 0.7643 (t0) REVERT: Z 230 ASP cc_start: 0.8020 (t0) cc_final: 0.7552 (t0) REVERT: Z 321 ASP cc_start: 0.8076 (t0) cc_final: 0.7821 (t70) REVERT: Z 381 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7923 (mm-30) REVERT: Z 426 MET cc_start: 0.6423 (mtt) cc_final: 0.5748 (mtt) REVERT: Z 502 LYS cc_start: 0.8335 (tttp) cc_final: 0.7977 (mtpp) outliers start: 57 outliers final: 30 residues processed: 394 average time/residue: 1.4125 time to fit residues: 624.1871 Evaluate side-chains 399 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 365 time to evaluate : 2.073 ------------------------------------------------------------------------------- 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 100 GLN Chi-restraints excluded: chain H residue 66 VAL 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 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain X residue 208 ILE 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 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 244 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 97 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 170 optimal weight: 0.0570 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN ** X 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 169 GLN Y 375 HIS Z 169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.118191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.102107 restraints weight = 30256.720| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.46 r_work: 0.3172 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20834 Z= 0.154 Angle : 0.575 6.985 28528 Z= 0.277 Chirality : 0.044 0.225 3546 Planarity : 0.004 0.083 3375 Dihedral : 8.368 70.834 5208 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.25 % Favored : 97.71 % Rotamer: Outliers : 2.71 % Allowed : 12.69 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.18), residues: 2316 helix: 2.53 (0.28), residues: 369 sheet: 0.92 (0.19), residues: 738 loop : -0.07 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 32 HIS 0.007 0.001 HIS Y 375 PHE 0.013 0.001 PHE X 53 TYR 0.016 0.001 TYR E 91 ARG 0.009 0.000 ARG Z 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 61) link_NAG-ASN : angle 1.83325 ( 183) link_ALPHA1-6 : bond 0.00243 ( 9) link_ALPHA1-6 : angle 1.88512 ( 27) link_BETA1-4 : bond 0.00428 ( 41) link_BETA1-4 : angle 1.60774 ( 123) link_ALPHA1-2 : bond 0.00385 ( 12) link_ALPHA1-2 : angle 1.57756 ( 36) link_ALPHA1-3 : bond 0.00917 ( 9) link_ALPHA1-3 : angle 1.75807 ( 27) hydrogen bonds : bond 0.04304 ( 570) hydrogen bonds : angle 4.38080 ( 1533) SS BOND : bond 0.00359 ( 38) SS BOND : angle 1.36642 ( 76) covalent geometry : bond 0.00365 (20664) covalent geometry : angle 0.53703 (28056) *********************** 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 429 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 373 time to evaluate : 2.116 Fit side-chains REVERT: A 74 THR cc_start: 0.8279 (t) cc_final: 0.8048 (t) REVERT: A 125 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8276 (p) REVERT: E 48 ILE cc_start: 0.8090 (mm) cc_final: 0.7880 (mp) REVERT: E 100 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6617 (pm20) REVERT: H 67 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7945 (tp) REVERT: L 29 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8485 (m) REVERT: R 624 ASN cc_start: 0.8362 (m110) cc_final: 0.8023 (m-40) REVERT: R 661 LEU cc_start: 0.8295 (mt) cc_final: 0.8055 (mp) REVERT: X 211 ASP cc_start: 0.7812 (t0) cc_final: 0.7518 (t0) REVERT: X 389 LYS cc_start: 0.8797 (ttmt) cc_final: 0.8537 (ttmm) REVERT: X 457 ASP cc_start: 0.8008 (t0) cc_final: 0.7730 (t0) REVERT: Y 111 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8085 (tp) REVERT: Y 121 LYS cc_start: 0.8520 (mtpm) cc_final: 0.8258 (mttp) REVERT: Y 207 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7570 (mtmm) REVERT: Y 426 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.5693 (mtp) REVERT: Y 456 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7452 (ttm170) REVERT: Z 107 ASP cc_start: 0.8254 (m-30) cc_final: 0.7977 (t0) REVERT: Z 164 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: Z 211 ASP cc_start: 0.7893 (t0) cc_final: 0.7638 (t0) REVERT: Z 240 LYS cc_start: 0.8130 (mppt) cc_final: 0.7864 (mtmm) REVERT: Z 381 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7713 (mm-30) REVERT: Z 426 MET cc_start: 0.6460 (mtt) cc_final: 0.5767 (mtt) REVERT: Z 502 LYS cc_start: 0.8301 (tttp) cc_final: 0.8090 (mmmm) outliers start: 56 outliers final: 32 residues processed: 395 average time/residue: 1.4185 time to fit residues: 629.6457 Evaluate side-chains 408 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 368 time to evaluate : 2.240 ------------------------------------------------------------------------------- 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 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 66 VAL 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 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 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 111 LEU Chi-restraints excluded: chain X residue 208 ILE 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 111 LEU Chi-restraints excluded: chain Y residue 163 THR 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 97 LYS Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 244 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 140 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 203 GLN Y 169 GLN Y 375 HIS Z 169 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101495 restraints weight = 30051.077| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.47 r_work: 0.3161 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: 0.7876 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20834 Z= 0.192 Angle : 0.617 7.265 28528 Z= 0.296 Chirality : 0.045 0.238 3546 Planarity : 0.004 0.086 3375 Dihedral : 8.301 70.876 5208 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.68 % Favored : 97.28 % Rotamer: Outliers : 2.86 % Allowed : 13.37 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.18), residues: 2316 helix: 2.46 (0.28), residues: 369 sheet: 0.87 (0.19), residues: 738 loop : -0.15 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 32 HIS 0.007 0.001 HIS Y 375 PHE 0.013 0.002 PHE X 53 TYR 0.018 0.002 TYR E 91 ARG 0.011 0.001 ARG Z 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 61) link_NAG-ASN : angle 2.02372 ( 183) link_ALPHA1-6 : bond 0.00175 ( 9) link_ALPHA1-6 : angle 1.90753 ( 27) link_BETA1-4 : bond 0.00430 ( 41) link_BETA1-4 : angle 1.69979 ( 123) link_ALPHA1-2 : bond 0.00351 ( 12) link_ALPHA1-2 : angle 1.63987 ( 36) link_ALPHA1-3 : bond 0.00894 ( 9) link_ALPHA1-3 : angle 1.81762 ( 27) hydrogen bonds : bond 0.04661 ( 570) hydrogen bonds : angle 4.44947 ( 1533) SS BOND : bond 0.00387 ( 38) SS BOND : angle 1.49611 ( 76) covalent geometry : bond 0.00456 (20664) covalent geometry : angle 0.57535 (28056) *********************** 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 435 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 376 time to evaluate : 2.039 Fit side-chains REVERT: A 74 THR cc_start: 0.8279 (t) cc_final: 0.8048 (t) REVERT: A 100 THR cc_start: 0.8674 (m) cc_final: 0.8352 (t) REVERT: A 125 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8296 (p) REVERT: E 100 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6625 (pm20) REVERT: H 67 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7954 (tp) REVERT: R 624 ASN cc_start: 0.8386 (m110) cc_final: 0.8011 (m-40) REVERT: X 211 ASP cc_start: 0.7826 (t0) cc_final: 0.7535 (t0) REVERT: X 389 LYS cc_start: 0.8790 (ttmt) cc_final: 0.8524 (ttmm) REVERT: X 457 ASP cc_start: 0.8025 (t0) cc_final: 0.7738 (t0) REVERT: Y 111 LEU cc_start: 0.8380 (tt) cc_final: 0.8131 (tp) REVERT: Y 207 LYS cc_start: 0.7828 (mtmm) cc_final: 0.7548 (mtmm) REVERT: Y 426 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.5769 (mtp) REVERT: Y 443 ILE cc_start: 0.8574 (mm) cc_final: 0.8355 (mp) REVERT: Y 456 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7492 (ttm170) REVERT: Y 492 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8305 (mt-10) REVERT: Z 107 ASP cc_start: 0.8229 (m-30) cc_final: 0.7941 (t0) REVERT: Z 111 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8077 (tp) REVERT: Z 211 ASP cc_start: 0.7906 (t0) cc_final: 0.7646 (t0) REVERT: Z 240 LYS cc_start: 0.8150 (mppt) cc_final: 0.7879 (mtmm) REVERT: Z 326 ILE cc_start: 0.8488 (pt) cc_final: 0.8023 (mm) REVERT: Z 381 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7829 (mm-30) REVERT: Z 426 MET cc_start: 0.6614 (mtt) cc_final: 0.5963 (mtt) REVERT: Z 502 LYS cc_start: 0.8287 (tttp) cc_final: 0.8072 (mmmm) outliers start: 59 outliers final: 42 residues processed: 400 average time/residue: 1.3568 time to fit residues: 609.2847 Evaluate side-chains 419 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 371 time to evaluate : 2.221 ------------------------------------------------------------------------------- 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 93 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain H residue 66 VAL 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 208 ILE 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 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 426 MET Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Y residue 501 CYS Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 111 LEU Chi-restraints excluded: chain Z residue 117 LYS Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 242 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 178 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 81 optimal weight: 0.0020 chunk 65 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- 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 Y 375 HIS Z 169 GLN Z 375 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101390 restraints weight = 30117.598| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.49 r_work: 0.3155 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20834 Z= 0.165 Angle : 0.593 7.106 28528 Z= 0.286 Chirality : 0.044 0.201 3546 Planarity : 0.004 0.082 3375 Dihedral : 8.095 70.333 5208 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.25 % Favored : 97.71 % Rotamer: Outliers : 2.66 % Allowed : 14.44 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2316 helix: 2.46 (0.28), residues: 369 sheet: 0.84 (0.19), residues: 738 loop : -0.15 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 479 HIS 0.008 0.001 HIS Y 375 PHE 0.012 0.001 PHE X 53 TYR 0.016 0.001 TYR E 91 ARG 0.012 0.001 ARG Z 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 61) link_NAG-ASN : angle 1.91014 ( 183) link_ALPHA1-6 : bond 0.00250 ( 9) link_ALPHA1-6 : angle 1.85888 ( 27) link_BETA1-4 : bond 0.00423 ( 41) link_BETA1-4 : angle 1.64710 ( 123) link_ALPHA1-2 : bond 0.00379 ( 12) link_ALPHA1-2 : angle 1.57730 ( 36) link_ALPHA1-3 : bond 0.00910 ( 9) link_ALPHA1-3 : angle 1.79099 ( 27) hydrogen bonds : bond 0.04413 ( 570) hydrogen bonds : angle 4.43014 ( 1533) SS BOND : bond 0.00418 ( 38) SS BOND : angle 1.45058 ( 76) covalent geometry : bond 0.00390 (20664) covalent geometry : angle 0.55379 (28056) *********************** 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 429 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 374 time to evaluate : 2.080 Fit side-chains REVERT: A 74 THR cc_start: 0.8272 (t) cc_final: 0.8040 (t) REVERT: A 100 THR cc_start: 0.8633 (m) cc_final: 0.8317 (t) REVERT: A 125 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8294 (p) REVERT: D 55 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7881 (mmtt) REVERT: E 100 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6634 (pm20) REVERT: H 67 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7974 (tp) REVERT: R 624 ASN cc_start: 0.8375 (m110) cc_final: 0.7998 (m-40) REVERT: X 211 ASP cc_start: 0.7814 (t0) cc_final: 0.7519 (t0) REVERT: X 389 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8517 (ttmm) REVERT: X 457 ASP cc_start: 0.8025 (t0) cc_final: 0.7739 (t0) REVERT: Y 111 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8069 (tp) REVERT: Y 121 LYS cc_start: 0.8508 (mtpm) cc_final: 0.8251 (mttp) REVERT: Y 164 GLU cc_start: 0.7752 (pm20) cc_final: 0.7400 (pm20) REVERT: Y 207 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7589 (mtmm) REVERT: Y 422 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: Y 426 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.5773 (mtp) REVERT: Y 456 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7477 (ttm170) REVERT: Y 503 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7766 (mtm-85) REVERT: Z 107 ASP cc_start: 0.8251 (m-30) cc_final: 0.7958 (t0) REVERT: Z 161 MET cc_start: 0.8294 (mmm) cc_final: 0.8029 (mmm) REVERT: Z 211 ASP cc_start: 0.7900 (t0) cc_final: 0.7646 (t0) REVERT: Z 240 LYS cc_start: 0.8166 (mppt) cc_final: 0.7889 (mtmm) REVERT: Z 321 ASP cc_start: 0.8064 (t0) cc_final: 0.7824 (t0) REVERT: Z 325 ASP cc_start: 0.8003 (m-30) cc_final: 0.7779 (t0) REVERT: Z 326 ILE cc_start: 0.8527 (pt) cc_final: 0.8087 (mm) REVERT: Z 381 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7780 (mm-30) REVERT: Z 426 MET cc_start: 0.6573 (mtt) cc_final: 0.5952 (mtt) REVERT: Z 502 LYS cc_start: 0.8195 (tttp) cc_final: 0.7969 (mmmm) outliers start: 55 outliers final: 38 residues processed: 397 average time/residue: 1.3884 time to fit residues: 617.5295 Evaluate side-chains 411 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 365 time to evaluate : 2.188 ------------------------------------------------------------------------------- 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 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 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 97 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 X residue 208 ILE 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 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 154 VAL Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL 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 164 GLU Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 242 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 112 optimal weight: 2.9990 chunk 22 optimal weight: 0.0370 chunk 81 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 48 optimal weight: 0.0570 chunk 156 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 195 optimal weight: 0.2980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN X 315 GLN Y 169 GLN Y 375 HIS Z 169 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 = 0.3568 r_free = 0.3568 target = 0.120336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104352 restraints weight = 30171.954| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.46 r_work: 0.3195 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20834 Z= 0.091 Angle : 0.535 8.425 28528 Z= 0.257 Chirality : 0.043 0.202 3546 Planarity : 0.004 0.079 3375 Dihedral : 7.556 68.003 5208 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.60 % Favored : 98.36 % Rotamer: Outliers : 2.13 % Allowed : 15.65 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.18), residues: 2316 helix: 2.66 (0.28), residues: 369 sheet: 0.78 (0.19), residues: 768 loop : -0.03 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 32 HIS 0.009 0.001 HIS Y 375 PHE 0.009 0.001 PHE Y 383 TYR 0.011 0.001 TYR E 91 ARG 0.013 0.000 ARG Z 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 61) link_NAG-ASN : angle 1.53879 ( 183) link_ALPHA1-6 : bond 0.00517 ( 9) link_ALPHA1-6 : angle 1.69902 ( 27) link_BETA1-4 : bond 0.00462 ( 41) link_BETA1-4 : angle 1.42906 ( 123) link_ALPHA1-2 : bond 0.00464 ( 12) link_ALPHA1-2 : angle 1.45148 ( 36) link_ALPHA1-3 : bond 0.01007 ( 9) link_ALPHA1-3 : angle 1.74236 ( 27) hydrogen bonds : bond 0.03399 ( 570) hydrogen bonds : angle 4.22309 ( 1533) SS BOND : bond 0.00414 ( 38) SS BOND : angle 1.11766 ( 76) covalent geometry : bond 0.00203 (20664) covalent geometry : angle 0.50497 (28056) *********************** 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 421 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 377 time to evaluate : 2.089 Fit side-chains REVERT: A 74 THR cc_start: 0.8276 (t) cc_final: 0.8057 (t) REVERT: A 100 THR cc_start: 0.8522 (m) cc_final: 0.8203 (t) REVERT: A 125 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8353 (p) REVERT: D 55 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7889 (mmtt) REVERT: D 116 MET cc_start: 0.8553 (mtp) cc_final: 0.8300 (mtp) REVERT: E 92 ASP cc_start: 0.8005 (t0) cc_final: 0.7785 (t0) REVERT: E 100 GLN cc_start: 0.6943 (OUTLIER) cc_final: 0.6632 (pm20) REVERT: R 624 ASN cc_start: 0.8375 (m110) cc_final: 0.8023 (m-40) REVERT: X 389 LYS cc_start: 0.8759 (ttmt) cc_final: 0.8515 (ttmm) REVERT: X 457 ASP cc_start: 0.7946 (t0) cc_final: 0.7702 (t0) REVERT: Y 111 LEU cc_start: 0.8349 (tt) cc_final: 0.8099 (tp) REVERT: Y 164 GLU cc_start: 0.7709 (pm20) cc_final: 0.7376 (pm20) REVERT: Y 207 LYS cc_start: 0.7722 (mtmm) cc_final: 0.7457 (mtmm) REVERT: Y 426 MET cc_start: 0.6450 (OUTLIER) cc_final: 0.5771 (mtp) REVERT: Y 427 TRP cc_start: 0.7836 (OUTLIER) cc_final: 0.7556 (m100) REVERT: Y 456 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7449 (ttm170) REVERT: Y 503 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7553 (mtm-85) REVERT: Z 83 GLU cc_start: 0.8302 (tt0) cc_final: 0.8092 (tt0) REVERT: Z 107 ASP cc_start: 0.8272 (m-30) cc_final: 0.7973 (t0) REVERT: Z 161 MET cc_start: 0.8216 (mmm) cc_final: 0.7941 (mmm) REVERT: Z 211 ASP cc_start: 0.7906 (t0) cc_final: 0.7653 (t0) REVERT: Z 230 ASP cc_start: 0.8048 (t0) cc_final: 0.7609 (t0) REVERT: Z 321 ASP cc_start: 0.8005 (t0) cc_final: 0.7750 (t0) REVERT: Z 325 ASP cc_start: 0.7943 (m-30) cc_final: 0.7690 (t0) REVERT: Z 326 ILE cc_start: 0.8488 (pt) cc_final: 0.8051 (mm) REVERT: Z 327 ARG cc_start: 0.8562 (mtm-85) cc_final: 0.7853 (mtm-85) REVERT: Z 381 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7766 (mm-30) REVERT: Z 426 MET cc_start: 0.6361 (mtt) cc_final: 0.5730 (mtt) REVERT: Z 502 LYS cc_start: 0.8201 (tttp) cc_final: 0.7987 (mmmm) outliers start: 44 outliers final: 23 residues processed: 394 average time/residue: 1.4519 time to fit residues: 653.0708 Evaluate side-chains 395 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 366 time to evaluate : 2.076 ------------------------------------------------------------------------------- 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 93 THR 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 125 THR 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 592 PHE 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 X residue 208 ILE 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 316 MET Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 427 TRP 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 208 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 122 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 194 optimal weight: 0.0770 chunk 32 optimal weight: 0.0030 chunk 126 optimal weight: 3.9990 chunk 146 optimal weight: 0.0000 chunk 213 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 171 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 overall best weight: 0.2352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 HIS A 50 GLN H 43 GLN T 577 GLN Y 375 HIS Z 169 GLN Z 315 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104878 restraints weight = 30088.459| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.46 r_work: 0.3204 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20834 Z= 0.088 Angle : 0.530 8.217 28528 Z= 0.255 Chirality : 0.043 0.200 3546 Planarity : 0.004 0.074 3375 Dihedral : 7.237 67.311 5208 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.81 % Favored : 98.14 % Rotamer: Outliers : 1.55 % Allowed : 16.57 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.18), residues: 2316 helix: 2.78 (0.28), residues: 369 sheet: 0.84 (0.19), residues: 765 loop : 0.02 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP L 32 HIS 0.008 0.001 HIS Y 375 PHE 0.012 0.001 PHE X 53 TYR 0.010 0.001 TYR E 91 ARG 0.014 0.000 ARG Z 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 61) link_NAG-ASN : angle 1.52513 ( 183) link_ALPHA1-6 : bond 0.00564 ( 9) link_ALPHA1-6 : angle 1.67066 ( 27) link_BETA1-4 : bond 0.00455 ( 41) link_BETA1-4 : angle 1.40370 ( 123) link_ALPHA1-2 : bond 0.00433 ( 12) link_ALPHA1-2 : angle 1.47642 ( 36) link_ALPHA1-3 : bond 0.00975 ( 9) link_ALPHA1-3 : angle 1.78379 ( 27) hydrogen bonds : bond 0.03197 ( 570) hydrogen bonds : angle 4.09688 ( 1533) SS BOND : bond 0.00372 ( 38) SS BOND : angle 1.39736 ( 76) covalent geometry : bond 0.00198 (20664) covalent geometry : angle 0.49793 (28056) *********************** 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 414 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 382 time to evaluate : 2.346 Fit side-chains revert: symmetry clash REVERT: A 74 THR cc_start: 0.8246 (t) cc_final: 0.8030 (t) REVERT: A 100 THR cc_start: 0.8504 (m) cc_final: 0.8172 (t) REVERT: D 55 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7846 (mmtt) REVERT: D 67 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7952 (tp) REVERT: D 116 MET cc_start: 0.8567 (mtp) cc_final: 0.8323 (mtp) REVERT: E 92 ASP cc_start: 0.8001 (t0) cc_final: 0.7771 (t0) REVERT: E 100 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6616 (pm20) REVERT: L 87 TYR cc_start: 0.8364 (m-80) cc_final: 0.7934 (m-80) REVERT: R 624 ASN cc_start: 0.8402 (m110) cc_final: 0.8017 (m-40) REVERT: X 161 MET cc_start: 0.8157 (ttp) cc_final: 0.7909 (ttm) REVERT: X 265 LEU cc_start: 0.8731 (mt) cc_final: 0.8399 (mp) REVERT: X 389 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8534 (ttmm) REVERT: X 457 ASP cc_start: 0.7904 (t0) cc_final: 0.7669 (t0) REVERT: Y 111 LEU cc_start: 0.8322 (tt) cc_final: 0.8056 (tp) REVERT: Y 164 GLU cc_start: 0.7691 (pm20) cc_final: 0.7358 (pm20) REVERT: Y 199 SER cc_start: 0.8361 (p) cc_final: 0.7744 (t) REVERT: Y 207 LYS cc_start: 0.7702 (mtmm) cc_final: 0.7441 (mtmm) REVERT: Y 264 SER cc_start: 0.8453 (m) cc_final: 0.8203 (p) REVERT: Y 283 ASN cc_start: 0.8728 (m-40) cc_final: 0.8514 (m-40) REVERT: Y 426 MET cc_start: 0.6360 (OUTLIER) cc_final: 0.5643 (mtp) REVERT: Y 503 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7709 (mtm-85) REVERT: Z 110 SER cc_start: 0.8590 (t) cc_final: 0.8234 (p) REVERT: Z 161 MET cc_start: 0.8224 (mmm) cc_final: 0.7964 (mmm) REVERT: Z 211 ASP cc_start: 0.7912 (t0) cc_final: 0.7652 (t0) REVERT: Z 230 ASP cc_start: 0.8019 (t0) cc_final: 0.7596 (t0) REVERT: Z 321 ASP cc_start: 0.8008 (t0) cc_final: 0.7738 (t0) REVERT: Z 325 ASP cc_start: 0.7928 (m-30) cc_final: 0.7666 (t0) REVERT: Z 326 ILE cc_start: 0.8444 (pt) cc_final: 0.8025 (mm) REVERT: Z 327 ARG cc_start: 0.8558 (mtm-85) cc_final: 0.7867 (mtm-85) REVERT: Z 347 GLU cc_start: 0.7710 (pp20) cc_final: 0.7374 (pp20) REVERT: Z 349 LEU cc_start: 0.8428 (mt) cc_final: 0.8199 (tp) REVERT: Z 381 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7679 (mm-30) REVERT: Z 426 MET cc_start: 0.6299 (mtt) cc_final: 0.5763 (mtt) REVERT: Z 502 LYS cc_start: 0.8188 (tttp) cc_final: 0.7982 (mmmm) outliers start: 32 outliers final: 19 residues processed: 396 average time/residue: 1.3297 time to fit residues: 593.1259 Evaluate side-chains 406 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 383 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR 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 125 THR 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 592 PHE Chi-restraints excluded: chain T residue 592 PHE Chi-restraints excluded: chain X residue 208 ILE 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 316 MET Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 208 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 117 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 186 optimal weight: 0.6980 chunk 209 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 195 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 143 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN H 43 GLN Y 375 HIS 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 = 0.3549 r_free = 0.3549 target = 0.118874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.102750 restraints weight = 30095.591| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.47 r_work: 0.3184 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20834 Z= 0.126 Angle : 0.564 8.676 28528 Z= 0.271 Chirality : 0.043 0.211 3546 Planarity : 0.004 0.077 3375 Dihedral : 7.301 68.562 5208 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.88 % Rotamer: Outliers : 1.26 % Allowed : 17.15 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.18), residues: 2316 helix: 2.73 (0.28), residues: 369 sheet: 0.83 (0.19), residues: 765 loop : -0.03 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP L 32 HIS 0.008 0.001 HIS Y 375 PHE 0.014 0.001 PHE X 53 TYR 0.013 0.001 TYR E 91 ARG 0.014 0.000 ARG X 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 61) link_NAG-ASN : angle 1.69781 ( 183) link_ALPHA1-6 : bond 0.00444 ( 9) link_ALPHA1-6 : angle 1.75237 ( 27) link_BETA1-4 : bond 0.00432 ( 41) link_BETA1-4 : angle 1.50346 ( 123) link_ALPHA1-2 : bond 0.00386 ( 12) link_ALPHA1-2 : angle 1.52803 ( 36) link_ALPHA1-3 : bond 0.00893 ( 9) link_ALPHA1-3 : angle 1.76697 ( 27) hydrogen bonds : bond 0.03701 ( 570) hydrogen bonds : angle 4.17312 ( 1533) SS BOND : bond 0.00396 ( 38) SS BOND : angle 1.54691 ( 76) covalent geometry : bond 0.00297 (20664) covalent geometry : angle 0.52828 (28056) ********************** 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 397 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 371 time to evaluate : 2.204 Fit side-chains revert: symmetry clash REVERT: A 74 THR cc_start: 0.8247 (t) cc_final: 0.8024 (t) REVERT: A 100 THR cc_start: 0.8570 (m) cc_final: 0.8246 (t) REVERT: D 55 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7851 (mmtt) REVERT: D 115 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8653 (t) REVERT: D 116 MET cc_start: 0.8599 (mtp) cc_final: 0.8362 (mtp) REVERT: E 100 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6644 (pm20) REVERT: L 87 TYR cc_start: 0.8375 (m-80) cc_final: 0.7927 (m-80) REVERT: R 624 ASN cc_start: 0.8420 (m110) cc_final: 0.8043 (m-40) REVERT: X 161 MET cc_start: 0.8266 (ttp) cc_final: 0.7964 (ttm) REVERT: X 211 ASP cc_start: 0.7788 (t0) cc_final: 0.7485 (t0) REVERT: X 265 LEU cc_start: 0.8729 (mt) cc_final: 0.8405 (mp) REVERT: X 389 LYS cc_start: 0.8717 (ttmt) cc_final: 0.8502 (ttmm) REVERT: X 457 ASP cc_start: 0.7935 (t0) cc_final: 0.7687 (t0) REVERT: Y 99 ASN cc_start: 0.8374 (t0) cc_final: 0.8088 (t0) REVERT: Y 111 LEU cc_start: 0.8319 (tt) cc_final: 0.8064 (tp) REVERT: Y 164 GLU cc_start: 0.7714 (pm20) cc_final: 0.7382 (pm20) REVERT: Y 207 LYS cc_start: 0.7725 (mtmm) cc_final: 0.7479 (mtmm) REVERT: Y 264 SER cc_start: 0.8496 (m) cc_final: 0.8250 (p) REVERT: Y 426 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.5789 (mtp) REVERT: Y 427 TRP cc_start: 0.7867 (OUTLIER) cc_final: 0.7499 (m100) REVERT: Y 503 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7621 (mtm-85) REVERT: Z 107 ASP cc_start: 0.8298 (m-30) cc_final: 0.8049 (t0) REVERT: Z 161 MET cc_start: 0.8249 (mmm) cc_final: 0.7994 (mmm) REVERT: Z 211 ASP cc_start: 0.7907 (t0) cc_final: 0.7647 (t0) REVERT: Z 230 ASP cc_start: 0.8007 (t0) cc_final: 0.7583 (t0) REVERT: Z 321 ASP cc_start: 0.8035 (t0) cc_final: 0.7767 (t0) REVERT: Z 325 ASP cc_start: 0.7946 (m-30) cc_final: 0.7677 (t0) REVERT: Z 326 ILE cc_start: 0.8483 (pt) cc_final: 0.8032 (mm) REVERT: Z 327 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.7869 (mtm-85) REVERT: Z 347 GLU cc_start: 0.7686 (pp20) cc_final: 0.7364 (pp20) REVERT: Z 381 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7686 (mm-30) REVERT: Z 426 MET cc_start: 0.6360 (mtt) cc_final: 0.5827 (mtt) outliers start: 26 outliers final: 20 residues processed: 381 average time/residue: 1.3716 time to fit residues: 589.1881 Evaluate side-chains 388 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 363 time to evaluate : 2.307 ------------------------------------------------------------------------------- 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 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 125 THR 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 592 PHE Chi-restraints excluded: chain X residue 208 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 316 MET Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 427 TRP 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 490 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 17 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN Y 375 HIS Z 315 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.118815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.102725 restraints weight = 30154.363| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.46 r_work: 0.3177 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20834 Z= 0.134 Angle : 0.576 8.724 28528 Z= 0.277 Chirality : 0.044 0.202 3546 Planarity : 0.004 0.078 3375 Dihedral : 7.313 68.964 5208 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.20 % Favored : 97.75 % Rotamer: Outliers : 1.36 % Allowed : 17.25 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.18), residues: 2316 helix: 2.68 (0.28), residues: 369 sheet: 0.81 (0.19), residues: 762 loop : -0.02 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP L 32 HIS 0.008 0.001 HIS Y 375 PHE 0.016 0.001 PHE X 53 TYR 0.014 0.001 TYR E 91 ARG 0.015 0.001 ARG X 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 61) link_NAG-ASN : angle 1.74953 ( 183) link_ALPHA1-6 : bond 0.00413 ( 9) link_ALPHA1-6 : angle 1.78884 ( 27) link_BETA1-4 : bond 0.00422 ( 41) link_BETA1-4 : angle 1.52628 ( 123) link_ALPHA1-2 : bond 0.00394 ( 12) link_ALPHA1-2 : angle 1.53239 ( 36) link_ALPHA1-3 : bond 0.00888 ( 9) link_ALPHA1-3 : angle 1.73441 ( 27) hydrogen bonds : bond 0.03867 ( 570) hydrogen bonds : angle 4.22896 ( 1533) SS BOND : bond 0.00375 ( 38) SS BOND : angle 1.50573 ( 76) covalent geometry : bond 0.00319 (20664) covalent geometry : angle 0.53989 (28056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15769.98 seconds wall clock time: 271 minutes 25.66 seconds (16285.66 seconds total)