Starting phenix.real_space_refine on Sun Aug 24 04:27:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9btv_44897/08_2025/9btv_44897.cif Found real_map, /net/cci-nas-00/data/ceres_data/9btv_44897/08_2025/9btv_44897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9btv_44897/08_2025/9btv_44897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9btv_44897/08_2025/9btv_44897.map" model { file = "/net/cci-nas-00/data/ceres_data/9btv_44897/08_2025/9btv_44897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9btv_44897/08_2025/9btv_44897.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 98 5.16 5 C 10524 2.51 5 N 2750 2.21 5 O 3480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16852 Number of models: 1 Model: "" Number of chains: 55 Chain: "A" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3489 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 962 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "C" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3462 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Chain: "E" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3467 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 3 Chain: "F" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 970 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "G" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 970 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1058 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 785 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "D" 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: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" 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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "j" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "k" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 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: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 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: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 3.35, per 1000 atoms: 0.20 Number of scatterers: 16852 At special positions: 0 Unit cell: (124.5, 128.65, 150.23, 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 98 16.00 O 3480 8.00 N 2750 7.00 C 10524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.01 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.09 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA I 3 " - " MAN I 4 " " BMA j 3 " - " MAN j 6 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " MAN j 4 " - " MAN j 5 " " BMA k 3 " - " MAN k 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " NAG-ASN " NAG A 601 " - " ASN A 339 " " NAG A 602 " - " ASN A 386 " " NAG A 603 " - " ASN A 448 " " NAG A 604 " - " ASN A 88 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 625 " " NAG C 601 " - " ASN C 339 " " NAG C 602 " - " ASN C 386 " " NAG C 603 " - " ASN C 448 " " NAG C 604 " - " ASN C 88 " " NAG D 1 " - " ASN A 160 " " NAG E 601 " - " ASN E 339 " " NAG E 602 " - " ASN E 386 " " NAG E 603 " - " ASN E 448 " " NAG E 604 " - " ASN E 465 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 625 " " NAG G 701 " - " ASN G 625 " " NAG G 702 " - " ASN G 611 " " NAG G 703 " - " ASN G 637 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 241 " " NAG K 1 " - " ASN A 234 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 465 " " NAG O 1 " - " ASN A 392 " " NAG P 1 " - " ASN A 363 " " NAG Q 1 " - " ASN A 332 " " NAG R 1 " - " ASN A 301 " " NAG S 1 " - " ASN A 133 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 197 " " NAG V 1 " - " ASN B 611 " " NAG W 1 " - " ASN C 156 " " NAG X 1 " - " ASN C 241 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 276 " " NAG a 1 " - " ASN C 465 " " NAG b 1 " - " ASN C 392 " " NAG c 1 " - " ASN C 363 " " NAG d 1 " - " ASN C 332 " " NAG e 1 " - " ASN C 301 " " NAG f 1 " - " ASN C 133 " " NAG g 1 " - " ASN C 262 " " NAG h 1 " - " ASN C 197 " " NAG i 1 " - " ASN C 160 " " NAG j 1 " - " ASN E 160 " " NAG k 1 " - " ASN E 156 " " NAG l 1 " - " ASN E 88 " " NAG m 1 " - " ASN E 241 " " NAG n 1 " - " ASN E 234 " " NAG o 1 " - " ASN E 276 " " NAG p 1 " - " ASN E 392 " " NAG q 1 " - " ASN E 363 " " NAG r 1 " - " ASN E 332 " " NAG s 1 " - " ASN E 301 " " NAG t 1 " - " ASN E 133 " " NAG u 1 " - " ASN E 262 " " NAG v 1 " - " ASN E 197 " " NAG w 1 " - " ASN F 611 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 431.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 34 sheets defined 24.8% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.766A pdb=" N THR A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 removed outlier: 4.321A pdb=" N GLY A 380 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 484 removed outlier: 4.016A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.286A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.827A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.607A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.074A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.884A pdb=" N THR C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 386 through 390 removed outlier: 4.369A pdb=" N GLY C 389 " --> pdb=" O ASN C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 4.116A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 334 through 353 removed outlier: 4.052A pdb=" N THR E 351 " --> pdb=" O GLU E 347 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 475 through 481 removed outlier: 4.210A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 484 No H-bonds generated for 'chain 'E' and resid 482 through 484' Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 544 Processing helix chain 'F' and resid 569 through 597 removed outlier: 3.950A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 removed outlier: 4.058A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 634 removed outlier: 3.512A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 648 removed outlier: 3.680A pdb=" N ILE F 646 " --> pdb=" O ILE F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 659 Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 543 removed outlier: 3.629A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN G 543 " --> pdb=" O VAL G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 569 through 596 removed outlier: 3.583A pdb=" N ASP G 589 " --> pdb=" O HIS G 585 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU G 592 " --> pdb=" O ARG G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 618 through 625 removed outlier: 3.572A pdb=" N ILE G 622 " --> pdb=" O SER G 618 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP G 623 " --> pdb=" O LEU G 619 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 635 removed outlier: 3.900A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE G 635 " --> pdb=" O TRP G 631 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 661 removed outlier: 4.214A pdb=" N ILE G 642 " --> pdb=" O TYR G 638 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR G 643 " --> pdb=" O THR G 639 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN G 652 " --> pdb=" O GLU G 648 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU G 654 " --> pdb=" O GLN G 650 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS G 655 " --> pdb=" O ASN G 651 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN G 656 " --> pdb=" O GLN G 652 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.564A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 27B through 31 removed outlier: 3.592A pdb=" N SER L 30 " --> pdb=" O ASN L 27B" (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN L 31 " --> pdb=" O ILE L 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 27B through 31' Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.408A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.658A pdb=" N LYS A 487 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.500A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.406A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.534A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLY A 451 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 10.879A pdb=" N GLN A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.782A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.873A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR A 293 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR A 334 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.085A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.873A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.782A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.879A pdb=" N GLN A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLY A 451 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 309 removed outlier: 6.431A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 39 Processing sheet with id=AB2, first strand: chain 'C' and resid 46 through 47 removed outlier: 3.800A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 245 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB4, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.354A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 9.376A pdb=" N ASN C 448 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 10.106A pdb=" N GLN C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 297 current: chain 'C' and resid 359 through 361 Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.115A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.106A pdb=" N GLN C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N ASN C 448 " --> pdb=" O GLN C 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 447 through 456 current: chain 'C' and resid 413 through 417 Processing sheet with id=AB9, first strand: chain 'C' and resid 302 through 309 removed outlier: 6.773A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.719A pdb=" N VAL E 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR G 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.800A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 76 removed outlier: 7.121A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AC7, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.422A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 256 through 257 removed outlier: 3.713A pdb=" N SER E 375 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.224A pdb=" N GLN E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N ASN E 448 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 10.650A pdb=" N VAL E 292 " --> pdb=" O GLU E 446 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N GLU E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.208A pdb=" N ILE E 294 " --> pdb=" O LYS E 444 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N LYS E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 260 through 261 removed outlier: 10.044A pdb=" N LYS E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.208A pdb=" N ILE E 294 " --> pdb=" O LYS E 444 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N GLU E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.650A pdb=" N VAL E 292 " --> pdb=" O GLU E 446 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N ASN E 448 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 10.224A pdb=" N GLN E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 358 through 361 Processing sheet with id=AD1, first strand: chain 'E' and resid 303 through 308 removed outlier: 7.221A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.810A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 95D through 100A removed outlier: 6.968A pdb=" N PHE H 100H" --> pdb=" O LEU H 100 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 20 through 24 removed outlier: 3.530A pdb=" N SER L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 44 through 48 removed outlier: 3.578A pdb=" N LEU L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 44 through 48 removed outlier: 3.578A pdb=" N LEU L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 2.21 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: 5059 1.35 - 1.47: 4414 1.47 - 1.60: 7577 1.60 - 1.72: 1 1.72 - 1.85: 124 Bond restraints: 17175 Sorted by residual: bond pdb=" N VAL F 608 " pdb=" CA VAL F 608 " ideal model delta sigma weight residual 1.457 1.491 -0.034 9.00e-03 1.23e+04 1.39e+01 bond pdb=" N ILE A 371 " pdb=" CA ILE A 371 " ideal model delta sigma weight residual 1.460 1.498 -0.039 1.09e-02 8.42e+03 1.26e+01 bond pdb=" N VAL C 496 " pdb=" CA VAL C 496 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.11e-02 8.12e+03 1.16e+01 bond pdb=" N VAL A 134 " pdb=" CA VAL A 134 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" N GLY C 495 " pdb=" CA GLY C 495 " ideal model delta sigma weight residual 1.445 1.477 -0.032 9.90e-03 1.02e+04 1.08e+01 ... (remaining 17170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 22879 3.07 - 6.14: 429 6.14 - 9.21: 11 9.21 - 12.28: 4 12.28 - 15.36: 1 Bond angle restraints: 23324 Sorted by residual: angle pdb=" N TYR A 191 " pdb=" CA TYR A 191 " pdb=" CB TYR A 191 " ideal model delta sigma weight residual 110.65 95.29 15.36 1.56e+00 4.11e-01 9.69e+01 angle pdb=" N ILE C 184 " pdb=" CA ILE C 184 " pdb=" C ILE C 184 " ideal model delta sigma weight residual 113.16 103.79 9.37 1.49e+00 4.50e-01 3.95e+01 angle pdb=" C CYS E 54 " pdb=" CA CYS E 54 " pdb=" CB CYS E 54 " ideal model delta sigma weight residual 110.51 99.22 11.29 1.89e+00 2.80e-01 3.57e+01 angle pdb=" C TYR A 191 " pdb=" CA TYR A 191 " pdb=" CB TYR A 191 " ideal model delta sigma weight residual 110.16 119.23 -9.07 1.66e+00 3.63e-01 2.99e+01 angle pdb=" CA GLU L 41 " pdb=" CB GLU L 41 " pdb=" CG GLU L 41 " ideal model delta sigma weight residual 114.10 124.27 -10.17 2.00e+00 2.50e-01 2.59e+01 ... (remaining 23319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.87: 11071 20.87 - 41.74: 648 41.74 - 62.61: 166 62.61 - 83.48: 32 83.48 - 104.35: 8 Dihedral angle restraints: 11925 sinusoidal: 6391 harmonic: 5534 Sorted by residual: dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -150.15 64.15 1 1.00e+01 1.00e-02 5.41e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 155.24 -62.24 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -144.53 58.53 1 1.00e+01 1.00e-02 4.59e+01 ... (remaining 11922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2564 0.074 - 0.149: 367 0.149 - 0.223: 45 0.223 - 0.297: 10 0.297 - 0.372: 2 Chirality restraints: 2988 Sorted by residual: chirality pdb=" C1 BMA j 3 " pdb=" O4 NAG j 2 " pdb=" C2 BMA j 3 " pdb=" O5 BMA j 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.27e+02 chirality pdb=" C1 MAN j 4 " pdb=" O6 BMA j 3 " pdb=" C2 MAN j 4 " pdb=" O5 MAN j 4 " both_signs ideal model delta sigma weight residual False 2.40 2.47 -0.07 2.00e-02 2.50e+03 1.40e+01 chirality pdb=" C1 MAN j 6 " pdb=" O3 BMA j 3 " pdb=" C2 MAN j 6 " pdb=" O5 MAN j 6 " both_signs ideal model delta sigma weight residual False 2.40 2.46 -0.06 2.00e-02 2.50e+03 9.73e+00 ... (remaining 2985 not shown) Planarity restraints: 2848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 88 " 0.106 2.00e-02 2.50e+03 1.45e-01 2.64e+02 pdb=" CG ASN E 88 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN E 88 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN E 88 " -0.254 2.00e-02 2.50e+03 pdb=" C1 NAG l 1 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 637 " 0.077 2.00e-02 2.50e+03 1.23e-01 1.88e+02 pdb=" CG ASN B 637 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN B 637 " 0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN B 637 " -0.219 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 2 " -0.087 2.00e-02 2.50e+03 7.21e-02 6.49e+01 pdb=" C7 NAG j 2 " 0.022 2.00e-02 2.50e+03 pdb=" C8 NAG j 2 " -0.065 2.00e-02 2.50e+03 pdb=" N2 NAG j 2 " 0.115 2.00e-02 2.50e+03 pdb=" O7 NAG j 2 " 0.016 2.00e-02 2.50e+03 ... (remaining 2845 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2851 2.78 - 3.31: 16532 3.31 - 3.84: 26902 3.84 - 4.37: 31430 4.37 - 4.90: 54124 Nonbonded interactions: 131839 Sorted by model distance: nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.244 3.040 nonbonded pdb=" OG SER B 528 " pdb=" O7 NAG A 604 " model vdw 2.249 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" O CYS G 604 " model vdw 2.255 3.040 nonbonded pdb=" O3 NAG D 2 " pdb=" O2 BMA D 3 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASN C 195 " pdb=" OG1 THR C 198 " model vdw 2.291 3.040 ... (remaining 131834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 57 or resid 65 through 135 or resid 152 through \ 186 or resid 189 through 604)) selection = (chain 'C' and (resid 33 through 57 or resid 65 through 135 or resid 152 through \ 604)) selection = (chain 'E' and (resid 33 through 186 or resid 189 through 604)) } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 520 through 545 or resid 569 through 702)) selection = (chain 'G' and (resid 520 through 545 or resid 569 through 702)) } ncs_group { reference = chain 'I' selection = chain 'i' selection = chain 'k' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'Q' selection = chain 'T' selection = chain 'X' selection = chain 'Y' selection = chain 'd' selection = chain 'g' selection = chain 'm' selection = chain 'n' selection = chain 'r' selection = chain 'u' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'v' selection = chain 'w' } 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: 4.580 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.280 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.006 0.080 17336 Z= 0.345 Angle : 1.128 31.610 23772 Z= 0.603 Chirality : 0.055 0.372 2988 Planarity : 0.006 0.121 2788 Dihedral : 13.449 104.347 8244 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.18), residues: 1870 helix: -0.66 (0.26), residues: 366 sheet: -0.99 (0.23), residues: 526 loop : -1.61 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 16 TYR 0.029 0.001 TYR H 100N PHE 0.021 0.001 PHE C 376 TRP 0.022 0.001 TRP H 47 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00549 (17175) covalent geometry : angle 0.97770 (23324) SS BOND : bond 0.01182 ( 35) SS BOND : angle 2.25785 ( 70) hydrogen bonds : bond 0.25080 ( 515) hydrogen bonds : angle 9.17121 ( 1437) link_ALPHA1-3 : bond 0.03085 ( 3) link_ALPHA1-3 : angle 6.14302 ( 9) link_ALPHA1-6 : bond 0.02495 ( 5) link_ALPHA1-6 : angle 3.62360 ( 15) link_BETA1-4 : bond 0.01516 ( 58) link_BETA1-4 : angle 4.55821 ( 174) link_NAG-ASN : bond 0.01156 ( 60) link_NAG-ASN : angle 4.35875 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8156 (tpt) cc_final: 0.7291 (tpt) REVERT: A 353 PHE cc_start: 0.6727 (p90) cc_final: 0.6503 (p90) REVERT: A 377 ASN cc_start: 0.7607 (t0) cc_final: 0.7110 (t0) REVERT: B 543 ASN cc_start: 0.7733 (m110) cc_final: 0.7195 (m-40) REVERT: B 584 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8328 (mt-10) REVERT: B 622 ILE cc_start: 0.9088 (tp) cc_final: 0.8864 (tp) REVERT: C 42 VAL cc_start: 0.7514 (t) cc_final: 0.7170 (p) REVERT: C 95 MET cc_start: 0.8326 (pmm) cc_final: 0.8084 (pmm) REVERT: C 112 TRP cc_start: 0.8715 (t-100) cc_final: 0.8259 (t-100) REVERT: C 434 MET cc_start: 0.8520 (ttp) cc_final: 0.7956 (ttm) REVERT: C 491 ILE cc_start: 0.8088 (mt) cc_final: 0.7879 (tt) REVERT: F 589 ASP cc_start: 0.8834 (p0) cc_final: 0.8633 (p0) REVERT: F 626 MET cc_start: 0.7693 (tpp) cc_final: 0.7414 (tpp) REVERT: F 653 GLN cc_start: 0.8527 (mm110) cc_final: 0.8144 (mm-40) REVERT: G 584 GLU cc_start: 0.8377 (tt0) cc_final: 0.8145 (tm-30) REVERT: G 632 ASP cc_start: 0.8572 (t70) cc_final: 0.8177 (t0) REVERT: G 657 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8825 (tm-30) REVERT: H 5 ARG cc_start: 0.8626 (ttm110) cc_final: 0.8300 (mtm-85) REVERT: H 13 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8570 (mtpp) REVERT: H 33 TYR cc_start: 0.8498 (m-80) cc_final: 0.8187 (m-80) REVERT: H 86 ASP cc_start: 0.7946 (m-30) cc_final: 0.7539 (m-30) REVERT: H 100 TYR cc_start: 0.8530 (p90) cc_final: 0.8130 (p90) REVERT: L 33 VAL cc_start: 0.9002 (t) cc_final: 0.8766 (p) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1296 time to fit residues: 30.2956 Evaluate side-chains 105 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 216 HIS A 246 GLN A 377 ASN C 130 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 302 ASN E 425 ASN F 570 HIS G 570 HIS G 590 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.067530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.052159 restraints weight = 63487.645| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 4.53 r_work: 0.2911 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17336 Z= 0.144 Angle : 0.761 16.678 23772 Z= 0.343 Chirality : 0.048 0.296 2988 Planarity : 0.004 0.047 2788 Dihedral : 8.907 76.853 4645 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.88 % Allowed : 11.09 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.18), residues: 1870 helix: 0.34 (0.27), residues: 383 sheet: -0.82 (0.22), residues: 510 loop : -1.27 (0.18), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 16 TYR 0.032 0.001 TYR H 100N PHE 0.011 0.001 PHE E 383 TRP 0.017 0.001 TRP H 47 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00308 (17175) covalent geometry : angle 0.67290 (23324) SS BOND : bond 0.00321 ( 35) SS BOND : angle 0.79301 ( 70) hydrogen bonds : bond 0.05021 ( 515) hydrogen bonds : angle 6.14151 ( 1437) link_ALPHA1-3 : bond 0.00996 ( 3) link_ALPHA1-3 : angle 3.05138 ( 9) link_ALPHA1-6 : bond 0.00892 ( 5) link_ALPHA1-6 : angle 1.95565 ( 15) link_BETA1-4 : bond 0.01045 ( 58) link_BETA1-4 : angle 3.31965 ( 174) link_NAG-ASN : bond 0.00362 ( 60) link_NAG-ASN : angle 2.47666 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8693 (tpt) cc_final: 0.7873 (tpt) REVERT: A 377 ASN cc_start: 0.8313 (t0) cc_final: 0.7893 (t0) REVERT: B 543 ASN cc_start: 0.7872 (m110) cc_final: 0.7336 (m-40) REVERT: B 584 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8397 (mt-10) REVERT: C 42 VAL cc_start: 0.7835 (t) cc_final: 0.7488 (p) REVERT: C 95 MET cc_start: 0.8320 (pmm) cc_final: 0.7841 (pmm) REVERT: C 434 MET cc_start: 0.8608 (ttp) cc_final: 0.8026 (ttm) REVERT: C 475 MET cc_start: 0.8732 (tpp) cc_final: 0.8409 (tpp) REVERT: E 499 THR cc_start: 0.7559 (OUTLIER) cc_final: 0.7281 (m) REVERT: F 530 MET cc_start: 0.7937 (mmt) cc_final: 0.6733 (mmt) REVERT: F 626 MET cc_start: 0.7455 (tpp) cc_final: 0.7066 (tpp) REVERT: F 653 GLN cc_start: 0.8483 (mm110) cc_final: 0.8160 (mm-40) REVERT: G 584 GLU cc_start: 0.8714 (tt0) cc_final: 0.8331 (tm-30) REVERT: G 616 ASN cc_start: 0.9253 (p0) cc_final: 0.8681 (m-40) REVERT: G 632 ASP cc_start: 0.8769 (t70) cc_final: 0.8538 (t70) REVERT: G 657 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8632 (tm-30) REVERT: H 100 TYR cc_start: 0.8811 (p90) cc_final: 0.8356 (p90) REVERT: L 13 GLU cc_start: 0.4405 (OUTLIER) cc_final: 0.4101 (pm20) REVERT: L 81 GLU cc_start: 0.9255 (tp30) cc_final: 0.9038 (mp0) REVERT: L 82 ASP cc_start: 0.8514 (m-30) cc_final: 0.7248 (m-30) outliers start: 15 outliers final: 8 residues processed: 129 average time/residue: 0.1239 time to fit residues: 24.4568 Evaluate side-chains 105 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain L residue 13 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 0 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 195 ASN A 330 HIS E 185 ASN E 195 ASN ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.065741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.050353 restraints weight = 64771.668| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 4.54 r_work: 0.2841 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17336 Z= 0.192 Angle : 0.727 16.711 23772 Z= 0.328 Chirality : 0.047 0.342 2988 Planarity : 0.004 0.054 2788 Dihedral : 8.621 68.919 4645 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.30 % Allowed : 11.33 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.19), residues: 1870 helix: 0.61 (0.27), residues: 381 sheet: -0.80 (0.22), residues: 521 loop : -1.18 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 16 TYR 0.033 0.002 TYR H 100N PHE 0.015 0.002 PHE C 376 TRP 0.013 0.001 TRP H 47 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00432 (17175) covalent geometry : angle 0.64918 (23324) SS BOND : bond 0.00393 ( 35) SS BOND : angle 0.90585 ( 70) hydrogen bonds : bond 0.04419 ( 515) hydrogen bonds : angle 5.66565 ( 1437) link_ALPHA1-3 : bond 0.00830 ( 3) link_ALPHA1-3 : angle 3.19560 ( 9) link_ALPHA1-6 : bond 0.00820 ( 5) link_ALPHA1-6 : angle 1.70759 ( 15) link_BETA1-4 : bond 0.00969 ( 58) link_BETA1-4 : angle 3.05556 ( 174) link_NAG-ASN : bond 0.00329 ( 60) link_NAG-ASN : angle 2.26879 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8752 (tpt) cc_final: 0.7858 (tpt) REVERT: A 377 ASN cc_start: 0.8387 (t0) cc_final: 0.8063 (t0) REVERT: A 426 MET cc_start: 0.8031 (pmm) cc_final: 0.7333 (ptp) REVERT: A 475 MET cc_start: 0.8286 (tpp) cc_final: 0.8030 (tpp) REVERT: B 543 ASN cc_start: 0.8007 (m110) cc_final: 0.7405 (m-40) REVERT: B 584 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8380 (mt-10) REVERT: B 589 ASP cc_start: 0.8901 (m-30) cc_final: 0.8526 (m-30) REVERT: B 626 MET cc_start: 0.8960 (pmm) cc_final: 0.8174 (pmm) REVERT: C 42 VAL cc_start: 0.8309 (t) cc_final: 0.7973 (p) REVERT: C 95 MET cc_start: 0.8447 (pmm) cc_final: 0.7780 (ptp) REVERT: C 475 MET cc_start: 0.8624 (tpp) cc_final: 0.8402 (tpp) REVERT: E 499 THR cc_start: 0.7722 (OUTLIER) cc_final: 0.7449 (m) REVERT: F 530 MET cc_start: 0.7894 (mmt) cc_final: 0.6678 (mmt) REVERT: F 626 MET cc_start: 0.7548 (tpp) cc_final: 0.7206 (tpp) REVERT: F 653 GLN cc_start: 0.8584 (mm110) cc_final: 0.8227 (mm-40) REVERT: G 584 GLU cc_start: 0.8805 (tt0) cc_final: 0.8328 (tm-30) REVERT: G 616 ASN cc_start: 0.9259 (p0) cc_final: 0.8676 (m-40) REVERT: G 632 ASP cc_start: 0.8689 (t70) cc_final: 0.8441 (t70) REVERT: H 100 TYR cc_start: 0.8930 (p90) cc_final: 0.8469 (p90) REVERT: L 17 LYS cc_start: 0.8891 (pttm) cc_final: 0.8458 (pttm) REVERT: L 81 GLU cc_start: 0.9375 (tp30) cc_final: 0.9094 (mp0) REVERT: L 82 ASP cc_start: 0.8122 (m-30) cc_final: 0.7277 (m-30) outliers start: 22 outliers final: 14 residues processed: 118 average time/residue: 0.1095 time to fit residues: 20.1937 Evaluate side-chains 105 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 118 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 147 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 195 ASN E 195 ASN E 377 ASN L 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.066663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.051233 restraints weight = 63895.938| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 4.53 r_work: 0.2887 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17336 Z= 0.113 Angle : 0.664 16.757 23772 Z= 0.297 Chirality : 0.046 0.340 2988 Planarity : 0.003 0.047 2788 Dihedral : 8.385 61.546 4645 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.53 % Allowed : 12.09 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.19), residues: 1870 helix: 0.85 (0.28), residues: 381 sheet: -0.66 (0.22), residues: 526 loop : -1.04 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 16 TYR 0.032 0.001 TYR H 100N PHE 0.011 0.001 PHE A 159 TRP 0.011 0.001 TRP A 112 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00235 (17175) covalent geometry : angle 0.59181 (23324) SS BOND : bond 0.00286 ( 35) SS BOND : angle 0.69012 ( 70) hydrogen bonds : bond 0.03697 ( 515) hydrogen bonds : angle 5.37359 ( 1437) link_ALPHA1-3 : bond 0.01006 ( 3) link_ALPHA1-3 : angle 3.00773 ( 9) link_ALPHA1-6 : bond 0.00988 ( 5) link_ALPHA1-6 : angle 1.63849 ( 15) link_BETA1-4 : bond 0.00987 ( 58) link_BETA1-4 : angle 2.85778 ( 174) link_NAG-ASN : bond 0.00291 ( 60) link_NAG-ASN : angle 2.00621 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8768 (tpt) cc_final: 0.7915 (tpt) REVERT: A 377 ASN cc_start: 0.8321 (t0) cc_final: 0.8026 (t0) REVERT: A 426 MET cc_start: 0.8162 (pmm) cc_final: 0.7266 (ptp) REVERT: B 543 ASN cc_start: 0.7899 (m110) cc_final: 0.7260 (m-40) REVERT: B 584 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8312 (mt-10) REVERT: B 626 MET cc_start: 0.8919 (pmm) cc_final: 0.8173 (pmm) REVERT: C 42 VAL cc_start: 0.8220 (t) cc_final: 0.7858 (p) REVERT: C 95 MET cc_start: 0.8427 (pmm) cc_final: 0.7733 (ptp) REVERT: C 434 MET cc_start: 0.8608 (ttp) cc_final: 0.8331 (tmm) REVERT: C 475 MET cc_start: 0.8608 (tpp) cc_final: 0.8370 (tpp) REVERT: E 195 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7556 (m-40) REVERT: E 499 THR cc_start: 0.7672 (OUTLIER) cc_final: 0.7394 (m) REVERT: F 530 MET cc_start: 0.7834 (mmt) cc_final: 0.6711 (mmt) REVERT: F 626 MET cc_start: 0.7674 (tpp) cc_final: 0.7365 (tpt) REVERT: F 633 LYS cc_start: 0.9475 (ptpt) cc_final: 0.9196 (mtmm) REVERT: F 653 GLN cc_start: 0.8519 (mm110) cc_final: 0.8170 (mm-40) REVERT: G 584 GLU cc_start: 0.8742 (tt0) cc_final: 0.8314 (tm-30) REVERT: G 616 ASN cc_start: 0.9237 (p0) cc_final: 0.8638 (m-40) REVERT: G 632 ASP cc_start: 0.8640 (t70) cc_final: 0.8414 (t70) REVERT: H 100 TYR cc_start: 0.8783 (p90) cc_final: 0.8354 (p90) REVERT: L 17 LYS cc_start: 0.8853 (pttm) cc_final: 0.8413 (pttm) REVERT: L 81 GLU cc_start: 0.9393 (tp30) cc_final: 0.9082 (mp0) REVERT: L 82 ASP cc_start: 0.8240 (m-30) cc_final: 0.7329 (m-30) outliers start: 26 outliers final: 11 residues processed: 125 average time/residue: 0.1163 time to fit residues: 22.9815 Evaluate side-chains 106 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 169 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 195 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.065359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.050156 restraints weight = 64202.791| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 4.46 r_work: 0.2835 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17336 Z= 0.179 Angle : 0.686 16.765 23772 Z= 0.309 Chirality : 0.045 0.344 2988 Planarity : 0.004 0.056 2788 Dihedral : 8.353 59.712 4645 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.71 % Allowed : 12.92 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.19), residues: 1870 helix: 0.87 (0.28), residues: 387 sheet: -0.68 (0.22), residues: 540 loop : -1.02 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 16 TYR 0.032 0.002 TYR H 100N PHE 0.014 0.001 PHE E 382 TRP 0.014 0.001 TRP F 596 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00405 (17175) covalent geometry : angle 0.61786 (23324) SS BOND : bond 0.00395 ( 35) SS BOND : angle 0.85495 ( 70) hydrogen bonds : bond 0.03719 ( 515) hydrogen bonds : angle 5.24708 ( 1437) link_ALPHA1-3 : bond 0.00831 ( 3) link_ALPHA1-3 : angle 3.02751 ( 9) link_ALPHA1-6 : bond 0.00873 ( 5) link_ALPHA1-6 : angle 1.54763 ( 15) link_BETA1-4 : bond 0.00935 ( 58) link_BETA1-4 : angle 2.79856 ( 174) link_NAG-ASN : bond 0.00308 ( 60) link_NAG-ASN : angle 2.03127 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8760 (tpt) cc_final: 0.7830 (tpt) REVERT: A 377 ASN cc_start: 0.8443 (t0) cc_final: 0.8123 (t0) REVERT: A 426 MET cc_start: 0.8253 (pmm) cc_final: 0.7505 (ptp) REVERT: A 475 MET cc_start: 0.8310 (tpp) cc_final: 0.7974 (tpp) REVERT: B 543 ASN cc_start: 0.7874 (m110) cc_final: 0.7237 (m-40) REVERT: B 581 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8251 (tt) REVERT: B 584 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8320 (mt-10) REVERT: B 626 MET cc_start: 0.8825 (pmm) cc_final: 0.8156 (pmm) REVERT: C 42 VAL cc_start: 0.8381 (t) cc_final: 0.8026 (p) REVERT: C 95 MET cc_start: 0.8417 (pmm) cc_final: 0.8071 (ptt) REVERT: C 426 MET cc_start: 0.8215 (pmm) cc_final: 0.7975 (pmm) REVERT: C 475 MET cc_start: 0.8575 (tpp) cc_final: 0.8314 (tpp) REVERT: E 499 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7384 (m) REVERT: F 530 MET cc_start: 0.7959 (mmt) cc_final: 0.6771 (mmt) REVERT: F 626 MET cc_start: 0.7705 (tpp) cc_final: 0.7363 (tpp) REVERT: F 652 GLN cc_start: 0.9095 (tp40) cc_final: 0.8447 (tm-30) REVERT: G 584 GLU cc_start: 0.8720 (tt0) cc_final: 0.8228 (tm-30) REVERT: G 616 ASN cc_start: 0.9252 (p0) cc_final: 0.8636 (m-40) REVERT: G 632 ASP cc_start: 0.8639 (t70) cc_final: 0.8410 (t70) REVERT: H 100 TYR cc_start: 0.8872 (p90) cc_final: 0.8388 (p90) REVERT: L 81 GLU cc_start: 0.9416 (tp30) cc_final: 0.9092 (mp0) REVERT: L 82 ASP cc_start: 0.8384 (m-30) cc_final: 0.7479 (m-30) outliers start: 29 outliers final: 19 residues processed: 116 average time/residue: 0.1160 time to fit residues: 20.8056 Evaluate side-chains 109 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 56 optimal weight: 0.0670 chunk 48 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.065489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.050040 restraints weight = 64597.764| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.32 r_work: 0.2860 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17336 Z= 0.153 Angle : 0.659 16.721 23772 Z= 0.298 Chirality : 0.045 0.343 2988 Planarity : 0.004 0.049 2788 Dihedral : 8.224 59.892 4645 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.59 % Allowed : 12.98 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.19), residues: 1870 helix: 1.00 (0.28), residues: 387 sheet: -0.63 (0.22), residues: 537 loop : -0.96 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 350 TYR 0.032 0.001 TYR H 100N PHE 0.015 0.001 PHE E 382 TRP 0.009 0.001 TRP A 479 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00340 (17175) covalent geometry : angle 0.59592 (23324) SS BOND : bond 0.00359 ( 35) SS BOND : angle 0.84081 ( 70) hydrogen bonds : bond 0.03475 ( 515) hydrogen bonds : angle 5.12632 ( 1437) link_ALPHA1-3 : bond 0.00897 ( 3) link_ALPHA1-3 : angle 2.95120 ( 9) link_ALPHA1-6 : bond 0.00963 ( 5) link_ALPHA1-6 : angle 1.42161 ( 15) link_BETA1-4 : bond 0.00935 ( 58) link_BETA1-4 : angle 2.67250 ( 174) link_NAG-ASN : bond 0.00265 ( 60) link_NAG-ASN : angle 1.89567 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8761 (tpt) cc_final: 0.7854 (tpt) REVERT: A 377 ASN cc_start: 0.8262 (t0) cc_final: 0.8017 (t0) REVERT: A 426 MET cc_start: 0.8285 (pmm) cc_final: 0.7444 (ptp) REVERT: A 475 MET cc_start: 0.8320 (tpp) cc_final: 0.7904 (tpp) REVERT: B 543 ASN cc_start: 0.8117 (m110) cc_final: 0.7444 (m-40) REVERT: B 581 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8423 (tt) REVERT: B 584 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8450 (mt-10) REVERT: B 626 MET cc_start: 0.8886 (pmm) cc_final: 0.8278 (pmm) REVERT: C 95 MET cc_start: 0.8496 (pmm) cc_final: 0.8166 (ptt) REVERT: C 475 MET cc_start: 0.8631 (tpp) cc_final: 0.8389 (tpp) REVERT: F 530 MET cc_start: 0.7916 (mmt) cc_final: 0.6774 (mmt) REVERT: F 626 MET cc_start: 0.7833 (tpp) cc_final: 0.7548 (tpp) REVERT: F 652 GLN cc_start: 0.9139 (tp40) cc_final: 0.8651 (tm-30) REVERT: G 584 GLU cc_start: 0.8804 (tt0) cc_final: 0.8330 (tm-30) REVERT: G 616 ASN cc_start: 0.9201 (p0) cc_final: 0.8590 (m-40) REVERT: G 632 ASP cc_start: 0.8661 (t70) cc_final: 0.8449 (t70) REVERT: H 100 TYR cc_start: 0.8894 (p90) cc_final: 0.8453 (p90) REVERT: L 17 LYS cc_start: 0.8675 (pttm) cc_final: 0.8332 (pttm) REVERT: L 81 GLU cc_start: 0.9427 (tp30) cc_final: 0.9125 (mp0) REVERT: L 82 ASP cc_start: 0.8430 (m-30) cc_final: 0.7581 (m-30) outliers start: 27 outliers final: 18 residues processed: 123 average time/residue: 0.1162 time to fit residues: 22.5032 Evaluate side-chains 111 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 31 optimal weight: 0.5980 chunk 102 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186AASN E 195 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.066136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.050942 restraints weight = 63889.891| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 4.29 r_work: 0.2882 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17336 Z= 0.116 Angle : 0.639 16.703 23772 Z= 0.289 Chirality : 0.045 0.339 2988 Planarity : 0.003 0.046 2788 Dihedral : 8.118 59.898 4645 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.30 % Allowed : 13.33 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.19), residues: 1870 helix: 1.02 (0.28), residues: 388 sheet: -0.62 (0.21), residues: 558 loop : -0.91 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 16 TYR 0.031 0.001 TYR H 100N PHE 0.009 0.001 PHE E 382 TRP 0.017 0.001 TRP F 596 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00248 (17175) covalent geometry : angle 0.57803 (23324) SS BOND : bond 0.00289 ( 35) SS BOND : angle 0.79893 ( 70) hydrogen bonds : bond 0.03301 ( 515) hydrogen bonds : angle 5.03609 ( 1437) link_ALPHA1-3 : bond 0.00924 ( 3) link_ALPHA1-3 : angle 2.84026 ( 9) link_ALPHA1-6 : bond 0.00997 ( 5) link_ALPHA1-6 : angle 1.39962 ( 15) link_BETA1-4 : bond 0.00944 ( 58) link_BETA1-4 : angle 2.61963 ( 174) link_NAG-ASN : bond 0.00244 ( 60) link_NAG-ASN : angle 1.78179 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8724 (tpt) cc_final: 0.7817 (tpt) REVERT: A 377 ASN cc_start: 0.8189 (t0) cc_final: 0.7939 (t0) REVERT: B 539 VAL cc_start: 0.9073 (p) cc_final: 0.8610 (p) REVERT: B 543 ASN cc_start: 0.8021 (m110) cc_final: 0.7345 (m-40) REVERT: B 581 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8370 (tt) REVERT: B 584 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8415 (mt-10) REVERT: B 626 MET cc_start: 0.8828 (pmm) cc_final: 0.8265 (pmm) REVERT: C 95 MET cc_start: 0.8483 (pmm) cc_final: 0.8136 (ptt) REVERT: C 475 MET cc_start: 0.8586 (tpp) cc_final: 0.8355 (tpp) REVERT: F 652 GLN cc_start: 0.9006 (tp40) cc_final: 0.8680 (tm-30) REVERT: G 584 GLU cc_start: 0.8775 (tt0) cc_final: 0.8356 (tm-30) REVERT: G 616 ASN cc_start: 0.9215 (p0) cc_final: 0.8578 (m-40) REVERT: G 632 ASP cc_start: 0.8647 (t70) cc_final: 0.8439 (t70) REVERT: H 100 TYR cc_start: 0.8825 (p90) cc_final: 0.8394 (p90) REVERT: L 81 GLU cc_start: 0.9428 (tp30) cc_final: 0.9123 (mp0) REVERT: L 82 ASP cc_start: 0.8504 (m-30) cc_final: 0.7645 (m-30) outliers start: 22 outliers final: 18 residues processed: 121 average time/residue: 0.1151 time to fit residues: 21.8370 Evaluate side-chains 113 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 129 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 55 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS C 355 ASN E 195 ASN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.065954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.050711 restraints weight = 64562.294| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.30 r_work: 0.2877 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17336 Z= 0.130 Angle : 0.646 16.760 23772 Z= 0.293 Chirality : 0.045 0.341 2988 Planarity : 0.003 0.045 2788 Dihedral : 8.086 59.642 4645 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.18 % Allowed : 13.39 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.19), residues: 1870 helix: 1.06 (0.28), residues: 388 sheet: -0.62 (0.21), residues: 555 loop : -0.88 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 16 TYR 0.032 0.001 TYR H 34 PHE 0.011 0.001 PHE E 382 TRP 0.024 0.001 TRP F 596 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00287 (17175) covalent geometry : angle 0.58651 (23324) SS BOND : bond 0.00320 ( 35) SS BOND : angle 0.78811 ( 70) hydrogen bonds : bond 0.03307 ( 515) hydrogen bonds : angle 5.00540 ( 1437) link_ALPHA1-3 : bond 0.00894 ( 3) link_ALPHA1-3 : angle 2.78077 ( 9) link_ALPHA1-6 : bond 0.00962 ( 5) link_ALPHA1-6 : angle 1.36127 ( 15) link_BETA1-4 : bond 0.00939 ( 58) link_BETA1-4 : angle 2.60030 ( 174) link_NAG-ASN : bond 0.00250 ( 60) link_NAG-ASN : angle 1.77877 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8721 (tpt) cc_final: 0.7808 (tpt) REVERT: A 377 ASN cc_start: 0.8167 (t0) cc_final: 0.7922 (t0) REVERT: B 539 VAL cc_start: 0.9099 (p) cc_final: 0.8633 (p) REVERT: B 543 ASN cc_start: 0.8046 (m110) cc_final: 0.7370 (m-40) REVERT: B 581 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8418 (tt) REVERT: B 584 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8474 (mt-10) REVERT: B 626 MET cc_start: 0.8833 (pmm) cc_final: 0.8275 (pmm) REVERT: C 95 MET cc_start: 0.8505 (pmm) cc_final: 0.8190 (ptt) REVERT: C 475 MET cc_start: 0.8595 (tpp) cc_final: 0.8365 (tpp) REVERT: E 502 LYS cc_start: 0.7696 (tmtt) cc_final: 0.7415 (tptt) REVERT: F 652 GLN cc_start: 0.9001 (tp40) cc_final: 0.8591 (tm-30) REVERT: F 653 GLN cc_start: 0.8733 (mm110) cc_final: 0.8392 (mm-40) REVERT: G 584 GLU cc_start: 0.8776 (tt0) cc_final: 0.8356 (tm-30) REVERT: G 616 ASN cc_start: 0.9198 (p0) cc_final: 0.8560 (m-40) REVERT: G 632 ASP cc_start: 0.8649 (t70) cc_final: 0.8444 (t70) REVERT: H 100 TYR cc_start: 0.8845 (p90) cc_final: 0.8419 (p90) REVERT: L 17 LYS cc_start: 0.8522 (pttm) cc_final: 0.8098 (pttm) REVERT: L 81 GLU cc_start: 0.9440 (tp30) cc_final: 0.9132 (mp0) REVERT: L 82 ASP cc_start: 0.8521 (m-30) cc_final: 0.7685 (m-30) outliers start: 20 outliers final: 18 residues processed: 122 average time/residue: 0.1096 time to fit residues: 20.8514 Evaluate side-chains 113 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 179 optimal weight: 30.0000 chunk 79 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 178 optimal weight: 0.4980 chunk 109 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186AASN E 195 ASN F 543 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.065713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.050543 restraints weight = 64185.860| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.26 r_work: 0.2873 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17336 Z= 0.136 Angle : 0.645 16.724 23772 Z= 0.293 Chirality : 0.045 0.340 2988 Planarity : 0.003 0.043 2788 Dihedral : 8.057 59.770 4645 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.24 % Allowed : 13.39 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.19), residues: 1870 helix: 1.04 (0.28), residues: 388 sheet: -0.57 (0.22), residues: 547 loop : -0.88 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 16 TYR 0.031 0.001 TYR H 100N PHE 0.011 0.001 PHE E 382 TRP 0.023 0.001 TRP F 596 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00301 (17175) covalent geometry : angle 0.58696 (23324) SS BOND : bond 0.00330 ( 35) SS BOND : angle 0.80162 ( 70) hydrogen bonds : bond 0.03279 ( 515) hydrogen bonds : angle 4.96820 ( 1437) link_ALPHA1-3 : bond 0.00878 ( 3) link_ALPHA1-3 : angle 2.73281 ( 9) link_ALPHA1-6 : bond 0.00948 ( 5) link_ALPHA1-6 : angle 1.32721 ( 15) link_BETA1-4 : bond 0.00925 ( 58) link_BETA1-4 : angle 2.57233 ( 174) link_NAG-ASN : bond 0.00257 ( 60) link_NAG-ASN : angle 1.76119 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8713 (tpt) cc_final: 0.7807 (tpt) REVERT: A 377 ASN cc_start: 0.8188 (t0) cc_final: 0.7947 (t0) REVERT: B 543 ASN cc_start: 0.8014 (m110) cc_final: 0.7374 (m-40) REVERT: B 581 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8427 (tt) REVERT: B 584 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8478 (mt-10) REVERT: B 626 MET cc_start: 0.8830 (pmm) cc_final: 0.8284 (pmm) REVERT: C 95 MET cc_start: 0.8512 (pmm) cc_final: 0.8239 (ptt) REVERT: C 475 MET cc_start: 0.8588 (tpp) cc_final: 0.8350 (tpp) REVERT: F 626 MET cc_start: 0.7096 (tpp) cc_final: 0.6833 (tpp) REVERT: F 647 GLU cc_start: 0.8552 (tt0) cc_final: 0.7882 (tp30) REVERT: F 652 GLN cc_start: 0.8961 (tp40) cc_final: 0.8583 (tm-30) REVERT: F 653 GLN cc_start: 0.8744 (mm110) cc_final: 0.8388 (mm-40) REVERT: G 584 GLU cc_start: 0.8810 (tt0) cc_final: 0.8364 (tm-30) REVERT: G 616 ASN cc_start: 0.9198 (p0) cc_final: 0.8541 (m-40) REVERT: G 632 ASP cc_start: 0.8657 (t70) cc_final: 0.8450 (t70) REVERT: H 100 TYR cc_start: 0.8853 (p90) cc_final: 0.8406 (p90) REVERT: L 17 LYS cc_start: 0.8514 (pttm) cc_final: 0.8101 (pttm) REVERT: L 81 GLU cc_start: 0.9438 (tp30) cc_final: 0.9135 (mp0) REVERT: L 82 ASP cc_start: 0.8531 (m-30) cc_final: 0.7713 (m-30) outliers start: 21 outliers final: 20 residues processed: 118 average time/residue: 0.1120 time to fit residues: 20.9317 Evaluate side-chains 117 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 127 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 173 optimal weight: 7.9990 chunk 179 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186AASN E 195 ASN F 607 ASN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.065963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050953 restraints weight = 63938.580| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 4.24 r_work: 0.2886 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17336 Z= 0.122 Angle : 0.638 16.689 23772 Z= 0.291 Chirality : 0.044 0.338 2988 Planarity : 0.003 0.043 2788 Dihedral : 8.009 59.793 4645 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.18 % Allowed : 14.04 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.19), residues: 1870 helix: 1.03 (0.28), residues: 388 sheet: -0.56 (0.22), residues: 555 loop : -0.87 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 16 TYR 0.031 0.001 TYR H 100N PHE 0.010 0.001 PHE E 382 TRP 0.023 0.001 TRP F 596 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00266 (17175) covalent geometry : angle 0.58159 (23324) SS BOND : bond 0.00308 ( 35) SS BOND : angle 0.75693 ( 70) hydrogen bonds : bond 0.03260 ( 515) hydrogen bonds : angle 4.94967 ( 1437) link_ALPHA1-3 : bond 0.00879 ( 3) link_ALPHA1-3 : angle 2.68852 ( 9) link_ALPHA1-6 : bond 0.00938 ( 5) link_ALPHA1-6 : angle 1.30388 ( 15) link_BETA1-4 : bond 0.00932 ( 58) link_BETA1-4 : angle 2.54547 ( 174) link_NAG-ASN : bond 0.00237 ( 60) link_NAG-ASN : angle 1.71754 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8722 (tpt) cc_final: 0.7774 (tpt) REVERT: A 377 ASN cc_start: 0.8144 (t0) cc_final: 0.7917 (t0) REVERT: B 543 ASN cc_start: 0.7995 (m110) cc_final: 0.7310 (m-40) REVERT: B 581 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8425 (tt) REVERT: B 584 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8481 (mt-10) REVERT: B 626 MET cc_start: 0.8832 (pmm) cc_final: 0.8285 (pmm) REVERT: C 95 MET cc_start: 0.8511 (pmm) cc_final: 0.8206 (ptt) REVERT: C 475 MET cc_start: 0.8604 (tpp) cc_final: 0.8383 (tpp) REVERT: E 502 LYS cc_start: 0.7722 (tmtt) cc_final: 0.7491 (tptt) REVERT: F 626 MET cc_start: 0.7230 (tpp) cc_final: 0.6934 (tpp) REVERT: F 647 GLU cc_start: 0.8482 (tt0) cc_final: 0.7935 (tp30) REVERT: F 652 GLN cc_start: 0.8930 (tp40) cc_final: 0.8603 (tm-30) REVERT: F 653 GLN cc_start: 0.8737 (mm110) cc_final: 0.8360 (mm-40) REVERT: G 616 ASN cc_start: 0.9194 (p0) cc_final: 0.8538 (m-40) REVERT: G 632 ASP cc_start: 0.8650 (t70) cc_final: 0.8444 (t70) REVERT: H 100 TYR cc_start: 0.8848 (p90) cc_final: 0.8415 (p90) REVERT: L 17 LYS cc_start: 0.8495 (pttm) cc_final: 0.8121 (pttm) REVERT: L 81 GLU cc_start: 0.9430 (tp30) cc_final: 0.9129 (mp0) REVERT: L 82 ASP cc_start: 0.8579 (m-30) cc_final: 0.7750 (m-30) outliers start: 20 outliers final: 19 residues processed: 117 average time/residue: 0.1403 time to fit residues: 25.5695 Evaluate side-chains 116 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 43 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186AASN E 195 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.065994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.050618 restraints weight = 64557.730| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 4.35 r_work: 0.2875 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17336 Z= 0.130 Angle : 0.637 16.649 23772 Z= 0.291 Chirality : 0.044 0.341 2988 Planarity : 0.003 0.043 2788 Dihedral : 7.994 59.903 4645 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.24 % Allowed : 14.16 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.19), residues: 1870 helix: 1.03 (0.28), residues: 387 sheet: -0.53 (0.22), residues: 547 loop : -0.86 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 43 TYR 0.031 0.001 TYR H 100N PHE 0.010 0.001 PHE E 382 TRP 0.020 0.001 TRP F 596 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00287 (17175) covalent geometry : angle 0.58141 (23324) SS BOND : bond 0.00315 ( 35) SS BOND : angle 0.76976 ( 70) hydrogen bonds : bond 0.03261 ( 515) hydrogen bonds : angle 4.93092 ( 1437) link_ALPHA1-3 : bond 0.00880 ( 3) link_ALPHA1-3 : angle 2.66434 ( 9) link_ALPHA1-6 : bond 0.00926 ( 5) link_ALPHA1-6 : angle 1.29951 ( 15) link_BETA1-4 : bond 0.00928 ( 58) link_BETA1-4 : angle 2.53267 ( 174) link_NAG-ASN : bond 0.00243 ( 60) link_NAG-ASN : angle 1.71137 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2892.57 seconds wall clock time: 50 minutes 54.63 seconds (3054.63 seconds total)