Starting phenix.real_space_refine on Wed Apr 8 20:10:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lua_23519/04_2026/7lua_23519_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lua_23519/04_2026/7lua_23519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lua_23519/04_2026/7lua_23519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lua_23519/04_2026/7lua_23519.map" model { file = "/net/cci-nas-00/data/ceres_data/7lua_23519/04_2026/7lua_23519_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lua_23519/04_2026/7lua_23519_trim.cif" } resolution = 4.7 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= 0.027 sd= 0.115 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: 5 Type Number sf(0) Gaussians S 129 5.16 5 C 13955 2.51 5 N 3627 2.21 5 O 4679 1.98 5 H 20105 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42495 Number of models: 1 Model: "" Number of chains: 56 Chain: "a" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7192 Classifications: {'peptide': 466} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 442} Chain: "b" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1985 Classifications: {'peptide': 126} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "c" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7192 Classifications: {'peptide': 466} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 442} Chain: "d" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1985 Classifications: {'peptide': 126} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "e" Number of atoms: 7195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7195 Classifications: {'peptide': 466} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 442} Chain: "f" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1985 Classifications: {'peptide': 126} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "g" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3275 Classifications: {'peptide': 218} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain: "h" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3295 Classifications: {'peptide': 219} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 203} Chain: "i" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3296 Classifications: {'peptide': 219} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 4, 'PTRANS': 11, 'TRANS': 203} Chain: "j" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3275 Classifications: {'peptide': 218} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "A" 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: "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: 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: "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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 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: "N" 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: "O" 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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 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: "p" 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: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 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: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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 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 Time building chain proxies: 7.95, per 1000 atoms: 0.19 Number of scatterers: 42495 At special positions: 0 Unit cell: (123.714, 123.714, 203.701, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 129 16.00 O 4679 8.00 N 3627 7.00 C 13955 6.00 H 20105 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS a 54 " - pdb=" SG CYS a 74 " distance=2.05 Simple disulfide: pdb=" SG CYS a 119 " - pdb=" SG CYS a 205 " distance=2.04 Simple disulfide: pdb=" SG CYS a 126 " - pdb=" SG CYS a 196 " distance=2.02 Simple disulfide: pdb=" SG CYS a 131 " - pdb=" SG CYS a 157 " distance=2.02 Simple disulfide: pdb=" SG CYS a 201 " - pdb=" SG CYS a 433 " distance=2.01 Simple disulfide: pdb=" SG CYS a 218 " - pdb=" SG CYS a 247 " distance=2.03 Simple disulfide: pdb=" SG CYS a 228 " - pdb=" SG CYS a 239 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS a 385 " - pdb=" SG CYS a 418 " distance=2.01 Simple disulfide: pdb=" SG CYS a 501 " - pdb=" SG CYS b 593 " distance=2.01 Simple disulfide: pdb=" SG CYS b 586 " - pdb=" SG CYS b 592 " distance=2.02 Simple disulfide: pdb=" SG CYS c 54 " - pdb=" SG CYS c 74 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 433 " distance=2.03 Simple disulfide: pdb=" SG CYS c 218 " - pdb=" SG CYS c 247 " distance=2.03 Simple disulfide: pdb=" SG CYS c 228 " - pdb=" SG CYS c 239 " distance=2.03 Simple disulfide: pdb=" SG CYS c 296 " - pdb=" SG CYS c 331 " distance=2.02 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 d 593 " distance=2.01 Simple disulfide: pdb=" SG CYS d 586 " - pdb=" SG CYS d 592 " distance=2.03 Simple disulfide: pdb=" SG CYS e 54 " - pdb=" SG CYS e 74 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 205 " distance=2.03 Simple disulfide: pdb=" SG CYS e 126 " - pdb=" SG CYS e 196 " distance=2.02 Simple disulfide: pdb=" SG CYS e 131 " - pdb=" SG CYS e 157 " distance=2.03 Simple disulfide: pdb=" SG CYS e 201 " - pdb=" SG CYS e 433 " distance=2.01 Simple disulfide: pdb=" SG CYS e 218 " - pdb=" SG CYS e 247 " distance=2.02 Simple disulfide: pdb=" SG CYS e 228 " - pdb=" SG CYS e 239 " distance=2.04 Simple disulfide: pdb=" SG CYS e 296 " - pdb=" SG CYS e 331 " distance=2.01 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=2.01 Simple disulfide: pdb=" SG CYS e 501 " - pdb=" SG CYS f 593 " distance=2.03 Simple disulfide: pdb=" SG CYS f 586 " - pdb=" SG CYS f 592 " distance=2.02 Simple disulfide: pdb=" SG CYS g 23 " - pdb=" SG CYS g 88 " distance=2.03 Simple disulfide: pdb=" SG CYS g 134 " - pdb=" SG CYS g 194 " distance=2.01 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.01 Simple disulfide: pdb=" SG CYS h 140 " - pdb=" SG CYS h 196 " distance=2.02 Simple disulfide: pdb=" SG CYS i 22 " - pdb=" SG CYS i 92 " distance=2.02 Simple disulfide: pdb=" SG CYS i 140 " - pdb=" SG CYS i 196 " distance=2.04 Simple disulfide: pdb=" SG CYS j 23 " - pdb=" SG CYS j 88 " distance=2.01 Simple disulfide: pdb=" SG CYS j 134 " - pdb=" SG CYS j 194 " distance=2.04 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 M 3 " - " MAN M 6 " " BMA N 3 " - " MAN N 4 " " BMA S 3 " - " MAN S 4 " " BMA p 3 " - " MAN p 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA M 3 " - " MAN M 4 " " MAN M 4 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA S 3 " - " MAN S 5 " " BMA p 3 " - " MAN p 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " 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 w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " NAG-ASN " NAG B 1 " - " ASN e 234 " " NAG D 1 " - " ASN e 262 " " NAG E 1 " - " ASN e 156 " " NAG G 1 " - " ASN e 301 " " NAG H 1 " - " ASN e 332 " " NAG I 1 " - " ASN e 339 " " NAG J 1 " - " ASN e 136 " " NAG K 1 " - " ASN e 160 " " NAG L 1 " - " ASN e 197 " " NAG N 1 " - " ASN e 276 " " NAG O 1 " - " ASN a 362 " " NAG P 1 " - " ASN a 392 " " NAG Q 1 " - " ASN a 234 " " NAG R 1 " - " ASN a 241 " " NAG S 1 " - " ASN a 262 " " NAG T 1 " - " ASN a 156 " " NAG V 1 " - " ASN a 301 " " NAG W 1 " - " ASN a 332 " " NAG X 1 " - " ASN a 339 " " NAG Y 1 " - " ASN a 136 " " NAG Z 1 " - " ASN a 160 " " NAG a 601 " - " ASN a 88 " " NAG a 602 " - " ASN a 276 " " NAG a 603 " - " ASN a 448 " " NAG a 604 " - " ASN a 442 " " NAG b 701 " - " ASN b 599 " " NAG b 702 " - " ASN b 625 " " NAG c 601 " - " ASN c 88 " " NAG c 602 " - " ASN c 276 " " NAG c 603 " - " ASN c 448 " " NAG c 604 " - " ASN c 442 " " NAG d 701 " - " ASN d 599 " " NAG d 702 " - " ASN d 625 " " NAG e 601 " - " ASN e 88 " " NAG e 602 " - " ASN e 448 " " NAG f 701 " - " ASN f 599 " " NAG f 702 " - " ASN f 625 " " NAG k 1 " - " ASN a 197 " " NAG l 1 " - " ASN c 362 " " NAG m 1 " - " ASN c 392 " " NAG n 1 " - " ASN c 234 " " NAG o 1 " - " ASN c 241 " " NAG p 1 " - " ASN c 262 " " NAG q 1 " - " ASN c 156 " " NAG s 1 " - " ASN c 301 " " NAG t 1 " - " ASN c 332 " " NAG u 1 " - " ASN c 339 " " NAG v 1 " - " ASN c 136 " " NAG w 1 " - " ASN c 160 " " NAG x 1 " - " ASN c 197 " NAG-SER " NAG F 1 " - " SER e 388 " " NAG U 1 " - " SER a 388 " " NAG r 1 " - " SER c 388 " Time building additional restraints: 4.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4926 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 46 sheets defined 21.2% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'a' and resid 58 through 63 Processing helix chain 'a' and resid 99 through 117 Processing helix chain 'a' and resid 123 through 126 Processing helix chain 'a' and resid 138 through 142 Processing helix chain 'a' and resid 335 through 353 Processing helix chain 'a' and resid 368 through 373 Processing helix chain 'a' and resid 377 through 381 Processing helix chain 'a' and resid 386 through 391 removed outlier: 4.026A pdb=" N LEU a 390 " --> pdb=" O ASN a 386 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 403 Processing helix chain 'a' and resid 474 through 484 removed outlier: 3.802A pdb=" N ASN a 478 " --> pdb=" O ASP a 474 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU a 482 " --> pdb=" O ASN a 478 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR a 484 " --> pdb=" O ARG a 480 " (cutoff:3.500A) Processing helix chain 'b' and resid 517 through 523 removed outlier: 4.155A pdb=" N MET b 523 " --> pdb=" O GLY b 519 " (cutoff:3.500A) Processing helix chain 'b' and resid 524 through 531 removed outlier: 3.770A pdb=" N GLN b 528 " --> pdb=" O THR b 524 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN b 531 " --> pdb=" O VAL b 527 " (cutoff:3.500A) Processing helix chain 'b' and resid 559 through 584 removed outlier: 3.801A pdb=" N LEU b 569 " --> pdb=" O GLN b 565 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU b 572 " --> pdb=" O VAL b 568 " (cutoff:3.500A) Processing helix chain 'b' and resid 606 through 612 removed outlier: 3.680A pdb=" N ILE b 610 " --> pdb=" O ASN b 606 " (cutoff:3.500A) Processing helix chain 'b' and resid 615 through 624 removed outlier: 4.092A pdb=" N LYS b 621 " --> pdb=" O LEU b 617 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU b 622 " --> pdb=" O GLN b 618 " (cutoff:3.500A) Processing helix chain 'b' and resid 625 through 627 No H-bonds generated for 'chain 'b' and resid 625 through 627' Processing helix chain 'b' and resid 628 through 636 Processing helix chain 'b' and resid 638 through 652 Processing helix chain 'c' and resid 96 through 98 No H-bonds generated for 'chain 'c' and resid 96 through 98' Processing helix chain 'c' and resid 99 through 117 Processing helix chain 'c' and resid 123 through 126 Processing helix chain 'c' and resid 335 through 353 Processing helix chain 'c' and resid 368 through 373 Processing helix chain 'c' and resid 386 through 391 Processing helix chain 'c' and resid 399 through 403 Processing helix chain 'c' and resid 474 through 484 removed outlier: 3.754A pdb=" N ASN c 478 " --> pdb=" O ASP c 474 " (cutoff:3.500A) Processing helix chain 'd' and resid 517 through 522 Processing helix chain 'd' and resid 524 through 531 removed outlier: 3.620A pdb=" N GLN d 528 " --> pdb=" O THR d 524 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN d 531 " --> pdb=" O VAL d 527 " (cutoff:3.500A) Processing helix chain 'd' and resid 558 through 584 removed outlier: 4.132A pdb=" N LYS d 562 " --> pdb=" O VAL d 558 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG d 567 " --> pdb=" O GLN d 563 " (cutoff:3.500A) Processing helix chain 'd' and resid 606 through 612 removed outlier: 3.681A pdb=" N ILE d 610 " --> pdb=" O ASN d 606 " (cutoff:3.500A) Processing helix chain 'd' and resid 615 through 624 removed outlier: 4.807A pdb=" N LYS d 621 " --> pdb=" O LEU d 617 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU d 622 " --> pdb=" O GLN d 618 " (cutoff:3.500A) Processing helix chain 'd' and resid 625 through 627 No H-bonds generated for 'chain 'd' and resid 625 through 627' Processing helix chain 'd' and resid 628 through 636 removed outlier: 3.855A pdb=" N LEU d 633 " --> pdb=" O ILE d 629 " (cutoff:3.500A) Processing helix chain 'd' and resid 638 through 652 Processing helix chain 'e' and resid 58 through 63 removed outlier: 3.503A pdb=" N TYR e 61 " --> pdb=" O ALA e 58 " (cutoff:3.500A) Processing helix chain 'e' and resid 99 through 117 removed outlier: 3.721A pdb=" N GLN e 114 " --> pdb=" O SER e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 122 through 126 Processing helix chain 'e' and resid 335 through 351 removed outlier: 3.849A pdb=" N LYS e 344 " --> pdb=" O ASP e 340 " (cutoff:3.500A) Processing helix chain 'e' and resid 368 through 372 Processing helix chain 'e' and resid 397 through 401 removed outlier: 3.671A pdb=" N SER e 401 " --> pdb=" O GLY e 398 " (cutoff:3.500A) Processing helix chain 'e' and resid 474 through 484 removed outlier: 3.649A pdb=" N GLU e 482 " --> pdb=" O ASN e 478 " (cutoff:3.500A) Processing helix chain 'f' and resid 517 through 523 removed outlier: 3.805A pdb=" N MET f 523 " --> pdb=" O GLY f 519 " (cutoff:3.500A) Processing helix chain 'f' and resid 524 through 532 removed outlier: 3.617A pdb=" N GLN f 528 " --> pdb=" O THR f 524 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN f 531 " --> pdb=" O VAL f 527 " (cutoff:3.500A) Processing helix chain 'f' and resid 558 through 584 removed outlier: 4.015A pdb=" N LYS f 562 " --> pdb=" O VAL f 558 " (cutoff:3.500A) Processing helix chain 'f' and resid 606 through 612 Processing helix chain 'f' and resid 615 through 624 removed outlier: 4.415A pdb=" N LYS f 621 " --> pdb=" O LEU f 617 " (cutoff:3.500A) Processing helix chain 'f' and resid 625 through 627 No H-bonds generated for 'chain 'f' and resid 625 through 627' Processing helix chain 'f' and resid 628 through 636 Processing helix chain 'f' and resid 638 through 651 Processing helix chain 'g' and resid 79 through 83 Processing helix chain 'g' and resid 121 through 127 removed outlier: 4.157A pdb=" N VAL g 125 " --> pdb=" O SER g 121 " (cutoff:3.500A) Processing helix chain 'g' and resid 183 through 189 Processing helix chain 'h' and resid 28 through 32 removed outlier: 3.537A pdb=" N TYR h 32 " --> pdb=" O PHE h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 60 through 65 removed outlier: 4.655A pdb=" N ASP h 65 " --> pdb=" O LYS h 61 " (cutoff:3.500A) Processing helix chain 'h' and resid 189 through 193 removed outlier: 3.686A pdb=" N GLN h 192 " --> pdb=" O LEU h 189 " (cutoff:3.500A) Processing helix chain 'h' and resid 201 through 204 Processing helix chain 'i' and resid 83 through 87 Processing helix chain 'i' and resid 98 through 100B Processing helix chain 'i' and resid 156 through 158 No H-bonds generated for 'chain 'i' and resid 156 through 158' Processing helix chain 'i' and resid 186 through 192 Processing helix chain 'j' and resid 79 through 83 removed outlier: 4.481A pdb=" N VAL j 83 " --> pdb=" O ALA j 80 " (cutoff:3.500A) Processing helix chain 'j' and resid 121 through 127 Processing helix chain 'j' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'a' and resid 494 through 499 removed outlier: 6.440A pdb=" N VAL a 36 " --> pdb=" O THR b 594 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 45 through 47 removed outlier: 3.864A pdb=" N ILE a 225 " --> pdb=" O VAL a 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'a' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'a' and resid 120 through 121 removed outlier: 6.117A pdb=" N THR a 202 " --> pdb=" O TYR a 435 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N ARG a 432 " --> pdb=" O MET a 426 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET a 426 " --> pdb=" O ARG a 432 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 169 through 177 Processing sheet with id=AA7, first strand: chain 'a' and resid 259 through 261 removed outlier: 6.305A pdb=" N LEU a 260 " --> pdb=" O THR a 450 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY a 451 " --> pdb=" O THR a 290 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR a 290 " --> pdb=" O GLY a 451 " (cutoff:3.500A) removed outlier: 12.028A pdb=" N LEU a 453 " --> pdb=" O LEU a 288 " (cutoff:3.500A) removed outlier: 11.979A pdb=" N LEU a 288 " --> pdb=" O LEU a 453 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N THR a 455 " --> pdb=" O VAL a 286 " (cutoff:3.500A) removed outlier: 10.257A pdb=" N VAL a 286 " --> pdb=" O THR a 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 284 through 297 current: chain 'a' and resid 358 through 361 Processing sheet with id=AA8, first strand: chain 'a' and resid 272 through 273 removed outlier: 10.257A pdb=" N VAL a 286 " --> pdb=" O THR a 455 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N THR a 455 " --> pdb=" O VAL a 286 " (cutoff:3.500A) removed outlier: 11.979A pdb=" N LEU a 288 " --> pdb=" O LEU a 453 " (cutoff:3.500A) removed outlier: 12.028A pdb=" N LEU a 453 " --> pdb=" O LEU a 288 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR a 290 " --> pdb=" O GLY a 451 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY a 451 " --> pdb=" O THR a 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 444 through 456 current: chain 'a' and resid 413 through 420 removed outlier: 3.848A pdb=" N PHE a 383 " --> pdb=" O PHE a 376 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE a 376 " --> pdb=" O PHE a 383 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 301 through 308 removed outlier: 6.225A pdb=" N ASN a 301 " --> pdb=" O ILE a 323 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE a 323 " --> pdb=" O ASN a 301 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N THR a 303 " --> pdb=" O GLY a 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 495 through 499 removed outlier: 5.046A pdb=" N VAL d 596 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL c 38 " --> pdb=" O THR d 594 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR d 594 " --> pdb=" O VAL c 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'c' and resid 75 through 76 removed outlier: 3.529A pdb=" N CYS c 218 " --> pdb=" O PHE c 53 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 91 through 94 removed outlier: 3.967A pdb=" N GLU c 91 " --> pdb=" O CYS c 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 120 through 121 removed outlier: 3.933A pdb=" N VAL c 120 " --> pdb=" O GLN c 203 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR c 202 " --> pdb=" O TYR c 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 169 through 177 removed outlier: 3.794A pdb=" N THR c 161 " --> pdb=" O LYS c 170 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 259 through 261 removed outlier: 6.505A pdb=" N LEU c 260 " --> pdb=" O THR c 450 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY c 451 " --> pdb=" O THR c 290 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N THR c 290 " --> pdb=" O GLY c 451 " (cutoff:3.500A) removed outlier: 11.637A pdb=" N LEU c 453 " --> pdb=" O LEU c 288 " (cutoff:3.500A) removed outlier: 11.474A pdb=" N LEU c 288 " --> pdb=" O LEU c 453 " (cutoff:3.500A) removed outlier: 11.034A pdb=" N THR c 455 " --> pdb=" O VAL c 286 " (cutoff:3.500A) removed outlier: 10.105A pdb=" N VAL c 286 " --> pdb=" O THR c 455 " (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 358 through 361 Processing sheet with id=AB8, first strand: chain 'c' and resid 272 through 273 removed outlier: 10.105A pdb=" N VAL c 286 " --> pdb=" O THR c 455 " (cutoff:3.500A) removed outlier: 11.034A pdb=" N THR c 455 " --> pdb=" O VAL c 286 " (cutoff:3.500A) removed outlier: 11.474A pdb=" N LEU c 288 " --> pdb=" O LEU c 453 " (cutoff:3.500A) removed outlier: 11.637A pdb=" N LEU c 453 " --> pdb=" O LEU c 288 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N THR c 290 " --> pdb=" O GLY c 451 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY c 451 " --> pdb=" O THR c 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 444 through 456 current: chain 'c' and resid 413 through 421 removed outlier: 3.814A pdb=" N LYS c 421 " --> pdb=" O PHE c 382 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE c 382 " --> pdb=" O LYS c 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'c' and resid 300 through 309 removed outlier: 6.416A pdb=" N ASN c 301 " --> pdb=" O ILE c 323 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE c 323 " --> pdb=" O ASN c 301 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N THR c 303 " --> pdb=" O GLY c 321 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'e' and resid 495 through 499 removed outlier: 5.140A pdb=" N VAL f 596 " --> pdb=" O VAL e 36 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N VAL e 38 " --> pdb=" O THR f 594 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N THR f 594 " --> pdb=" O VAL e 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'e' and resid 45 through 47 removed outlier: 3.641A pdb=" N ILE e 225 " --> pdb=" O VAL e 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'e' and resid 53 through 56 Processing sheet with id=AC4, first strand: chain 'e' and resid 91 through 92 removed outlier: 3.920A pdb=" N GLU e 91 " --> pdb=" O CYS e 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'e' and resid 169 through 177 removed outlier: 3.842A pdb=" N LYS e 170 " --> pdb=" O THR e 161 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR e 161 " --> pdb=" O LYS e 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 201 through 203 removed outlier: 6.365A pdb=" N THR e 202 " --> pdb=" O TYR e 435 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ARG e 432 " --> pdb=" O ASN e 425 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASN e 425 " --> pdb=" O ARG e 432 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N MET e 434 " --> pdb=" O ILE e 423 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE e 423 " --> pdb=" O MET e 434 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'e' and resid 259 through 261 removed outlier: 3.898A pdb=" N GLY e 451 " --> pdb=" O LEU e 260 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR e 444 " --> pdb=" O ILE e 294 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N ILE e 294 " --> pdb=" O THR e 444 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N ARG e 446 " --> pdb=" O VAL e 292 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N VAL e 292 " --> pdb=" O ARG e 446 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ASN e 448 " --> pdb=" O THR e 290 " (cutoff:3.500A) removed outlier: 10.739A pdb=" N THR e 290 " --> pdb=" O ASN e 448 " (cutoff:3.500A) removed outlier: 6.594A 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=AC8, first strand: chain 'e' and resid 271 through 273 removed outlier: 4.302A pdb=" N VAL e 271 " --> pdb=" O HIS e 287 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS e 287 " --> pdb=" O VAL e 271 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR e 450 " --> pdb=" O LEU e 288 " (cutoff:3.500A) removed outlier: 10.739A pdb=" N THR e 290 " --> pdb=" O ASN e 448 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ASN e 448 " --> pdb=" O THR e 290 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N VAL e 292 " --> pdb=" O ARG e 446 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N ARG e 446 " --> pdb=" O VAL e 292 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N ILE e 294 " --> pdb=" O THR e 444 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR e 444 " --> pdb=" O ILE e 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 443 through 456 current: chain 'e' and resid 413 through 419 removed outlier: 4.338A pdb=" N GLN e 417 " --> pdb=" O ASN e 386 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'e' and resid 301 through 305 removed outlier: 6.993A pdb=" N ASN e 301 " --> pdb=" O ILE e 323 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE e 323 " --> pdb=" O ASN e 301 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR e 303 " --> pdb=" O GLY e 321 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'g' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'g' and resid 10 through 13 removed outlier: 5.994A pdb=" N LEU g 33 " --> pdb=" O PHE g 49 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE g 49 " --> pdb=" O LEU g 33 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP g 35 " --> pdb=" O LEU g 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'g' and resid 114 through 118 removed outlier: 3.656A pdb=" N PHE g 116 " --> pdb=" O LEU g 135 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'g' and resid 144 through 150 Processing sheet with id=AD5, first strand: chain 'h' and resid 4 through 6 Processing sheet with id=AD6, first strand: chain 'h' and resid 10 through 12 removed outlier: 4.090A pdb=" N HIS h 35 " --> pdb=" O THR h 93 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG h 38 " --> pdb=" O TRP h 47 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP h 47 " --> pdb=" O ARG h 38 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LYS h 52 " --> pdb=" O VAL h 56 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL h 56 " --> pdb=" O LYS h 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'h' and resid 10 through 12 Processing sheet with id=AD8, first strand: chain 'h' and resid 122 through 124 removed outlier: 5.480A pdb=" N ALA h 137 " --> pdb=" O VAL h 184 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL h 184 " --> pdb=" O ALA h 137 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY h 139 " --> pdb=" O VAL h 182 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL h 182 " --> pdb=" O GLY h 139 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU h 141 " --> pdb=" O SER h 180 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER h 180 " --> pdb=" O LEU h 141 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYS h 143 " --> pdb=" O LEU h 178 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU h 178 " --> pdb=" O LYS h 143 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'h' and resid 122 through 124 removed outlier: 5.480A pdb=" N ALA h 137 " --> pdb=" O VAL h 184 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL h 184 " --> pdb=" O ALA h 137 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY h 139 " --> pdb=" O VAL h 182 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL h 182 " --> pdb=" O GLY h 139 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU h 141 " --> pdb=" O SER h 180 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER h 180 " --> pdb=" O LEU h 141 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYS h 143 " --> pdb=" O LEU h 178 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU h 178 " --> pdb=" O LYS h 143 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU h 175 " --> pdb=" O GLN h 171 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'h' and resid 151 through 153 Processing sheet with id=AE2, first strand: chain 'i' and resid 5 through 6 Processing sheet with id=AE3, first strand: chain 'i' and resid 10 through 12 removed outlier: 3.836A pdb=" N GLU i 10 " --> pdb=" O LEU i 108 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE i 34 " --> pdb=" O GLU i 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU i 50 " --> pdb=" O ILE i 34 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP i 36 " --> pdb=" O LEU i 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'i' and resid 120 through 122 removed outlier: 5.476A pdb=" N TYR i 176 " --> pdb=" O ASP i 144 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER i 179 " --> pdb=" O PRO i 167 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL i 181 " --> pdb=" O THR i 165 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR i 165 " --> pdb=" O VAL i 181 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'i' and resid 151 through 154 Processing sheet with id=AE6, first strand: chain 'j' and resid 5 through 7 removed outlier: 3.507A pdb=" N ASN j 70 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'j' and resid 10 through 13 removed outlier: 6.319A pdb=" N TRP j 35 " --> pdb=" O LEU j 47 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY j 50 " --> pdb=" O LYS j 53 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'j' and resid 114 through 117 removed outlier: 5.093A pdb=" N TYR j 173 " --> pdb=" O ASN j 138 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'j' and resid 145 through 146 Processing sheet with id=AF1, first strand: chain 'j' and resid 145 through 146 749 hydrogen bonds defined for protein. 1953 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: 11.19 Time building geometry restraints manager: 5.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.70 - 0.92: 36 0.92 - 1.15: 20069 1.15 - 1.37: 7178 1.37 - 1.60: 15489 1.60 - 1.82: 170 Bond restraints: 42942 Sorted by residual: bond pdb=" N LEU f 556 " pdb=" H LEU f 556 " ideal model delta sigma weight residual 0.860 0.696 0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" N GLN c 82 " pdb=" H GLN c 82 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" N ARG c 476 " pdb=" H ARG c 476 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" N ILE a 333 " pdb=" H ILE a 333 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" CD1 TYR e 486 " pdb=" HD1 TYR e 486 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.60e+01 ... (remaining 42937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 70108 3.60 - 7.20: 6135 7.20 - 10.81: 476 10.81 - 14.41: 1 14.41 - 18.01: 1 Bond angle restraints: 76721 Sorted by residual: angle pdb=" CA HIS a 374 " pdb=" CB HIS a 374 " pdb=" CG HIS a 374 " ideal model delta sigma weight residual 113.80 105.93 7.87 1.00e+00 1.00e+00 6.19e+01 angle pdb=" CB HIS c 374 " pdb=" CG HIS c 374 " pdb=" CD2 HIS c 374 " ideal model delta sigma weight residual 131.20 122.25 8.95 1.30e+00 5.92e-01 4.74e+01 angle pdb=" CA HIS c 374 " pdb=" CB HIS c 374 " pdb=" CG HIS c 374 " ideal model delta sigma weight residual 113.80 107.08 6.72 1.00e+00 1.00e+00 4.51e+01 angle pdb=" N ALA e 497 " pdb=" CA ALA e 497 " pdb=" C ALA e 497 " ideal model delta sigma weight residual 108.22 114.25 -6.03 9.00e-01 1.23e+00 4.49e+01 angle pdb=" CA ASP a 325 " pdb=" CB ASP a 325 " pdb=" CG ASP a 325 " ideal model delta sigma weight residual 112.60 119.20 -6.60 1.00e+00 1.00e+00 4.36e+01 ... (remaining 76716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 19995 21.63 - 43.25: 1384 43.25 - 64.88: 611 64.88 - 86.51: 278 86.51 - 108.14: 132 Dihedral angle restraints: 22400 sinusoidal: 13488 harmonic: 8912 Sorted by residual: 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 93.00 146.62 -53.62 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CA VAL e 65 " pdb=" C VAL e 65 " pdb=" N HIS e 66 " pdb=" CA HIS e 66 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ALA i 137 " pdb=" C ALA i 137 " pdb=" N LEU i 138 " pdb=" CA LEU i 138 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 22397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2176 0.090 - 0.181: 1363 0.181 - 0.271: 332 0.271 - 0.362: 55 0.362 - 0.452: 19 Chirality restraints: 3945 Sorted by residual: chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.45e+02 chirality pdb=" C1 BMA Z 3 " pdb=" O4 NAG Z 2 " pdb=" C2 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.19e+02 chirality pdb=" C1 BMA w 3 " pdb=" O4 NAG w 2 " pdb=" C2 BMA w 3 " pdb=" O5 BMA w 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.18e+02 ... (remaining 3942 not shown) Planarity restraints: 6333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP g 35 " -0.375 2.00e-02 2.50e+03 1.39e-01 7.76e+02 pdb=" CG TRP g 35 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP g 35 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 TRP g 35 " 0.062 2.00e-02 2.50e+03 pdb=" NE1 TRP g 35 " 0.146 2.00e-02 2.50e+03 pdb=" CE2 TRP g 35 " 0.040 2.00e-02 2.50e+03 pdb=" CE3 TRP g 35 " 0.105 2.00e-02 2.50e+03 pdb=" CZ2 TRP g 35 " -0.090 2.00e-02 2.50e+03 pdb=" CZ3 TRP g 35 " 0.067 2.00e-02 2.50e+03 pdb=" CH2 TRP g 35 " -0.074 2.00e-02 2.50e+03 pdb=" HD1 TRP g 35 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP g 35 " 0.161 2.00e-02 2.50e+03 pdb=" HE3 TRP g 35 " 0.148 2.00e-02 2.50e+03 pdb=" HZ2 TRP g 35 " -0.166 2.00e-02 2.50e+03 pdb=" HZ3 TRP g 35 " 0.101 2.00e-02 2.50e+03 pdb=" HH2 TRP g 35 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP i 47 " -0.220 2.00e-02 2.50e+03 1.32e-01 6.95e+02 pdb=" CG TRP i 47 " -0.105 2.00e-02 2.50e+03 pdb=" CD1 TRP i 47 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP i 47 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP i 47 " 0.076 2.00e-02 2.50e+03 pdb=" CE2 TRP i 47 " -0.039 2.00e-02 2.50e+03 pdb=" CE3 TRP i 47 " 0.078 2.00e-02 2.50e+03 pdb=" CZ2 TRP i 47 " -0.119 2.00e-02 2.50e+03 pdb=" CZ3 TRP i 47 " 0.070 2.00e-02 2.50e+03 pdb=" CH2 TRP i 47 " -0.035 2.00e-02 2.50e+03 pdb=" HD1 TRP i 47 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 TRP i 47 " 0.332 2.00e-02 2.50e+03 pdb=" HE3 TRP i 47 " 0.116 2.00e-02 2.50e+03 pdb=" HZ2 TRP i 47 " -0.212 2.00e-02 2.50e+03 pdb=" HZ3 TRP i 47 " 0.108 2.00e-02 2.50e+03 pdb=" HH2 TRP i 47 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP f 598 " -0.331 2.00e-02 2.50e+03 1.26e-01 6.32e+02 pdb=" CG TRP f 598 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP f 598 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 TRP f 598 " 0.113 2.00e-02 2.50e+03 pdb=" NE1 TRP f 598 " 0.123 2.00e-02 2.50e+03 pdb=" CE2 TRP f 598 " 0.071 2.00e-02 2.50e+03 pdb=" CE3 TRP f 598 " 0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP f 598 " -0.043 2.00e-02 2.50e+03 pdb=" CZ3 TRP f 598 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP f 598 " -0.057 2.00e-02 2.50e+03 pdb=" HD1 TRP f 598 " -0.118 2.00e-02 2.50e+03 pdb=" HE1 TRP f 598 " 0.128 2.00e-02 2.50e+03 pdb=" HE3 TRP f 598 " 0.122 2.00e-02 2.50e+03 pdb=" HZ2 TRP f 598 " -0.137 2.00e-02 2.50e+03 pdb=" HZ3 TRP f 598 " 0.021 2.00e-02 2.50e+03 pdb=" HH2 TRP f 598 " -0.148 2.00e-02 2.50e+03 ... (remaining 6330 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 3546 2.19 - 2.79: 75063 2.79 - 3.40: 120887 3.40 - 4.00: 160150 4.00 - 4.60: 231296 Nonbonded interactions: 590942 Sorted by model distance: nonbonded pdb=" OE1 GLU i 133 " pdb=" HG SER i 186 " model vdw 1.588 2.450 nonbonded pdb=" HG SER i 127 " pdb=" O GLU i 212 " model vdw 1.595 2.450 nonbonded pdb=" OE2 GLU g 161 " pdb=" HG SER g 177 " model vdw 1.599 2.450 nonbonded pdb=" OD2 ASP g 167 " pdb=" HG1 THR g 172 " model vdw 1.605 2.450 nonbonded pdb=" OD1 ASP i 72 " pdb=" HG SER i 74 " model vdw 1.607 2.450 ... (remaining 590937 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'J' selection = chain 'Q' selection = chain 'V' selection = chain 'Y' selection = chain 'n' selection = chain 's' selection = chain 'v' } ncs_group { reference = chain 'D' selection = chain 'N' selection = chain 'S' selection = chain 'p' } ncs_group { reference = (chain 'a' and (resid 31 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 250 through 603)) selection = (chain 'c' and (resid 31 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 250 through 603)) selection = (chain 'e' and (resid 31 through 240 or (resid 241 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 242 through 361 or (resid 362 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 363 \ through 391 or (resid 392 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 \ or name HD21)) or resid 393 through 441 or (resid 442 and (name N or name CA or \ name C or name O or name CB or name CG or name OD1 or name ND2 or name H or nam \ e HA or name HB2 or name HB3 or name HD21)) or resid 443 through 603)) } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' } ncs_group { reference = chain 'g' selection = chain 'j' } ncs_group { reference = chain 'h' selection = (chain 'i' and (resid 1 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 36 through 212)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.230 Extract box with map and model: 0.530 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 40.830 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 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 : 0.015 0.083 23016 Z= 0.869 Angle : 2.059 21.599 31570 Z= 1.250 Chirality : 0.115 0.452 3945 Planarity : 0.018 0.169 3770 Dihedral : 20.573 108.135 10442 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 1.11 % Allowed : 9.11 % Favored : 89.79 % Rotamer: Outliers : 2.85 % Allowed : 6.91 % Favored : 90.25 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 8.87 % 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 are not related in a simple way. whole: -2.53 (0.14), residues: 2624 helix: -1.85 (0.21), residues: 385 sheet: -1.22 (0.23), residues: 488 loop : -1.87 (0.13), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG g 54 TYR 0.195 0.029 TYR g 140 PHE 0.149 0.020 PHE h 122 TRP 0.241 0.037 TRP f 598 HIS 0.029 0.006 HIS h 200 Details of bonding type rmsd covalent geometry : bond 0.01523 (22837) covalent geometry : angle 1.96619 (31080) SS BOND : bond 0.01223 ( 44) SS BOND : angle 2.02997 ( 88) hydrogen bonds : bond 0.16129 ( 719) hydrogen bonds : angle 9.42435 ( 1953) link_ALPHA1-3 : bond 0.02461 ( 5) link_ALPHA1-3 : angle 4.76324 ( 15) link_ALPHA1-6 : bond 0.01848 ( 6) link_ALPHA1-6 : angle 3.65513 ( 18) link_BETA1-4 : bond 0.02958 ( 71) link_BETA1-4 : angle 6.69980 ( 213) link_NAG-ASN : bond 0.00882 ( 50) link_NAG-ASN : angle 4.45396 ( 150) link_NAG-SER : bond 0.03440 ( 3) link_NAG-SER : angle 5.28558 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 59 time to evaluate : 1.146 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 104 MET cc_start: 0.8749 (ttm) cc_final: 0.8069 (ttm) REVERT: a 479 TRP cc_start: 0.8713 (OUTLIER) cc_final: 0.7304 (m100) REVERT: b 518 MET cc_start: 0.8686 (mtm) cc_final: 0.8351 (mtm) REVERT: b 583 ILE cc_start: 0.9626 (mt) cc_final: 0.9417 (tt) REVERT: c 158 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8777 (p) REVERT: c 475 MET cc_start: 0.8117 (ptp) cc_final: 0.7887 (ptt) REVERT: d 518 MET cc_start: 0.8693 (mtm) cc_final: 0.8190 (mtm) REVERT: g 13 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7672 (p) REVERT: g 92 VAL cc_start: 0.4544 (OUTLIER) cc_final: 0.4283 (t) REVERT: h 74 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8725 (p) REVERT: h 75 THR cc_start: 0.7190 (OUTLIER) cc_final: 0.6657 (m) REVERT: i 150 VAL cc_start: 0.5110 (OUTLIER) cc_final: 0.4785 (p) REVERT: j 14 THR cc_start: 0.6877 (OUTLIER) cc_final: 0.6620 (m) outliers start: 66 outliers final: 34 residues processed: 123 average time/residue: 0.3816 time to fit residues: 71.9759 Evaluate side-chains 93 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 51 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 300 ASN c 328 GLN c 422 GLN d 528 GLN d 578 GLN ** f 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 6 GLN j 124 GLN j 138 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.033067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.026010 restraints weight = 958653.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.026958 restraints weight = 485695.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.027562 restraints weight = 305362.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.027958 restraints weight = 221391.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.028215 restraints weight = 177336.609| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 : 0.011 1.130 23016 Z= 0.447 Angle : 1.046 28.746 31570 Z= 0.508 Chirality : 0.051 0.379 3945 Planarity : 0.006 0.125 3770 Dihedral : 17.277 80.142 5670 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.12 % Favored : 91.65 % Rotamer: Outliers : 0.17 % Allowed : 2.11 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 are not related in a simple way. whole: -2.67 (0.15), residues: 2624 helix: -1.44 (0.22), residues: 407 sheet: -1.64 (0.20), residues: 627 loop : -1.97 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG i 129 TYR 0.047 0.003 TYR e 396 PHE 0.019 0.003 PHE j 49 TRP 0.028 0.003 TRP c 479 HIS 0.017 0.002 HIS a 374 Details of bonding type rmsd covalent geometry : bond 0.01061 (22837) covalent geometry : angle 0.96011 (31080) SS BOND : bond 0.00385 ( 44) SS BOND : angle 1.22945 ( 88) hydrogen bonds : bond 0.07300 ( 719) hydrogen bonds : angle 8.18690 ( 1953) link_ALPHA1-3 : bond 0.00411 ( 5) link_ALPHA1-3 : angle 2.73366 ( 15) link_ALPHA1-6 : bond 0.00595 ( 6) link_ALPHA1-6 : angle 1.76285 ( 18) link_BETA1-4 : bond 0.01264 ( 71) link_BETA1-4 : angle 4.29696 ( 213) link_NAG-ASN : bond 0.00637 ( 50) link_NAG-ASN : angle 3.33466 ( 150) link_NAG-SER : bond 0.01003 ( 3) link_NAG-SER : angle 1.49886 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 1.151 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 577 ASP cc_start: 0.9682 (m-30) cc_final: 0.9466 (m-30) REVERT: d 518 MET cc_start: 0.8816 (mtm) cc_final: 0.8473 (mtm) REVERT: h 80 MET cc_start: 0.9325 (ppp) cc_final: 0.8931 (ppp) outliers start: 4 outliers final: 4 residues processed: 62 average time/residue: 0.4178 time to fit residues: 39.3156 Evaluate side-chains 56 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 82 optimal weight: 0.0670 chunk 196 optimal weight: 20.0000 chunk 239 optimal weight: 0.2980 chunk 64 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 188 optimal weight: 40.0000 overall best weight: 4.2724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 639 ASN ** f 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.033130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.026105 restraints weight = 968572.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.027054 restraints weight = 489923.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.027667 restraints weight = 306907.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.028063 restraints weight = 221786.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.028289 restraints weight = 177899.775| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 23016 Z= 0.169 Angle : 0.855 20.095 31570 Z= 0.408 Chirality : 0.050 0.318 3945 Planarity : 0.005 0.073 3770 Dihedral : 12.584 64.089 5670 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.50 % Favored : 91.39 % Rotamer: Outliers : 0.17 % Allowed : 1.99 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -2.52 (0.15), residues: 2624 helix: -0.89 (0.24), residues: 414 sheet: -1.71 (0.19), residues: 659 loop : -1.91 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG h 94 TYR 0.046 0.002 TYR g 36 PHE 0.021 0.002 PHE j 62 TRP 0.020 0.002 TRP c 479 HIS 0.016 0.002 HIS g 34 Details of bonding type rmsd covalent geometry : bond 0.00356 (22837) covalent geometry : angle 0.79040 (31080) SS BOND : bond 0.00271 ( 44) SS BOND : angle 0.91178 ( 88) hydrogen bonds : bond 0.05563 ( 719) hydrogen bonds : angle 7.59904 ( 1953) link_ALPHA1-3 : bond 0.00818 ( 5) link_ALPHA1-3 : angle 2.18890 ( 15) link_ALPHA1-6 : bond 0.00567 ( 6) link_ALPHA1-6 : angle 1.66633 ( 18) link_BETA1-4 : bond 0.00987 ( 71) link_BETA1-4 : angle 3.45906 ( 213) link_NAG-ASN : bond 0.00367 ( 50) link_NAG-ASN : angle 2.43410 ( 150) link_NAG-SER : bond 0.00865 ( 3) link_NAG-SER : angle 1.55919 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 1.177 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: e 369 MET cc_start: 0.7907 (ptm) cc_final: 0.7578 (ptm) outliers start: 4 outliers final: 4 residues processed: 59 average time/residue: 0.3998 time to fit residues: 36.1025 Evaluate side-chains 56 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 228 optimal weight: 9.9990 chunk 208 optimal weight: 50.0000 chunk 159 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 245 optimal weight: 30.0000 chunk 86 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 230 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 82 GLN a 478 ASN b 639 ASN ** c 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 389 ASN ** f 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 30 ASN g 199 GLN j 27DHIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.032752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.025789 restraints weight = 976396.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.026707 restraints weight = 496733.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.027292 restraints weight = 312473.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.027676 restraints weight = 227294.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.027921 restraints weight = 183288.357| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 23016 Z= 0.242 Angle : 0.837 12.431 31570 Z= 0.403 Chirality : 0.047 0.351 3945 Planarity : 0.005 0.070 3770 Dihedral : 10.140 59.551 5670 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.68 % Favored : 90.21 % Rotamer: Outliers : 0.22 % Allowed : 1.81 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % Cis-general : 0.00 % Twisted Proline : 0.81 % 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 are not related in a simple way. whole: -2.75 (0.15), residues: 2624 helix: -0.97 (0.23), residues: 416 sheet: -1.91 (0.19), residues: 670 loop : -2.07 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG f 573 TYR 0.043 0.002 TYR c 217 PHE 0.014 0.002 PHE j 118 TRP 0.018 0.002 TRP e 35 HIS 0.018 0.002 HIS i 35 Details of bonding type rmsd covalent geometry : bond 0.00504 (22837) covalent geometry : angle 0.77295 (31080) SS BOND : bond 0.00384 ( 44) SS BOND : angle 1.33984 ( 88) hydrogen bonds : bond 0.05351 ( 719) hydrogen bonds : angle 7.55741 ( 1953) link_ALPHA1-3 : bond 0.00638 ( 5) link_ALPHA1-3 : angle 2.93402 ( 15) link_ALPHA1-6 : bond 0.00546 ( 6) link_ALPHA1-6 : angle 1.97726 ( 18) link_BETA1-4 : bond 0.00807 ( 71) link_BETA1-4 : angle 3.23113 ( 213) link_NAG-ASN : bond 0.00721 ( 50) link_NAG-ASN : angle 2.48270 ( 150) link_NAG-SER : bond 0.00905 ( 3) link_NAG-SER : angle 2.00186 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 1.153 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 426 MET cc_start: 0.9530 (tpt) cc_final: 0.9145 (tpt) REVERT: d 518 MET cc_start: 0.8429 (mtm) cc_final: 0.8221 (mtm) REVERT: e 369 MET cc_start: 0.7915 (ptm) cc_final: 0.7549 (ptm) REVERT: h 69 MET cc_start: 0.7938 (ttp) cc_final: 0.7401 (ttp) outliers start: 5 outliers final: 4 residues processed: 60 average time/residue: 0.3740 time to fit residues: 35.5025 Evaluate side-chains 54 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 188 optimal weight: 40.0000 chunk 116 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 236 optimal weight: 8.9990 chunk 93 optimal weight: 30.0000 chunk 107 optimal weight: 6.9990 chunk 245 optimal weight: 30.0000 chunk 237 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 225 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 164 HIS ** j 34 HIS ** 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 = 0.3319 r_free = 0.3319 target = 0.032772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.025744 restraints weight = 993344.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.026667 restraints weight = 501787.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.027257 restraints weight = 314927.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.027636 restraints weight = 228915.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.027886 restraints weight = 184983.889| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23016 Z= 0.197 Angle : 0.761 12.063 31570 Z= 0.369 Chirality : 0.046 0.349 3945 Planarity : 0.005 0.106 3770 Dihedral : 9.303 59.930 5670 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.91 % Favored : 89.98 % Rotamer: Outliers : 0.17 % Allowed : 1.60 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % Cis-general : 0.00 % Twisted Proline : 0.81 % 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 are not related in a simple way. whole: -2.71 (0.15), residues: 2624 helix: -0.85 (0.24), residues: 417 sheet: -1.90 (0.19), residues: 657 loop : -2.07 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG h 94 TYR 0.024 0.002 TYR a 384 PHE 0.018 0.002 PHE j 85 TRP 0.015 0.002 TRP e 35 HIS 0.010 0.002 HIS i 35 Details of bonding type rmsd covalent geometry : bond 0.00401 (22837) covalent geometry : angle 0.70498 (31080) SS BOND : bond 0.00331 ( 44) SS BOND : angle 1.12178 ( 88) hydrogen bonds : bond 0.04860 ( 719) hydrogen bonds : angle 7.40622 ( 1953) link_ALPHA1-3 : bond 0.00814 ( 5) link_ALPHA1-3 : angle 2.73797 ( 15) link_ALPHA1-6 : bond 0.00627 ( 6) link_ALPHA1-6 : angle 1.78112 ( 18) link_BETA1-4 : bond 0.00779 ( 71) link_BETA1-4 : angle 2.85638 ( 213) link_NAG-ASN : bond 0.00460 ( 50) link_NAG-ASN : angle 2.26176 ( 150) link_NAG-SER : bond 0.00461 ( 3) link_NAG-SER : angle 2.32079 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.880 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: c 426 MET cc_start: 0.9547 (tpt) cc_final: 0.9187 (tpt) REVERT: h 69 MET cc_start: 0.8029 (ttp) cc_final: 0.7673 (ttp) outliers start: 4 outliers final: 4 residues processed: 59 average time/residue: 0.3717 time to fit residues: 34.3229 Evaluate side-chains 54 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 234 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 229 optimal weight: 50.0000 chunk 179 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 363 GLN ** e 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.032698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.025636 restraints weight = 987729.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.026549 restraints weight = 502379.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.027132 restraints weight = 318313.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.027510 restraints weight = 232453.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.027754 restraints weight = 188253.574| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23016 Z= 0.211 Angle : 0.751 12.037 31570 Z= 0.365 Chirality : 0.045 0.348 3945 Planarity : 0.005 0.063 3770 Dihedral : 8.877 59.375 5670 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.59 % Favored : 89.29 % Rotamer: Outliers : 0.17 % Allowed : 1.47 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % 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 are not related in a simple way. whole: -2.74 (0.15), residues: 2624 helix: -0.69 (0.24), residues: 416 sheet: -1.92 (0.19), residues: 660 loop : -2.14 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 573 TYR 0.027 0.002 TYR a 384 PHE 0.014 0.002 PHE i 29 TRP 0.014 0.002 TRP e 35 HIS 0.010 0.002 HIS c 105 Details of bonding type rmsd covalent geometry : bond 0.00432 (22837) covalent geometry : angle 0.69863 (31080) SS BOND : bond 0.00309 ( 44) SS BOND : angle 0.95501 ( 88) hydrogen bonds : bond 0.04864 ( 719) hydrogen bonds : angle 7.33588 ( 1953) link_ALPHA1-3 : bond 0.00719 ( 5) link_ALPHA1-3 : angle 2.83977 ( 15) link_ALPHA1-6 : bond 0.00658 ( 6) link_ALPHA1-6 : angle 1.83140 ( 18) link_BETA1-4 : bond 0.00736 ( 71) link_BETA1-4 : angle 2.74789 ( 213) link_NAG-ASN : bond 0.00547 ( 50) link_NAG-ASN : angle 2.24845 ( 150) link_NAG-SER : bond 0.00370 ( 3) link_NAG-SER : angle 1.53660 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 1.162 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: symmetry clash 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: symmetry clash 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: c 426 MET cc_start: 0.9532 (tpt) cc_final: 0.9116 (tpt) outliers start: 4 outliers final: 4 residues processed: 57 average time/residue: 0.3509 time to fit residues: 31.9639 Evaluate side-chains 53 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 227 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 228 optimal weight: 40.0000 chunk 138 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.032828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.025756 restraints weight = 974805.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.026693 restraints weight = 493484.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.027284 restraints weight = 310193.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.027663 restraints weight = 226340.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.027878 restraints weight = 183494.097| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23016 Z= 0.160 Angle : 0.709 11.661 31570 Z= 0.343 Chirality : 0.045 0.335 3945 Planarity : 0.005 0.060 3770 Dihedral : 8.529 59.571 5670 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.98 % Favored : 89.90 % Rotamer: Outliers : 0.17 % Allowed : 0.65 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % 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 are not related in a simple way. whole: -2.63 (0.15), residues: 2624 helix: -0.47 (0.24), residues: 416 sheet: -1.86 (0.19), residues: 650 loop : -2.11 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 446 TYR 0.028 0.002 TYR d 626 PHE 0.012 0.002 PHE j 209 TRP 0.011 0.002 TRP c 427 HIS 0.010 0.002 HIS c 105 Details of bonding type rmsd covalent geometry : bond 0.00329 (22837) covalent geometry : angle 0.65847 (31080) SS BOND : bond 0.00279 ( 44) SS BOND : angle 1.00707 ( 88) hydrogen bonds : bond 0.04516 ( 719) hydrogen bonds : angle 7.12435 ( 1953) link_ALPHA1-3 : bond 0.00779 ( 5) link_ALPHA1-3 : angle 2.62615 ( 15) link_ALPHA1-6 : bond 0.00713 ( 6) link_ALPHA1-6 : angle 1.87702 ( 18) link_BETA1-4 : bond 0.00754 ( 71) link_BETA1-4 : angle 2.58957 ( 213) link_NAG-ASN : bond 0.00376 ( 50) link_NAG-ASN : angle 2.12823 ( 150) link_NAG-SER : bond 0.00592 ( 3) link_NAG-SER : angle 2.07720 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 1.130 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: symmetry clash 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: symmetry clash 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: c 426 MET cc_start: 0.9541 (tpt) cc_final: 0.9329 (tpp) REVERT: h 69 MET cc_start: 0.8021 (ttm) cc_final: 0.7231 (ttm) REVERT: h 80 MET cc_start: 0.8426 (ptt) cc_final: 0.7852 (ptt) outliers start: 4 outliers final: 4 residues processed: 58 average time/residue: 0.3576 time to fit residues: 33.1829 Evaluate side-chains 54 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 23 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.032605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.025500 restraints weight = 987085.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.026426 restraints weight = 495174.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.027018 restraints weight = 309559.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.027389 restraints weight = 225734.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.027634 restraints weight = 182646.686| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 23016 Z= 0.221 Angle : 0.745 11.766 31570 Z= 0.361 Chirality : 0.044 0.345 3945 Planarity : 0.005 0.063 3770 Dihedral : 8.449 59.421 5670 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.62 % Favored : 88.26 % Rotamer: Outliers : 0.17 % Allowed : 0.65 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % 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 are not related in a simple way. whole: -2.76 (0.15), residues: 2624 helix: -0.58 (0.23), residues: 426 sheet: -1.89 (0.19), residues: 648 loop : -2.23 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 573 TYR 0.026 0.002 TYR a 384 PHE 0.016 0.002 PHE h 68 TRP 0.046 0.002 TRP j 96 HIS 0.010 0.002 HIS a 374 Details of bonding type rmsd covalent geometry : bond 0.00453 (22837) covalent geometry : angle 0.69386 (31080) SS BOND : bond 0.00406 ( 44) SS BOND : angle 1.33200 ( 88) hydrogen bonds : bond 0.04596 ( 719) hydrogen bonds : angle 7.20201 ( 1953) link_ALPHA1-3 : bond 0.00619 ( 5) link_ALPHA1-3 : angle 2.76964 ( 15) link_ALPHA1-6 : bond 0.00683 ( 6) link_ALPHA1-6 : angle 1.87745 ( 18) link_BETA1-4 : bond 0.00715 ( 71) link_BETA1-4 : angle 2.63514 ( 213) link_NAG-ASN : bond 0.00586 ( 50) link_NAG-ASN : angle 2.19860 ( 150) link_NAG-SER : bond 0.00496 ( 3) link_NAG-SER : angle 2.16237 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 1.107 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 434 MET cc_start: 0.9176 (ttp) cc_final: 0.8907 (ttp) REVERT: c 426 MET cc_start: 0.9508 (tpt) cc_final: 0.9275 (tpp) REVERT: e 475 MET cc_start: 0.8176 (pmm) cc_final: 0.7916 (mpp) REVERT: h 51 MET cc_start: 0.8634 (ttp) cc_final: 0.8392 (ttp) REVERT: h 80 MET cc_start: 0.8487 (ptt) cc_final: 0.7867 (ptt) outliers start: 4 outliers final: 4 residues processed: 56 average time/residue: 0.3482 time to fit residues: 31.9051 Evaluate side-chains 53 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 102 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 196 optimal weight: 0.5980 chunk 153 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.032741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.025693 restraints weight = 987011.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.026614 restraints weight = 499727.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.027202 restraints weight = 314969.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.027580 restraints weight = 230058.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.027823 restraints weight = 186459.418| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23016 Z= 0.166 Angle : 0.700 11.427 31570 Z= 0.339 Chirality : 0.044 0.335 3945 Planarity : 0.004 0.064 3770 Dihedral : 8.218 58.586 5670 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.52 % Favored : 89.37 % Rotamer: Outliers : 0.17 % Allowed : 0.26 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % 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 are not related in a simple way. whole: -2.64 (0.15), residues: 2624 helix: -0.36 (0.24), residues: 425 sheet: -1.87 (0.19), residues: 650 loop : -2.16 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 446 TYR 0.043 0.002 TYR e 396 PHE 0.012 0.002 PHE j 209 TRP 0.026 0.002 TRP j 96 HIS 0.008 0.001 HIS a 374 Details of bonding type rmsd covalent geometry : bond 0.00342 (22837) covalent geometry : angle 0.65106 (31080) SS BOND : bond 0.00256 ( 44) SS BOND : angle 1.10576 ( 88) hydrogen bonds : bond 0.04382 ( 719) hydrogen bonds : angle 7.04752 ( 1953) link_ALPHA1-3 : bond 0.00673 ( 5) link_ALPHA1-3 : angle 2.56118 ( 15) link_ALPHA1-6 : bond 0.00693 ( 6) link_ALPHA1-6 : angle 1.80543 ( 18) link_BETA1-4 : bond 0.00709 ( 71) link_BETA1-4 : angle 2.54235 ( 213) link_NAG-ASN : bond 0.00397 ( 50) link_NAG-ASN : angle 2.06584 ( 150) link_NAG-SER : bond 0.00466 ( 3) link_NAG-SER : angle 1.78353 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 1.165 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 426 MET cc_start: 0.9514 (tpt) cc_final: 0.9282 (tpp) REVERT: d 518 MET cc_start: 0.8566 (mtm) cc_final: 0.8331 (mtm) REVERT: e 475 MET cc_start: 0.8123 (pmm) cc_final: 0.7852 (mpp) REVERT: h 80 MET cc_start: 0.8522 (ptt) cc_final: 0.7926 (ptt) outliers start: 4 outliers final: 4 residues processed: 56 average time/residue: 0.3409 time to fit residues: 31.2495 Evaluate side-chains 52 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 103 optimal weight: 0.8980 chunk 228 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 200 optimal weight: 0.6980 chunk 232 optimal weight: 30.0000 chunk 102 optimal weight: 9.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 422 GLN ** e 392 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 = 0.3329 r_free = 0.3329 target = 0.032889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.025819 restraints weight = 977618.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.026778 restraints weight = 489426.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.027382 restraints weight = 306217.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.027774 restraints weight = 222623.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.028032 restraints weight = 179406.496| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23016 Z= 0.120 Angle : 0.660 11.226 31570 Z= 0.319 Chirality : 0.044 0.299 3945 Planarity : 0.005 0.119 3770 Dihedral : 7.833 58.556 5670 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.83 % Favored : 90.05 % Rotamer: Outliers : 0.17 % Allowed : 0.04 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % 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 are not related in a simple way. whole: -2.32 (0.16), residues: 2624 helix: 0.23 (0.25), residues: 408 sheet: -1.73 (0.20), residues: 640 loop : -2.00 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 446 TYR 0.036 0.002 TYR e 396 PHE 0.015 0.001 PHE h 122 TRP 0.024 0.002 TRP e 479 HIS 0.007 0.001 HIS a 374 Details of bonding type rmsd covalent geometry : bond 0.00253 (22837) covalent geometry : angle 0.61407 (31080) SS BOND : bond 0.00215 ( 44) SS BOND : angle 0.91185 ( 88) hydrogen bonds : bond 0.04070 ( 719) hydrogen bonds : angle 6.77730 ( 1953) link_ALPHA1-3 : bond 0.00693 ( 5) link_ALPHA1-3 : angle 2.41117 ( 15) link_ALPHA1-6 : bond 0.00689 ( 6) link_ALPHA1-6 : angle 1.67894 ( 18) link_BETA1-4 : bond 0.00708 ( 71) link_BETA1-4 : angle 2.44167 ( 213) link_NAG-ASN : bond 0.00247 ( 50) link_NAG-ASN : angle 1.91869 ( 150) link_NAG-SER : bond 0.00445 ( 3) link_NAG-SER : angle 1.58292 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 1.190 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 426 MET cc_start: 0.9521 (tpt) cc_final: 0.9305 (tpp) REVERT: e 475 MET cc_start: 0.8002 (pmm) cc_final: 0.7714 (mpp) REVERT: h 51 MET cc_start: 0.8650 (ttp) cc_final: 0.8370 (ttp) REVERT: h 80 MET cc_start: 0.8597 (ptt) cc_final: 0.7925 (ptt) outliers start: 4 outliers final: 4 residues processed: 57 average time/residue: 0.3315 time to fit residues: 30.6753 Evaluate side-chains 53 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 14 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 82 optimal weight: 30.0000 chunk 150 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.032707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.025601 restraints weight = 966809.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.026561 restraints weight = 479637.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.027165 restraints weight = 298130.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.027555 restraints weight = 216552.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.027779 restraints weight = 174254.218| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23016 Z= 0.152 Angle : 0.661 11.307 31570 Z= 0.319 Chirality : 0.043 0.296 3945 Planarity : 0.004 0.067 3770 Dihedral : 7.705 57.979 5670 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.06 % Favored : 89.82 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % 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 are not related in a simple way. whole: -2.29 (0.16), residues: 2624 helix: 0.37 (0.25), residues: 408 sheet: -1.75 (0.20), residues: 653 loop : -2.00 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG j 38 TYR 0.036 0.002 TYR e 396 PHE 0.013 0.001 PHE j 118 TRP 0.026 0.002 TRP e 479 HIS 0.008 0.001 HIS a 374 Details of bonding type rmsd covalent geometry : bond 0.00314 (22837) covalent geometry : angle 0.61478 (31080) SS BOND : bond 0.00235 ( 44) SS BOND : angle 0.90715 ( 88) hydrogen bonds : bond 0.04025 ( 719) hydrogen bonds : angle 6.75321 ( 1953) link_ALPHA1-3 : bond 0.00584 ( 5) link_ALPHA1-3 : angle 2.46000 ( 15) link_ALPHA1-6 : bond 0.00624 ( 6) link_ALPHA1-6 : angle 1.69493 ( 18) link_BETA1-4 : bond 0.00708 ( 71) link_BETA1-4 : angle 2.44950 ( 213) link_NAG-ASN : bond 0.00360 ( 50) link_NAG-ASN : angle 1.93396 ( 150) link_NAG-SER : bond 0.00414 ( 3) link_NAG-SER : angle 1.50066 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5733.96 seconds wall clock time: 99 minutes 30.32 seconds (5970.32 seconds total)