Starting phenix.real_space_refine on Wed Nov 19 05:06:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5v8m_8644/11_2025/5v8m_8644.cif Found real_map, /net/cci-nas-00/data/ceres_data/5v8m_8644/11_2025/5v8m_8644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5v8m_8644/11_2025/5v8m_8644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5v8m_8644/11_2025/5v8m_8644.map" model { file = "/net/cci-nas-00/data/ceres_data/5v8m_8644/11_2025/5v8m_8644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5v8m_8644/11_2025/5v8m_8644.cif" } resolution = 4.4 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 12987 2.51 5 N 3423 2.21 5 O 4305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20835 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3493 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "B" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "F" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3493 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "I" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "R" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "T" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "G" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3493 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "J" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "S" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "U" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "N" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" 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: "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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "e" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "r" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 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: "w" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "x" 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: "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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 Residues with excluded nonbonded symmetry interactions: 60 residue: pdb=" C1 NAG K 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG K 1 " occ=0.00 residue: pdb=" C1 NAG K 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG K 2 " occ=0.00 residue: pdb=" C1 NAG M 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG M 1 " occ=0.00 residue: pdb=" C1 NAG M 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG M 2 " occ=0.00 residue: pdb=" C1 BMA M 3 " occ=0.00 ... (9 atoms not shown) pdb=" O6 BMA M 3 " occ=0.00 residue: pdb=" C1 MAN M 4 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN M 4 " occ=0.00 residue: pdb=" C1 MAN M 5 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN M 5 " occ=0.00 residue: pdb=" C1 MAN M 6 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN M 6 " occ=0.00 residue: pdb=" C1 MAN M 7 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN M 7 " occ=0.00 residue: pdb=" C1 MAN N 6 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN N 6 " occ=0.00 residue: pdb=" C1 MAN N 7 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN N 7 " occ=0.00 residue: pdb=" C1 MAN N 8 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN N 8 " occ=0.00 ... (remaining 48 not shown) Time building chain proxies: 5.32, per 1000 atoms: 0.26 Number of scatterers: 20835 At special positions: 0 Unit cell: (149.34, 144.1, 121.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4305 8.00 N 3423 7.00 C 12987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.19 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.11 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.19 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.11 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.04 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.04 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.07 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.19 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.11 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.04 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN N 4 " - " MAN N 5 " " MAN d 4 " - " MAN d 5 " " MAN e 4 " - " MAN e 5 " " MAN q 4 " - " MAN q 5 " " MAN r 4 " - " MAN r 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " MAN M 6 " - " MAN M 7 " " BMA N 3 " - " MAN N 4 " " MAN N 6 " - " MAN N 7 " " BMA V 3 " - " MAN V 6 " " MAN V 4 " - " MAN V 5 " " BMA d 3 " - " MAN d 4 " " MAN d 6 " - " MAN d 7 " " BMA e 3 " - " MAN e 4 " " MAN e 6 " - " MAN e 7 " " BMA i 3 " - " MAN i 6 " " MAN i 4 " - " MAN i 5 " " BMA q 3 " - " MAN q 4 " " MAN q 6 " - " MAN q 7 " " BMA r 3 " - " MAN r 4 " " MAN r 6 " - " MAN r 7 " " BMA v 3 " - " MAN v 6 " " MAN v 4 " - " MAN v 5 " ALPHA1-6 " BMA M 3 " - " MAN M 6 " " BMA N 3 " - " MAN N 6 " " MAN N 6 " - " MAN N 8 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA d 3 " - " MAN d 6 " " BMA e 3 " - " MAN e 6 " " MAN e 6 " - " MAN e 8 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " BMA q 3 " - " MAN q 6 " " BMA r 3 " - " MAN r 6 " " MAN r 6 " - " MAN r 8 " " BMA v 3 " - " MAN v 4 " " BMA w 3 " - " MAN w 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 604 " - " ASN A 133 " " NAG A 611 " - " ASN A 234 " " NAG A 633 " - " ASN A 339 " " NAG A 634 " - " ASN A 355 " " NAG A 645 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 1 " - " ASN A 88 " " NAG D 1 " - " ASN A 156 " " NAG E 1 " - " ASN A 160 " " NAG F 604 " - " ASN F 133 " " NAG F 611 " - " ASN F 234 " " NAG F 631 " - " ASN F 355 " " NAG F 634 " - " ASN F 339 " " NAG F 645 " - " ASN F 392 " " NAG G 604 " - " ASN G 133 " " NAG G 611 " - " ASN G 234 " " NAG G 633 " - " ASN G 339 " " NAG G 634 " - " ASN G 355 " " NAG G 645 " - " ASN G 392 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 637 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 637 " " NAG K 1 " - " ASN A 197 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 276 " " NAG O 1 " - " ASN A 295 " " NAG P 1 " - " ASN A 301 " " NAG Q 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 363 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN L 72 " " NAG Z 1 " - " ASN F 88 " " NAG a 1 " - " ASN F 156 " " NAG b 1 " - " ASN F 160 " " NAG c 1 " - " ASN F 197 " " NAG d 1 " - " ASN F 262 " " NAG e 1 " - " ASN F 276 " " NAG f 1 " - " ASN F 295 " " NAG g 1 " - " ASN F 301 " " NAG h 1 " - " ASN F 332 " " NAG i 1 " - " ASN F 363 " " NAG j 1 " - " ASN F 386 " " NAG k 1 " - " ASN F 448 " " NAG l 1 " - " ASN T 72 " " NAG m 1 " - " ASN G 88 " " NAG n 1 " - " ASN G 156 " " NAG o 1 " - " ASN G 160 " " NAG p 1 " - " ASN G 197 " " NAG q 1 " - " ASN G 262 " " NAG r 1 " - " ASN G 276 " " NAG s 1 " - " ASN G 295 " " NAG t 1 " - " ASN G 301 " " NAG u 1 " - " ASN G 332 " " NAG v 1 " - " ASN G 363 " " NAG w 1 " - " ASN G 386 " " NAG x 1 " - " ASN G 448 " " NAG y 1 " - " ASN U 72 " Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 825.9 milliseconds 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4422 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 54 sheets defined 24.0% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.824A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.865A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.500A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.967A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.745A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.582A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 597 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'F' and resid 99 through 117 removed outlier: 3.824A pdb=" N ILE F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 removed outlier: 3.864A pdb=" N VAL F 127 " --> pdb=" O PRO F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 151 Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 377 through 381 removed outlier: 3.501A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 392 Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.967A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 528 Processing helix chain 'I' and resid 529 through 534 removed outlier: 3.745A pdb=" N SER I 534 " --> pdb=" O MET I 530 " (cutoff:3.500A) Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.581A pdb=" N ARG I 542 " --> pdb=" O THR I 538 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 597 Processing helix chain 'I' and resid 611 through 615 Processing helix chain 'I' and resid 618 through 624 Processing helix chain 'I' and resid 627 through 636 Processing helix chain 'I' and resid 638 through 649 Processing helix chain 'I' and resid 650 through 663 Processing helix chain 'R' and resid 28 through 32 Processing helix chain 'R' and resid 60 through 64 Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'T' and resid 79 through 83 Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.824A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.864A pdb=" N VAL G 127 " --> pdb=" O PRO G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 151 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 377 through 381 removed outlier: 3.500A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 392 Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.966A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 528 Processing helix chain 'J' and resid 529 through 534 removed outlier: 3.745A pdb=" N SER J 534 " --> pdb=" O MET J 530 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.581A pdb=" N ARG J 542 " --> pdb=" O THR J 538 " (cutoff:3.500A) Processing helix chain 'J' and resid 571 through 597 Processing helix chain 'J' and resid 611 through 615 Processing helix chain 'J' and resid 618 through 624 Processing helix chain 'J' and resid 627 through 636 Processing helix chain 'J' and resid 638 through 649 Processing helix chain 'J' and resid 650 through 663 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 83 through 87 Processing helix chain 'U' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.863A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.056A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 394 through 395 removed outlier: 6.669A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.198A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 376 removed outlier: 4.339A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 316 through 323 removed outlier: 4.411A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.820A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.198A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.593A pdb=" N ALA H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.593A pdb=" N ALA H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.730A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AC1, first strand: chain 'F' and resid 35 through 40 Processing sheet with id=AC2, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.863A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 91 through 92 Processing sheet with id=AC5, first strand: chain 'F' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain 'F' and resid 181 through 183 Processing sheet with id=AC7, first strand: chain 'F' and resid 201 through 202 Processing sheet with id=AC8, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.056A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 394 through 395 removed outlier: 6.668A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.197A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 374 through 376 removed outlier: 4.339A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 316 through 323 removed outlier: 4.410A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.819A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.197A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AD5, first strand: chain 'R' and resid 10 through 11 removed outlier: 6.593A pdb=" N ALA R 10 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 10 through 11 removed outlier: 6.593A pdb=" N ALA R 10 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL R 102 " --> pdb=" O ARG R 94 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 4 through 6 Processing sheet with id=AD8, first strand: chain 'T' and resid 10 through 11 removed outlier: 6.729A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 10 through 11 Processing sheet with id=AE1, first strand: chain 'G' and resid 35 through 40 Processing sheet with id=AE2, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AE3, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.863A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 91 through 92 Processing sheet with id=AE5, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AE6, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AE7, first strand: chain 'G' and resid 201 through 202 Processing sheet with id=AE8, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.057A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 394 through 395 removed outlier: 6.669A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.197A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 374 through 376 removed outlier: 4.339A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 316 through 323 removed outlier: 4.411A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 271 through 273 removed outlier: 6.820A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.197A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 5 through 6 Processing sheet with id=AF5, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.594A pdb=" N ALA S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE S 34 " --> pdb=" O TRP S 50 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TRP S 50 " --> pdb=" O ILE S 34 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.594A pdb=" N ALA S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL S 102 " --> pdb=" O ARG S 94 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 4 through 6 Processing sheet with id=AF8, first strand: chain 'U' and resid 10 through 11 removed outlier: 6.730A pdb=" N TRP U 35 " --> pdb=" O LEU U 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 10 through 11 849 hydrogen bonds defined for protein. 2025 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: 4.53 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5451 1.33 - 1.45: 5952 1.45 - 1.58: 9675 1.58 - 1.71: 9 1.71 - 1.83: 162 Bond restraints: 21249 Sorted by residual: bond pdb=" CA PHE S 78 " pdb=" C PHE S 78 " ideal model delta sigma weight residual 1.522 1.465 0.056 1.21e-02 6.83e+03 2.15e+01 bond pdb=" CA PHE H 78 " pdb=" C PHE H 78 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.21e-02 6.83e+03 2.11e+01 bond pdb=" CA PHE R 78 " pdb=" C PHE R 78 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.21e-02 6.83e+03 2.06e+01 bond pdb=" C3 MAN e 5 " pdb=" C4 MAN e 5 " ideal model delta sigma weight residual 1.524 1.615 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C3 MAN N 5 " pdb=" C4 MAN N 5 " ideal model delta sigma weight residual 1.524 1.615 -0.091 2.00e-02 2.50e+03 2.05e+01 ... (remaining 21244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 24900 2.53 - 5.05: 3213 5.05 - 7.58: 630 7.58 - 10.11: 105 10.11 - 12.63: 21 Bond angle restraints: 28869 Sorted by residual: angle pdb=" C LYS G 252 " pdb=" N PRO G 253 " pdb=" CA PRO G 253 " ideal model delta sigma weight residual 120.12 131.59 -11.47 1.11e+00 8.12e-01 1.07e+02 angle pdb=" C LYS A 252 " pdb=" N PRO A 253 " pdb=" CA PRO A 253 " ideal model delta sigma weight residual 120.12 131.53 -11.41 1.11e+00 8.12e-01 1.06e+02 angle pdb=" C LYS F 252 " pdb=" N PRO F 253 " pdb=" CA PRO F 253 " ideal model delta sigma weight residual 120.12 131.52 -11.40 1.11e+00 8.12e-01 1.05e+02 angle pdb=" C CYS A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta sigma weight residual 119.56 129.03 -9.47 1.01e+00 9.80e-01 8.79e+01 angle pdb=" C CYS F 239 " pdb=" N PRO F 240 " pdb=" CA PRO F 240 " ideal model delta sigma weight residual 119.56 129.00 -9.44 1.01e+00 9.80e-01 8.74e+01 ... (remaining 28864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 13890 22.84 - 45.68: 456 45.68 - 68.52: 162 68.52 - 91.37: 96 91.37 - 114.21: 42 Dihedral angle restraints: 14646 sinusoidal: 7794 harmonic: 6852 Sorted by residual: dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.22 44.22 1 1.00e+01 1.00e-02 2.72e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.22 44.22 1 1.00e+01 1.00e-02 2.72e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.22 44.22 1 1.00e+01 1.00e-02 2.72e+01 ... (remaining 14643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.176: 3318 0.176 - 0.351: 282 0.351 - 0.527: 51 0.527 - 0.702: 3 0.702 - 0.878: 3 Chirality restraints: 3657 Sorted by residual: chirality pdb=" C1 MAN e 6 " pdb=" O6 BMA e 3 " pdb=" C2 MAN e 6 " pdb=" O5 MAN e 6 " both_signs ideal model delta sigma weight residual False 2.40 1.52 0.88 2.00e-02 2.50e+03 1.93e+03 chirality pdb=" C1 MAN N 6 " pdb=" O6 BMA N 3 " pdb=" C2 MAN N 6 " pdb=" O5 MAN N 6 " both_signs ideal model delta sigma weight residual False 2.40 1.52 0.88 2.00e-02 2.50e+03 1.92e+03 chirality pdb=" C1 MAN r 6 " pdb=" O6 BMA r 3 " pdb=" C2 MAN r 6 " pdb=" O5 MAN r 6 " both_signs ideal model delta sigma weight residual False 2.40 1.53 0.87 2.00e-02 2.50e+03 1.91e+03 ... (remaining 3654 not shown) Planarity restraints: 3534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 363 " -0.195 2.00e-02 2.50e+03 2.62e-01 8.61e+02 pdb=" CG ASN A 363 " 0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN A 363 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 363 " 0.443 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.319 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 363 " 0.195 2.00e-02 2.50e+03 2.62e-01 8.61e+02 pdb=" CG ASN G 363 " -0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN G 363 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN G 363 " -0.443 2.00e-02 2.50e+03 pdb=" C1 NAG v 1 " 0.319 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 363 " -0.195 2.00e-02 2.50e+03 2.62e-01 8.60e+02 pdb=" CG ASN F 363 " 0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN F 363 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN F 363 " 0.443 2.00e-02 2.50e+03 pdb=" C1 NAG i 1 " -0.319 2.00e-02 2.50e+03 ... (remaining 3531 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 1204 2.68 - 3.23: 21423 3.23 - 3.79: 33682 3.79 - 4.34: 43612 4.34 - 4.90: 69605 Nonbonded interactions: 169526 Sorted by model distance: nonbonded pdb=" OD1 ASN A 363 " pdb=" O SER A 364 " model vdw 2.124 3.040 nonbonded pdb=" OD1 ASN F 363 " pdb=" O SER F 364 " model vdw 2.124 3.040 nonbonded pdb=" OD1 ASN G 363 " pdb=" O SER G 364 " model vdw 2.124 3.040 nonbonded pdb=" O ARG L 66 " pdb=" CD1 TRP L 67 " model vdw 2.212 3.260 nonbonded pdb=" O ARG T 66 " pdb=" CD1 TRP T 67 " model vdw 2.212 3.260 ... (remaining 169521 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'Z' selection = chain 'm' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'H' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'L' selection = chain 'T' selection = chain 'U' } ncs_group { reference = (chain 'M' and resid 5 through 7) selection = (chain 'N' and resid 6 through 8) selection = (chain 'V' and resid 4 through 6) selection = (chain 'd' and resid 5 through 7) selection = (chain 'e' and resid 6 through 8) selection = (chain 'i' and resid 4 through 6) selection = (chain 'q' and resid 5 through 7) selection = (chain 'r' and resid 6 through 8) selection = (chain 'v' and resid 4 through 6) } ncs_group { reference = chain 'W' selection = chain 'j' selection = chain 'w' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.97 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.430 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 : 0.016 0.161 21441 Z= 0.977 Angle : 2.096 25.650 29406 Z= 1.194 Chirality : 0.114 0.878 3657 Planarity : 0.012 0.087 3474 Dihedral : 15.328 114.207 10107 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.14 % Allowed : 0.43 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.18), residues: 2328 helix: -0.54 (0.23), residues: 390 sheet: 0.73 (0.18), residues: 717 loop : 3.10 (0.19), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 298 TYR 0.048 0.005 TYR R 76 PHE 0.022 0.005 PHE S 78 TRP 0.052 0.008 TRP F 479 HIS 0.009 0.003 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.01548 (21249) covalent geometry : angle 1.86044 (28869) SS BOND : bond 0.05067 ( 39) SS BOND : angle 2.92557 ( 78) hydrogen bonds : bond 0.16905 ( 729) hydrogen bonds : angle 8.97720 ( 2025) link_ALPHA1-2 : bond 0.02155 ( 6) link_ALPHA1-2 : angle 3.75042 ( 18) link_ALPHA1-3 : bond 0.03218 ( 18) link_ALPHA1-3 : angle 3.19944 ( 54) link_ALPHA1-6 : bond 0.02868 ( 15) link_ALPHA1-6 : angle 6.75404 ( 45) link_BETA1-4 : bond 0.03127 ( 54) link_BETA1-4 : angle 5.05798 ( 162) link_NAG-ASN : bond 0.02690 ( 60) link_NAG-ASN : angle 10.96745 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 391 time to evaluate : 0.851 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: A 95 MET cc_start: 0.8165 (ttt) cc_final: 0.7890 (ttm) REVERT: A 117 LYS cc_start: 0.9082 (mttt) cc_final: 0.8835 (mmmm) REVERT: A 150 MET cc_start: 0.8458 (mmm) cc_final: 0.8248 (mmm) REVERT: A 161 MET cc_start: 0.8982 (tmm) cc_final: 0.8693 (tmm) REVERT: B 633 LYS cc_start: 0.9162 (mttt) cc_final: 0.8820 (tppt) REVERT: B 647 GLU cc_start: 0.8918 (tt0) cc_final: 0.8406 (tt0) REVERT: H 73 PHE cc_start: 0.8529 (m-80) cc_final: 0.8192 (m-80) REVERT: L 33 LEU cc_start: 0.9481 (tp) cc_final: 0.9222 (tp) REVERT: F 180 ASP cc_start: 0.8685 (m-30) cc_final: 0.8474 (m-30) REVERT: F 217 TYR cc_start: 0.8413 (m-80) cc_final: 0.8029 (m-80) REVERT: F 434 MET cc_start: 0.8610 (ptm) cc_final: 0.8164 (ppp) REVERT: F 435 TYR cc_start: 0.8897 (t80) cc_final: 0.8638 (t80) REVERT: I 633 LYS cc_start: 0.9158 (mttt) cc_final: 0.8793 (tppp) REVERT: I 647 GLU cc_start: 0.8891 (tt0) cc_final: 0.8366 (tt0) REVERT: R 73 PHE cc_start: 0.8412 (m-80) cc_final: 0.8110 (m-80) REVERT: T 33 LEU cc_start: 0.9514 (tp) cc_final: 0.9105 (tp) REVERT: T 58 VAL cc_start: 0.8125 (t) cc_final: 0.7807 (t) REVERT: G 217 TYR cc_start: 0.8322 (m-80) cc_final: 0.7959 (m-80) REVERT: J 538 THR cc_start: 0.8248 (p) cc_final: 0.8044 (p) REVERT: J 610 TRP cc_start: 0.7018 (p-90) cc_final: 0.6696 (p-90) REVERT: J 633 LYS cc_start: 0.9103 (mttt) cc_final: 0.8871 (tppp) REVERT: S 73 PHE cc_start: 0.8519 (m-80) cc_final: 0.8136 (m-80) REVERT: U 33 LEU cc_start: 0.9538 (tp) cc_final: 0.9280 (tp) REVERT: U 104 LEU cc_start: 0.8905 (mt) cc_final: 0.8630 (mt) outliers start: 3 outliers final: 3 residues processed: 394 average time/residue: 0.1807 time to fit residues: 104.9197 Evaluate side-chains 197 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 428 GLN F 80 ASN F 428 GLN G 80 ASN S 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.059822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.050864 restraints weight = 112127.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.052313 restraints weight = 63711.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.053311 restraints weight = 42996.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.053919 restraints weight = 32420.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.054422 restraints weight = 27090.437| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21441 Z= 0.189 Angle : 0.994 19.250 29406 Z= 0.455 Chirality : 0.051 0.317 3657 Planarity : 0.006 0.075 3474 Dihedral : 14.414 75.308 5661 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.38 % Allowed : 0.91 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 1.83 (0.18), residues: 2328 helix: 1.10 (0.27), residues: 372 sheet: 0.41 (0.18), residues: 750 loop : 2.11 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 298 TYR 0.019 0.002 TYR J 586 PHE 0.027 0.002 PHE U 62 TRP 0.024 0.002 TRP S 103 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00404 (21249) covalent geometry : angle 0.86496 (28869) SS BOND : bond 0.00235 ( 39) SS BOND : angle 0.99777 ( 78) hydrogen bonds : bond 0.05261 ( 729) hydrogen bonds : angle 6.57812 ( 2025) link_ALPHA1-2 : bond 0.00104 ( 6) link_ALPHA1-2 : angle 1.89068 ( 18) link_ALPHA1-3 : bond 0.00656 ( 18) link_ALPHA1-3 : angle 1.96686 ( 54) link_ALPHA1-6 : bond 0.00970 ( 15) link_ALPHA1-6 : angle 2.42187 ( 45) link_BETA1-4 : bond 0.00633 ( 54) link_BETA1-4 : angle 2.74340 ( 162) link_NAG-ASN : bond 0.00538 ( 60) link_NAG-ASN : angle 5.60154 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 310 time to evaluate : 0.816 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: A 45 TRP cc_start: 0.7403 (m-10) cc_final: 0.7198 (m-10) REVERT: A 150 MET cc_start: 0.8358 (mmm) cc_final: 0.7994 (mmm) REVERT: A 434 MET cc_start: 0.8409 (ppp) cc_final: 0.7826 (ppp) REVERT: B 584 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8045 (tm-30) REVERT: B 586 TYR cc_start: 0.8931 (t80) cc_final: 0.8727 (t80) REVERT: B 610 TRP cc_start: 0.7276 (p-90) cc_final: 0.6875 (p-90) REVERT: B 658 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8794 (pp30) REVERT: H 43 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8266 (mp-120) REVERT: H 71 TRP cc_start: 0.8225 (p-90) cc_final: 0.7821 (p-90) REVERT: H 80 MET cc_start: 0.8639 (tmm) cc_final: 0.8286 (tmm) REVERT: H 100 TRP cc_start: 0.9422 (m-10) cc_final: 0.8890 (m-10) REVERT: L 33 LEU cc_start: 0.9583 (tp) cc_final: 0.9042 (tp) REVERT: L 34 ASN cc_start: 0.8723 (m-40) cc_final: 0.8427 (t0) REVERT: L 46 LEU cc_start: 0.8075 (tt) cc_final: 0.6992 (tt) REVERT: L 62 PHE cc_start: 0.9079 (m-10) cc_final: 0.8873 (m-80) REVERT: F 150 MET cc_start: 0.7600 (mmm) cc_final: 0.6991 (mmm) REVERT: F 434 MET cc_start: 0.8530 (ptm) cc_final: 0.8227 (ptm) REVERT: I 584 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8088 (tm-30) REVERT: I 648 GLU cc_start: 0.8927 (tp30) cc_final: 0.8335 (tp30) REVERT: R 71 TRP cc_start: 0.7956 (p-90) cc_final: 0.7458 (p-90) REVERT: R 80 MET cc_start: 0.8702 (tmm) cc_final: 0.8459 (tmm) REVERT: R 100 TRP cc_start: 0.9437 (m-10) cc_final: 0.8629 (m-10) REVERT: T 33 LEU cc_start: 0.9565 (tp) cc_final: 0.9035 (tp) REVERT: T 34 ASN cc_start: 0.8392 (m-40) cc_final: 0.8107 (t0) REVERT: T 42 LYS cc_start: 0.9396 (mtmt) cc_final: 0.9191 (mtmm) REVERT: T 46 LEU cc_start: 0.8086 (tt) cc_final: 0.7299 (tt) REVERT: G 45 TRP cc_start: 0.7589 (m-10) cc_final: 0.7379 (m-10) REVERT: J 574 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8699 (mtmm) REVERT: J 584 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7970 (tm-30) REVERT: J 610 TRP cc_start: 0.7398 (p-90) cc_final: 0.6845 (p-90) REVERT: J 634 GLU cc_start: 0.8482 (tt0) cc_final: 0.8268 (mt-10) REVERT: J 648 GLU cc_start: 0.8913 (tp30) cc_final: 0.8378 (tp30) REVERT: S 71 TRP cc_start: 0.8155 (p-90) cc_final: 0.7688 (p-90) REVERT: S 80 MET cc_start: 0.8713 (tmm) cc_final: 0.8501 (tmm) REVERT: S 82 LYS cc_start: 0.8603 (mttt) cc_final: 0.8310 (mptt) REVERT: S 100 TRP cc_start: 0.9343 (m-10) cc_final: 0.8791 (m-10) REVERT: S 109 VAL cc_start: 0.9451 (t) cc_final: 0.9104 (t) REVERT: U 42 LYS cc_start: 0.9319 (mtmt) cc_final: 0.9118 (mtmm) REVERT: U 62 PHE cc_start: 0.9056 (m-10) cc_final: 0.8705 (m-80) outliers start: 8 outliers final: 0 residues processed: 318 average time/residue: 0.1628 time to fit residues: 78.9056 Evaluate side-chains 198 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 172 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 210 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 184 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 overall best weight: 3.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN B 618 ASN H 56 GLN L 24 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 ASN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 618 ASN S 28 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.057645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.048674 restraints weight = 114768.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.050006 restraints weight = 66353.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.050941 restraints weight = 45734.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.051588 restraints weight = 34938.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.052040 restraints weight = 28885.761| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 21441 Z= 0.205 Angle : 0.900 18.849 29406 Z= 0.415 Chirality : 0.055 1.203 3657 Planarity : 0.005 0.047 3474 Dihedral : 11.553 65.529 5661 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.19 % Allowed : 1.20 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.17), residues: 2328 helix: 1.44 (0.27), residues: 366 sheet: 0.25 (0.17), residues: 762 loop : 1.42 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 585 TYR 0.034 0.002 TYR U 49 PHE 0.032 0.002 PHE R 73 TRP 0.017 0.002 TRP S 103 HIS 0.005 0.001 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00445 (21249) covalent geometry : angle 0.79791 (28869) SS BOND : bond 0.00489 ( 39) SS BOND : angle 0.86958 ( 78) hydrogen bonds : bond 0.04561 ( 729) hydrogen bonds : angle 5.79253 ( 2025) link_ALPHA1-2 : bond 0.00273 ( 6) link_ALPHA1-2 : angle 2.00431 ( 18) link_ALPHA1-3 : bond 0.00852 ( 18) link_ALPHA1-3 : angle 1.63867 ( 54) link_ALPHA1-6 : bond 0.00909 ( 15) link_ALPHA1-6 : angle 2.44800 ( 45) link_BETA1-4 : bond 0.00578 ( 54) link_BETA1-4 : angle 2.69112 ( 162) link_NAG-ASN : bond 0.00434 ( 60) link_NAG-ASN : angle 4.55367 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 260 time to evaluate : 0.920 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: A 45 TRP cc_start: 0.7484 (m-10) cc_final: 0.7268 (m-10) REVERT: A 104 MET cc_start: 0.8842 (tpp) cc_final: 0.8385 (tpp) REVERT: A 150 MET cc_start: 0.8520 (mmm) cc_final: 0.8149 (mmm) REVERT: A 377 ASN cc_start: 0.8560 (t0) cc_final: 0.8343 (t0) REVERT: A 434 MET cc_start: 0.8680 (ppp) cc_final: 0.7989 (ppp) REVERT: B 584 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8081 (tm-30) REVERT: B 626 MET cc_start: 0.7519 (ptm) cc_final: 0.7268 (ptm) REVERT: B 633 LYS cc_start: 0.9479 (mttt) cc_final: 0.9230 (mtpt) REVERT: H 80 MET cc_start: 0.8729 (tmm) cc_final: 0.8505 (tmm) REVERT: L 33 LEU cc_start: 0.9482 (tp) cc_final: 0.9016 (tp) REVERT: L 34 ASN cc_start: 0.9321 (m-40) cc_final: 0.8650 (t0) REVERT: L 42 LYS cc_start: 0.9220 (mtmt) cc_final: 0.8879 (ptmm) REVERT: F 95 MET cc_start: 0.7879 (ttp) cc_final: 0.7638 (ttm) REVERT: F 150 MET cc_start: 0.8095 (mmm) cc_final: 0.7716 (mmm) REVERT: F 377 ASN cc_start: 0.8458 (t0) cc_final: 0.8227 (t0) REVERT: F 434 MET cc_start: 0.8696 (ptm) cc_final: 0.8304 (ptm) REVERT: I 530 MET cc_start: 0.8120 (mmm) cc_final: 0.7809 (mmm) REVERT: I 584 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8036 (tm-30) REVERT: I 610 TRP cc_start: 0.7061 (p-90) cc_final: 0.6760 (p-90) REVERT: I 633 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8873 (tppp) REVERT: T 33 LEU cc_start: 0.9554 (tp) cc_final: 0.9141 (tp) REVERT: T 34 ASN cc_start: 0.9244 (m-40) cc_final: 0.8817 (t0) REVERT: G 150 MET cc_start: 0.8427 (mmm) cc_final: 0.8190 (mmm) REVERT: G 434 MET cc_start: 0.9040 (ptm) cc_final: 0.8759 (ppp) REVERT: J 584 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8069 (tm-30) REVERT: J 633 LYS cc_start: 0.9192 (mtpt) cc_final: 0.8973 (tppp) REVERT: U 33 LEU cc_start: 0.9618 (tp) cc_final: 0.9191 (tp) REVERT: U 34 ASN cc_start: 0.9244 (m-40) cc_final: 0.8897 (t0) REVERT: U 46 LEU cc_start: 0.6689 (tt) cc_final: 0.6122 (tt) outliers start: 4 outliers final: 0 residues processed: 264 average time/residue: 0.1635 time to fit residues: 65.8343 Evaluate side-chains 169 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 43 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 ASN T 24 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 374 HIS ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.055976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.047036 restraints weight = 115547.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.048337 restraints weight = 67170.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.049222 restraints weight = 46171.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.049862 restraints weight = 35591.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.050326 restraints weight = 29447.568| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21441 Z= 0.245 Angle : 0.877 18.467 29406 Z= 0.405 Chirality : 0.052 0.937 3657 Planarity : 0.005 0.039 3474 Dihedral : 9.888 59.964 5661 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.14 % Allowed : 1.34 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 0.93 (0.17), residues: 2328 helix: 1.14 (0.26), residues: 387 sheet: 0.09 (0.17), residues: 732 loop : 1.02 (0.19), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 298 TYR 0.017 0.002 TYR T 49 PHE 0.018 0.002 PHE H 73 TRP 0.017 0.002 TRP A 96 HIS 0.006 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00530 (21249) covalent geometry : angle 0.78393 (28869) SS BOND : bond 0.00241 ( 39) SS BOND : angle 0.89618 ( 78) hydrogen bonds : bond 0.04409 ( 729) hydrogen bonds : angle 5.66077 ( 2025) link_ALPHA1-2 : bond 0.00049 ( 6) link_ALPHA1-2 : angle 2.01848 ( 18) link_ALPHA1-3 : bond 0.00851 ( 18) link_ALPHA1-3 : angle 1.68760 ( 54) link_ALPHA1-6 : bond 0.00992 ( 15) link_ALPHA1-6 : angle 2.78467 ( 45) link_BETA1-4 : bond 0.00356 ( 54) link_BETA1-4 : angle 2.36483 ( 162) link_NAG-ASN : bond 0.00439 ( 60) link_NAG-ASN : angle 4.30981 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 229 time to evaluate : 0.864 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: A 95 MET cc_start: 0.8167 (ttp) cc_final: 0.7874 (ttm) REVERT: A 377 ASN cc_start: 0.8391 (t0) cc_final: 0.8183 (t0) REVERT: B 548 ILE cc_start: 0.7520 (tp) cc_final: 0.7298 (tp) REVERT: B 584 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8184 (tm-30) REVERT: B 633 LYS cc_start: 0.9495 (mttt) cc_final: 0.9065 (mmmm) REVERT: H 80 MET cc_start: 0.8830 (tmm) cc_final: 0.8608 (tmm) REVERT: H 82 LYS cc_start: 0.8733 (mttt) cc_final: 0.8412 (mmtt) REVERT: L 33 LEU cc_start: 0.9644 (tp) cc_final: 0.8990 (tp) REVERT: L 34 ASN cc_start: 0.9262 (m-40) cc_final: 0.8204 (t0) REVERT: L 42 LYS cc_start: 0.9317 (mtmt) cc_final: 0.9115 (mtmm) REVERT: L 62 PHE cc_start: 0.9273 (m-80) cc_final: 0.8928 (m-80) REVERT: F 95 MET cc_start: 0.8064 (ttp) cc_final: 0.7572 (ttm) REVERT: F 150 MET cc_start: 0.8148 (mmm) cc_final: 0.7902 (mmm) REVERT: F 434 MET cc_start: 0.8925 (ptm) cc_final: 0.8503 (ptm) REVERT: I 530 MET cc_start: 0.8305 (mmm) cc_final: 0.8100 (mmm) REVERT: I 584 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8203 (tm-30) REVERT: I 610 TRP cc_start: 0.7283 (p-90) cc_final: 0.6510 (p-90) REVERT: T 33 LEU cc_start: 0.9655 (tp) cc_final: 0.9098 (tp) REVERT: T 34 ASN cc_start: 0.9134 (m-40) cc_final: 0.8767 (t0) REVERT: G 434 MET cc_start: 0.9087 (ptm) cc_final: 0.8683 (ptm) REVERT: J 584 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8237 (tm-30) REVERT: J 610 TRP cc_start: 0.7347 (p-90) cc_final: 0.6627 (p-90) REVERT: S 61 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8465 (ttp80) REVERT: S 71 TRP cc_start: 0.8246 (p-90) cc_final: 0.7721 (p-90) REVERT: S 82 LYS cc_start: 0.8654 (mttt) cc_final: 0.8444 (mttp) REVERT: U 42 LYS cc_start: 0.9302 (mtmt) cc_final: 0.8691 (ptmm) outliers start: 3 outliers final: 2 residues processed: 232 average time/residue: 0.1639 time to fit residues: 58.3095 Evaluate side-chains 168 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 125 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN F 374 HIS ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 575 GLN ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 ASN U 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.056839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.047764 restraints weight = 113303.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.049137 restraints weight = 64285.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.050076 restraints weight = 43594.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.050755 restraints weight = 33136.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.051264 restraints weight = 27138.473| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21441 Z= 0.142 Angle : 0.783 18.236 29406 Z= 0.358 Chirality : 0.050 0.791 3657 Planarity : 0.004 0.037 3474 Dihedral : 9.253 58.600 5661 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.14 % Allowed : 2.01 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.14 (0.18), residues: 2328 helix: 1.63 (0.27), residues: 369 sheet: 0.23 (0.17), residues: 792 loop : 1.08 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 61 TYR 0.012 0.001 TYR U 49 PHE 0.012 0.001 PHE L 62 TRP 0.015 0.002 TRP A 45 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00302 (21249) covalent geometry : angle 0.68485 (28869) SS BOND : bond 0.00228 ( 39) SS BOND : angle 0.70051 ( 78) hydrogen bonds : bond 0.04012 ( 729) hydrogen bonds : angle 5.32499 ( 2025) link_ALPHA1-2 : bond 0.00237 ( 6) link_ALPHA1-2 : angle 1.86709 ( 18) link_ALPHA1-3 : bond 0.00929 ( 18) link_ALPHA1-3 : angle 1.62549 ( 54) link_ALPHA1-6 : bond 0.00986 ( 15) link_ALPHA1-6 : angle 2.51534 ( 45) link_BETA1-4 : bond 0.00429 ( 54) link_BETA1-4 : angle 2.18873 ( 162) link_NAG-ASN : bond 0.00249 ( 60) link_NAG-ASN : angle 4.20421 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 0.731 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: A 95 MET cc_start: 0.8024 (ttp) cc_final: 0.7658 (ttm) REVERT: A 150 MET cc_start: 0.8350 (mmm) cc_final: 0.7828 (mmm) REVERT: A 434 MET cc_start: 0.8894 (ptm) cc_final: 0.8618 (ptm) REVERT: B 571 TRP cc_start: 0.7718 (m-10) cc_final: 0.7388 (m-10) REVERT: B 584 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B 626 MET cc_start: 0.7724 (ptp) cc_final: 0.7521 (ptp) REVERT: H 71 TRP cc_start: 0.8218 (p-90) cc_final: 0.7740 (p-90) REVERT: H 80 MET cc_start: 0.8888 (tmm) cc_final: 0.8558 (tmm) REVERT: H 82 LYS cc_start: 0.8681 (mttt) cc_final: 0.8421 (mmtt) REVERT: L 33 LEU cc_start: 0.9589 (tp) cc_final: 0.9054 (tp) REVERT: L 34 ASN cc_start: 0.9168 (m-40) cc_final: 0.8148 (t0) REVERT: L 62 PHE cc_start: 0.8997 (m-80) cc_final: 0.8731 (m-80) REVERT: F 95 MET cc_start: 0.7823 (ttp) cc_final: 0.7561 (ttm) REVERT: F 434 MET cc_start: 0.8902 (ptm) cc_final: 0.8635 (ptm) REVERT: I 548 ILE cc_start: 0.7536 (tp) cc_final: 0.7320 (tp) REVERT: I 584 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8179 (tm-30) REVERT: I 610 TRP cc_start: 0.7397 (p-90) cc_final: 0.6755 (p-90) REVERT: I 626 MET cc_start: 0.7620 (ptp) cc_final: 0.7403 (ptt) REVERT: R 71 TRP cc_start: 0.8225 (p-90) cc_final: 0.7768 (p-90) REVERT: R 80 MET cc_start: 0.8917 (tmm) cc_final: 0.8655 (tmm) REVERT: T 33 LEU cc_start: 0.9593 (tp) cc_final: 0.9142 (tp) REVERT: T 34 ASN cc_start: 0.9067 (m-40) cc_final: 0.8692 (t0) REVERT: T 42 LYS cc_start: 0.9463 (mtmt) cc_final: 0.9137 (ptmm) REVERT: T 47 LEU cc_start: 0.8882 (mm) cc_final: 0.7969 (tp) REVERT: G 377 ASN cc_start: 0.8637 (t0) cc_final: 0.8412 (t0) REVERT: J 584 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8165 (tm-30) REVERT: J 586 TYR cc_start: 0.8996 (t80) cc_final: 0.8786 (t80) REVERT: J 610 TRP cc_start: 0.7210 (p-90) cc_final: 0.6605 (p-90) REVERT: S 31 ASP cc_start: 0.8046 (t0) cc_final: 0.7768 (t0) REVERT: S 32 TYR cc_start: 0.9070 (m-80) cc_final: 0.8457 (m-80) REVERT: S 71 TRP cc_start: 0.8277 (p-90) cc_final: 0.7812 (p-90) REVERT: S 98 ASP cc_start: 0.9102 (p0) cc_final: 0.8413 (t0) REVERT: S 100 ASP cc_start: 0.8363 (t0) cc_final: 0.7886 (p0) REVERT: U 42 LYS cc_start: 0.9285 (mtmt) cc_final: 0.8745 (ptmm) outliers start: 3 outliers final: 1 residues processed: 241 average time/residue: 0.1613 time to fit residues: 59.4901 Evaluate side-chains 178 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 203 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN B 651 ASN H 56 GLN F 130 GLN F 203 GLN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN I 575 GLN I 640 GLN ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN G 99 ASN G 130 GLN G 203 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 640 GLN ** J 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.054624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.045690 restraints weight = 119938.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.046917 restraints weight = 71845.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.047767 restraints weight = 50522.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.048368 restraints weight = 39570.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.048817 restraints weight = 33205.370| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 21441 Z= 0.324 Angle : 0.976 16.271 29406 Z= 0.446 Chirality : 0.053 0.844 3657 Planarity : 0.005 0.041 3474 Dihedral : 9.278 59.024 5661 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.14 % Allowed : 1.05 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.17), residues: 2328 helix: 0.99 (0.27), residues: 366 sheet: -0.05 (0.18), residues: 735 loop : 0.52 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 65 TYR 0.021 0.002 TYR A 217 PHE 0.016 0.002 PHE A 53 TRP 0.030 0.003 TRP B 628 HIS 0.009 0.002 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00703 (21249) covalent geometry : angle 0.88533 (28869) SS BOND : bond 0.00378 ( 39) SS BOND : angle 1.05236 ( 78) hydrogen bonds : bond 0.04598 ( 729) hydrogen bonds : angle 5.63290 ( 2025) link_ALPHA1-2 : bond 0.00288 ( 6) link_ALPHA1-2 : angle 2.21515 ( 18) link_ALPHA1-3 : bond 0.00769 ( 18) link_ALPHA1-3 : angle 1.94303 ( 54) link_ALPHA1-6 : bond 0.01008 ( 15) link_ALPHA1-6 : angle 3.11194 ( 45) link_BETA1-4 : bond 0.00361 ( 54) link_BETA1-4 : angle 2.33919 ( 162) link_NAG-ASN : bond 0.00653 ( 60) link_NAG-ASN : angle 4.51596 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 195 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8292 (ttp) cc_final: 0.7652 (ttm) REVERT: A 104 MET cc_start: 0.9128 (tpp) cc_final: 0.8797 (tpt) REVERT: A 150 MET cc_start: 0.8439 (mmm) cc_final: 0.7961 (mmm) REVERT: A 434 MET cc_start: 0.8883 (ptm) cc_final: 0.8539 (ptm) REVERT: B 546 SER cc_start: 0.8732 (m) cc_final: 0.8230 (p) REVERT: B 584 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8218 (tm-30) REVERT: B 610 TRP cc_start: 0.7319 (p-90) cc_final: 0.6752 (p-90) REVERT: B 633 LYS cc_start: 0.9314 (mmmt) cc_final: 0.8942 (mtpt) REVERT: H 45 LEU cc_start: 0.9295 (mt) cc_final: 0.9082 (mt) REVERT: L 33 LEU cc_start: 0.9660 (tp) cc_final: 0.9323 (tp) REVERT: L 34 ASN cc_start: 0.9267 (m-40) cc_final: 0.8849 (t0) REVERT: L 42 LYS cc_start: 0.9381 (mtmt) cc_final: 0.9121 (ptmm) REVERT: F 95 MET cc_start: 0.7995 (ttp) cc_final: 0.7331 (ttm) REVERT: F 434 MET cc_start: 0.8890 (ptm) cc_final: 0.8579 (ptm) REVERT: I 546 SER cc_start: 0.8889 (m) cc_final: 0.8369 (p) REVERT: I 584 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8193 (tm-30) REVERT: I 610 TRP cc_start: 0.7486 (p-90) cc_final: 0.6459 (p-90) REVERT: I 626 MET cc_start: 0.7776 (ptp) cc_final: 0.7520 (ptt) REVERT: R 71 TRP cc_start: 0.8342 (p-90) cc_final: 0.7920 (p-90) REVERT: T 33 LEU cc_start: 0.9605 (tp) cc_final: 0.9265 (tp) REVERT: T 34 ASN cc_start: 0.9211 (m-40) cc_final: 0.8876 (t0) REVERT: T 53 LYS cc_start: 0.9487 (mtmt) cc_final: 0.9225 (mtmm) REVERT: G 377 ASN cc_start: 0.8601 (t0) cc_final: 0.8386 (t0) REVERT: G 434 MET cc_start: 0.8766 (ptm) cc_final: 0.8520 (ptm) REVERT: J 584 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8225 (tm-30) REVERT: J 610 TRP cc_start: 0.7260 (p-90) cc_final: 0.6399 (p-90) REVERT: J 626 MET cc_start: 0.8178 (ptp) cc_final: 0.7971 (ptp) REVERT: S 71 TRP cc_start: 0.8429 (p-90) cc_final: 0.7914 (p-90) REVERT: S 82 LYS cc_start: 0.8097 (mptt) cc_final: 0.7853 (mmtm) REVERT: U 42 LYS cc_start: 0.9323 (mtmt) cc_final: 0.8950 (ptmm) outliers start: 3 outliers final: 0 residues processed: 198 average time/residue: 0.1481 time to fit residues: 45.8616 Evaluate side-chains 149 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 188 optimal weight: 0.0770 chunk 113 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN H 108 GLN F 374 HIS I 575 GLN ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.056556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.047583 restraints weight = 113600.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.048903 restraints weight = 65325.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.049837 restraints weight = 44765.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.050516 restraints weight = 34249.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.051005 restraints weight = 28075.612| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21441 Z= 0.122 Angle : 0.780 17.129 29406 Z= 0.357 Chirality : 0.049 0.720 3657 Planarity : 0.004 0.040 3474 Dihedral : 8.464 56.607 5661 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.14 % Allowed : 0.81 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.18), residues: 2328 helix: 1.69 (0.28), residues: 363 sheet: 0.20 (0.17), residues: 780 loop : 0.70 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 61 TYR 0.014 0.001 TYR F 217 PHE 0.021 0.001 PHE T 62 TRP 0.034 0.002 TRP I 571 HIS 0.005 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00253 (21249) covalent geometry : angle 0.68770 (28869) SS BOND : bond 0.00300 ( 39) SS BOND : angle 0.92925 ( 78) hydrogen bonds : bond 0.03849 ( 729) hydrogen bonds : angle 5.21757 ( 2025) link_ALPHA1-2 : bond 0.00384 ( 6) link_ALPHA1-2 : angle 1.81036 ( 18) link_ALPHA1-3 : bond 0.00956 ( 18) link_ALPHA1-3 : angle 1.72858 ( 54) link_ALPHA1-6 : bond 0.01015 ( 15) link_ALPHA1-6 : angle 2.42632 ( 45) link_BETA1-4 : bond 0.00431 ( 54) link_BETA1-4 : angle 2.09674 ( 162) link_NAG-ASN : bond 0.00270 ( 60) link_NAG-ASN : angle 4.07578 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 233 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8019 (ttp) cc_final: 0.7708 (ttm) REVERT: A 104 MET cc_start: 0.9253 (tpp) cc_final: 0.8478 (tpt) REVERT: A 150 MET cc_start: 0.8406 (mmm) cc_final: 0.8073 (mmm) REVERT: A 217 TYR cc_start: 0.8635 (m-80) cc_final: 0.7471 (m-80) REVERT: B 546 SER cc_start: 0.8533 (m) cc_final: 0.8041 (p) REVERT: B 548 ILE cc_start: 0.7547 (tp) cc_final: 0.7281 (tp) REVERT: B 571 TRP cc_start: 0.7767 (m-10) cc_final: 0.7493 (m-10) REVERT: B 584 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8303 (tm-30) REVERT: B 633 LYS cc_start: 0.9169 (mtpp) cc_final: 0.8718 (mmmm) REVERT: B 651 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8206 (t0) REVERT: H 51 ILE cc_start: 0.9462 (tt) cc_final: 0.9247 (tp) REVERT: H 71 TRP cc_start: 0.8377 (p-90) cc_final: 0.7907 (p-90) REVERT: H 80 MET cc_start: 0.8948 (tmm) cc_final: 0.8694 (tmm) REVERT: H 82 LEU cc_start: 0.9226 (mt) cc_final: 0.9013 (mt) REVERT: L 33 LEU cc_start: 0.9658 (tp) cc_final: 0.9220 (tp) REVERT: L 34 ASN cc_start: 0.9117 (m-40) cc_final: 0.8167 (t0) REVERT: L 42 LYS cc_start: 0.9367 (mtmt) cc_final: 0.9068 (ptmm) REVERT: L 47 LEU cc_start: 0.9165 (mm) cc_final: 0.8235 (tp) REVERT: F 150 MET cc_start: 0.8009 (mmm) cc_final: 0.7643 (mmm) REVERT: I 530 MET cc_start: 0.8304 (mmm) cc_final: 0.8056 (mmm) REVERT: I 546 SER cc_start: 0.8753 (m) cc_final: 0.8118 (p) REVERT: I 574 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8758 (mtmm) REVERT: I 584 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8220 (tm-30) REVERT: I 610 TRP cc_start: 0.7151 (p-90) cc_final: 0.6423 (p-90) REVERT: R 71 TRP cc_start: 0.8223 (p-90) cc_final: 0.7873 (p-90) REVERT: R 80 MET cc_start: 0.8965 (tmm) cc_final: 0.8710 (tmm) REVERT: T 33 LEU cc_start: 0.9608 (tp) cc_final: 0.9228 (tp) REVERT: T 34 ASN cc_start: 0.8960 (m-40) cc_final: 0.8705 (t0) REVERT: T 42 LYS cc_start: 0.9476 (mtmt) cc_final: 0.9139 (ptmm) REVERT: G 150 MET cc_start: 0.8281 (mmm) cc_final: 0.7988 (mmm) REVERT: J 530 MET cc_start: 0.8955 (mmm) cc_final: 0.8506 (mmm) REVERT: J 571 TRP cc_start: 0.7765 (m-10) cc_final: 0.7366 (m-10) REVERT: J 584 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8168 (tm-30) REVERT: J 610 TRP cc_start: 0.7083 (p-90) cc_final: 0.6394 (p-90) REVERT: S 32 TYR cc_start: 0.8810 (m-80) cc_final: 0.8254 (m-80) REVERT: S 71 TRP cc_start: 0.8288 (p-90) cc_final: 0.7979 (p-90) REVERT: S 98 ASP cc_start: 0.9114 (p0) cc_final: 0.8471 (t0) REVERT: U 42 LYS cc_start: 0.9277 (mtmt) cc_final: 0.8831 (ptmm) outliers start: 3 outliers final: 0 residues processed: 236 average time/residue: 0.1560 time to fit residues: 57.4385 Evaluate side-chains 173 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 199 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN F 99 ASN I 575 GLN ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN G 99 ASN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 ASN U 26 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.054959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.046088 restraints weight = 118331.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.047316 restraints weight = 70144.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.048197 restraints weight = 49274.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.048815 restraints weight = 38170.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.049272 restraints weight = 31737.376| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 21441 Z= 0.275 Angle : 0.881 15.363 29406 Z= 0.409 Chirality : 0.050 0.751 3657 Planarity : 0.004 0.037 3474 Dihedral : 8.558 56.132 5661 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.10 % Allowed : 0.72 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2328 helix: 1.11 (0.28), residues: 369 sheet: 0.03 (0.18), residues: 738 loop : 0.39 (0.19), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 61 TYR 0.020 0.002 TYR A 217 PHE 0.013 0.002 PHE A 353 TRP 0.047 0.003 TRP I 628 HIS 0.008 0.002 HIS G 85 Details of bonding type rmsd covalent geometry : bond 0.00596 (21249) covalent geometry : angle 0.80135 (28869) SS BOND : bond 0.00496 ( 39) SS BOND : angle 1.03578 ( 78) hydrogen bonds : bond 0.04360 ( 729) hydrogen bonds : angle 5.46082 ( 2025) link_ALPHA1-2 : bond 0.00201 ( 6) link_ALPHA1-2 : angle 2.10994 ( 18) link_ALPHA1-3 : bond 0.00798 ( 18) link_ALPHA1-3 : angle 1.95332 ( 54) link_ALPHA1-6 : bond 0.00974 ( 15) link_ALPHA1-6 : angle 2.84498 ( 45) link_BETA1-4 : bond 0.00366 ( 54) link_BETA1-4 : angle 2.08351 ( 162) link_NAG-ASN : bond 0.00533 ( 60) link_NAG-ASN : angle 3.96150 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8198 (ttp) cc_final: 0.7761 (ttm) REVERT: A 104 MET cc_start: 0.9082 (tpp) cc_final: 0.8622 (tpt) REVERT: A 150 MET cc_start: 0.8338 (mmm) cc_final: 0.7869 (mmm) REVERT: A 434 MET cc_start: 0.8866 (ptm) cc_final: 0.8637 (ptm) REVERT: B 530 MET cc_start: 0.8132 (mmp) cc_final: 0.7166 (mmp) REVERT: B 546 SER cc_start: 0.8835 (m) cc_final: 0.8308 (p) REVERT: B 548 ILE cc_start: 0.7502 (tp) cc_final: 0.7258 (tp) REVERT: B 584 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8353 (tm-30) REVERT: B 610 TRP cc_start: 0.7081 (p-90) cc_final: 0.6541 (p-90) REVERT: B 633 LYS cc_start: 0.9165 (mtpp) cc_final: 0.8759 (mmmm) REVERT: H 45 LEU cc_start: 0.9283 (mt) cc_final: 0.9006 (mt) REVERT: H 80 MET cc_start: 0.8899 (tmm) cc_final: 0.8691 (tmm) REVERT: H 82 LEU cc_start: 0.9259 (mt) cc_final: 0.9049 (mt) REVERT: L 33 LEU cc_start: 0.9701 (tp) cc_final: 0.9241 (tp) REVERT: L 34 ASN cc_start: 0.9267 (m-40) cc_final: 0.8279 (t0) REVERT: F 150 MET cc_start: 0.8010 (mmm) cc_final: 0.7648 (mmm) REVERT: I 546 SER cc_start: 0.8717 (m) cc_final: 0.8106 (p) REVERT: I 584 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8338 (tm-30) REVERT: I 610 TRP cc_start: 0.7516 (p-90) cc_final: 0.6474 (p-90) REVERT: R 71 TRP cc_start: 0.8307 (p-90) cc_final: 0.7985 (p-90) REVERT: T 33 LEU cc_start: 0.9628 (tp) cc_final: 0.9276 (tp) REVERT: T 34 ASN cc_start: 0.9185 (m-40) cc_final: 0.8844 (t0) REVERT: J 530 MET cc_start: 0.9062 (mmm) cc_final: 0.8843 (mmm) REVERT: J 584 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8225 (tm-30) REVERT: J 610 TRP cc_start: 0.7375 (p-90) cc_final: 0.6458 (p-90) REVERT: S 71 TRP cc_start: 0.8368 (p-90) cc_final: 0.7943 (p-90) REVERT: S 100 ASP cc_start: 0.8830 (t70) cc_final: 0.8599 (t0) REVERT: U 42 LYS cc_start: 0.9275 (mtmt) cc_final: 0.8881 (ptmm) outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.1538 time to fit residues: 49.3051 Evaluate side-chains 150 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 95 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 575 GLN ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN G 94 ASN G 99 ASN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.054995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.046063 restraints weight = 116209.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.047365 restraints weight = 67538.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.048259 restraints weight = 46430.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.048784 restraints weight = 35767.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.049278 restraints weight = 30317.456| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 21441 Z= 0.210 Angle : 0.823 16.094 29406 Z= 0.380 Chirality : 0.049 0.717 3657 Planarity : 0.004 0.040 3474 Dihedral : 8.319 54.335 5661 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.14 % Allowed : 0.62 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.17), residues: 2328 helix: 1.29 (0.28), residues: 366 sheet: 0.13 (0.18), residues: 741 loop : 0.33 (0.19), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 61 TYR 0.031 0.002 TYR G 217 PHE 0.013 0.001 PHE T 62 TRP 0.047 0.002 TRP I 628 HIS 0.009 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00459 (21249) covalent geometry : angle 0.73400 (28869) SS BOND : bond 0.00250 ( 39) SS BOND : angle 1.12500 ( 78) hydrogen bonds : bond 0.04078 ( 729) hydrogen bonds : angle 5.36792 ( 2025) link_ALPHA1-2 : bond 0.00144 ( 6) link_ALPHA1-2 : angle 1.95519 ( 18) link_ALPHA1-3 : bond 0.00870 ( 18) link_ALPHA1-3 : angle 1.88559 ( 54) link_ALPHA1-6 : bond 0.00941 ( 15) link_ALPHA1-6 : angle 2.67987 ( 45) link_BETA1-4 : bond 0.00370 ( 54) link_BETA1-4 : angle 2.11033 ( 162) link_NAG-ASN : bond 0.00312 ( 60) link_NAG-ASN : angle 4.06102 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 193 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8073 (ttp) cc_final: 0.7763 (ttm) REVERT: A 98 ASN cc_start: 0.9130 (t0) cc_final: 0.8884 (t0) REVERT: A 104 MET cc_start: 0.9311 (tpp) cc_final: 0.9013 (tpt) REVERT: A 150 MET cc_start: 0.8398 (mmm) cc_final: 0.7979 (mmm) REVERT: B 530 MET cc_start: 0.7767 (mmp) cc_final: 0.6885 (mmp) REVERT: B 546 SER cc_start: 0.8750 (m) cc_final: 0.8216 (p) REVERT: B 548 ILE cc_start: 0.7488 (tp) cc_final: 0.7279 (tp) REVERT: B 584 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8416 (tm-30) REVERT: B 610 TRP cc_start: 0.7141 (p-90) cc_final: 0.6489 (p-90) REVERT: H 45 LEU cc_start: 0.9360 (mt) cc_final: 0.9098 (mt) REVERT: H 71 TRP cc_start: 0.8458 (p-90) cc_final: 0.7986 (p-90) REVERT: H 80 MET cc_start: 0.8979 (tmm) cc_final: 0.8697 (tmm) REVERT: H 82 LEU cc_start: 0.9262 (mt) cc_final: 0.9032 (mt) REVERT: L 33 LEU cc_start: 0.9572 (tp) cc_final: 0.9141 (tp) REVERT: L 34 ASN cc_start: 0.9224 (m-40) cc_final: 0.8270 (t0) REVERT: F 150 MET cc_start: 0.7926 (mmm) cc_final: 0.7559 (mmm) REVERT: I 546 SER cc_start: 0.8753 (m) cc_final: 0.8155 (p) REVERT: I 574 LYS cc_start: 0.9216 (mtpt) cc_final: 0.8920 (mttp) REVERT: I 584 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8402 (tm-30) REVERT: I 610 TRP cc_start: 0.7463 (p-90) cc_final: 0.6443 (p-90) REVERT: I 626 MET cc_start: 0.7869 (ptp) cc_final: 0.7269 (ptt) REVERT: R 71 TRP cc_start: 0.8269 (p-90) cc_final: 0.7992 (p-90) REVERT: R 80 MET cc_start: 0.8974 (tmm) cc_final: 0.8751 (tmm) REVERT: T 4 MET cc_start: 0.8188 (ptp) cc_final: 0.7557 (ptt) REVERT: T 33 LEU cc_start: 0.9640 (tp) cc_final: 0.9269 (tp) REVERT: T 34 ASN cc_start: 0.9042 (m-40) cc_final: 0.8775 (t0) REVERT: T 42 LYS cc_start: 0.9343 (mtmt) cc_final: 0.9087 (ptmm) REVERT: G 98 ASN cc_start: 0.9070 (t0) cc_final: 0.8747 (t0) REVERT: G 150 MET cc_start: 0.8183 (mmm) cc_final: 0.7927 (mmm) REVERT: J 530 MET cc_start: 0.8829 (mmm) cc_final: 0.8609 (mmm) REVERT: J 543 ASN cc_start: 0.8895 (m-40) cc_final: 0.8632 (m-40) REVERT: J 571 TRP cc_start: 0.7812 (m-10) cc_final: 0.7436 (m-10) REVERT: J 584 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8256 (tm-30) REVERT: J 610 TRP cc_start: 0.7374 (p-90) cc_final: 0.6460 (p-90) REVERT: S 23 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8297 (mm-30) REVERT: S 71 TRP cc_start: 0.8348 (p-90) cc_final: 0.8033 (p-90) REVERT: U 42 LYS cc_start: 0.9315 (mtmt) cc_final: 0.8899 (ptmm) REVERT: U 47 LEU cc_start: 0.9210 (mp) cc_final: 0.8991 (mp) REVERT: U 69 GLN cc_start: 0.8123 (pm20) cc_final: 0.7880 (pm20) outliers start: 3 outliers final: 0 residues processed: 196 average time/residue: 0.1419 time to fit residues: 44.4561 Evaluate side-chains 155 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 19 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 164 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN F 99 ASN F 425 ASN R 28 ASN G 99 ASN G 293 GLN S 28 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.056159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.047134 restraints weight = 114232.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.048486 restraints weight = 64724.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.049429 restraints weight = 44029.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.050115 restraints weight = 33468.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.050593 restraints weight = 27384.433| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21441 Z= 0.129 Angle : 0.779 15.876 29406 Z= 0.361 Chirality : 0.048 0.659 3657 Planarity : 0.004 0.036 3474 Dihedral : 7.874 54.951 5661 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2328 helix: 1.52 (0.29), residues: 369 sheet: 0.23 (0.18), residues: 777 loop : 0.45 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 61 TYR 0.030 0.001 TYR G 217 PHE 0.021 0.001 PHE G 233 TRP 0.035 0.002 TRP I 628 HIS 0.007 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00272 (21249) covalent geometry : angle 0.68987 (28869) SS BOND : bond 0.00321 ( 39) SS BOND : angle 1.09205 ( 78) hydrogen bonds : bond 0.03826 ( 729) hydrogen bonds : angle 5.22635 ( 2025) link_ALPHA1-2 : bond 0.00341 ( 6) link_ALPHA1-2 : angle 1.78107 ( 18) link_ALPHA1-3 : bond 0.00921 ( 18) link_ALPHA1-3 : angle 1.81505 ( 54) link_ALPHA1-6 : bond 0.00982 ( 15) link_ALPHA1-6 : angle 2.33011 ( 45) link_BETA1-4 : bond 0.00421 ( 54) link_BETA1-4 : angle 2.03141 ( 162) link_NAG-ASN : bond 0.00328 ( 60) link_NAG-ASN : angle 3.98261 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7962 (ttp) cc_final: 0.7725 (ttm) REVERT: A 98 ASN cc_start: 0.9041 (t0) cc_final: 0.8815 (t0) REVERT: A 104 MET cc_start: 0.9277 (tpp) cc_final: 0.8950 (tpt) REVERT: A 150 MET cc_start: 0.8342 (mmm) cc_final: 0.7957 (mmm) REVERT: B 546 SER cc_start: 0.8748 (m) cc_final: 0.8233 (p) REVERT: B 548 ILE cc_start: 0.7368 (tp) cc_final: 0.7120 (tp) REVERT: B 584 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8454 (tm-30) REVERT: H 45 LEU cc_start: 0.9340 (mt) cc_final: 0.9140 (mt) REVERT: H 71 TRP cc_start: 0.8408 (p-90) cc_final: 0.7968 (p-90) REVERT: H 80 MET cc_start: 0.8968 (tmm) cc_final: 0.8693 (tmm) REVERT: L 21 ILE cc_start: 0.8876 (pt) cc_final: 0.8641 (pt) REVERT: L 33 LEU cc_start: 0.9661 (tp) cc_final: 0.9220 (tp) REVERT: L 34 ASN cc_start: 0.9164 (m-40) cc_final: 0.8421 (t0) REVERT: L 46 LEU cc_start: 0.9041 (pt) cc_final: 0.8344 (tt) REVERT: L 47 LEU cc_start: 0.9246 (mp) cc_final: 0.8998 (mp) REVERT: F 150 MET cc_start: 0.8179 (mmm) cc_final: 0.7832 (mmm) REVERT: I 546 SER cc_start: 0.8688 (m) cc_final: 0.8061 (p) REVERT: I 574 LYS cc_start: 0.9200 (mtpt) cc_final: 0.8849 (mttp) REVERT: I 584 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8322 (tm-30) REVERT: I 610 TRP cc_start: 0.7360 (p-90) cc_final: 0.6489 (p-90) REVERT: I 626 MET cc_start: 0.7365 (ptp) cc_final: 0.6990 (ptp) REVERT: R 71 TRP cc_start: 0.8252 (p-90) cc_final: 0.7929 (p-90) REVERT: R 80 MET cc_start: 0.8961 (tmm) cc_final: 0.8693 (tmm) REVERT: R 98 ASP cc_start: 0.9112 (p0) cc_final: 0.8387 (t0) REVERT: T 33 LEU cc_start: 0.9636 (tp) cc_final: 0.9226 (tp) REVERT: T 34 ASN cc_start: 0.9015 (m-40) cc_final: 0.8721 (t0) REVERT: T 42 LYS cc_start: 0.9456 (mtmt) cc_final: 0.9171 (ptmm) REVERT: G 98 ASN cc_start: 0.8875 (t0) cc_final: 0.8648 (t0) REVERT: G 150 MET cc_start: 0.8093 (mmm) cc_final: 0.7851 (mmm) REVERT: G 217 TYR cc_start: 0.9222 (m-10) cc_final: 0.8774 (m-80) REVERT: J 543 ASN cc_start: 0.8899 (m-40) cc_final: 0.8620 (m-40) REVERT: J 571 TRP cc_start: 0.7715 (m-10) cc_final: 0.7340 (m-10) REVERT: J 584 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8263 (tm-30) REVERT: J 610 TRP cc_start: 0.7105 (p-90) cc_final: 0.6330 (p-90) REVERT: S 23 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8204 (mm-30) REVERT: S 32 TYR cc_start: 0.9011 (m-80) cc_final: 0.8341 (m-80) REVERT: S 71 TRP cc_start: 0.8284 (p-90) cc_final: 0.8013 (p-90) REVERT: S 98 ASP cc_start: 0.9106 (p0) cc_final: 0.8588 (t0) REVERT: U 42 LYS cc_start: 0.9286 (mtmt) cc_final: 0.8863 (ptmm) REVERT: U 47 LEU cc_start: 0.9199 (mp) cc_final: 0.8980 (mp) outliers start: 2 outliers final: 0 residues processed: 220 average time/residue: 0.1476 time to fit residues: 51.0270 Evaluate side-chains 164 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 168 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 195 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 13 optimal weight: 0.3980 chunk 167 optimal weight: 0.2980 chunk 98 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN R 28 ASN G 99 ASN S 28 ASN S 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.047945 restraints weight = 113365.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.049330 restraints weight = 64473.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.050274 restraints weight = 43818.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.050968 restraints weight = 33412.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.051468 restraints weight = 27373.946| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21441 Z= 0.118 Angle : 0.752 15.543 29406 Z= 0.347 Chirality : 0.047 0.625 3657 Planarity : 0.004 0.035 3474 Dihedral : 7.458 55.156 5661 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.10 % Allowed : 0.05 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.18), residues: 2328 helix: 1.59 (0.29), residues: 366 sheet: 0.32 (0.18), residues: 759 loop : 0.52 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 61 TYR 0.038 0.001 TYR G 217 PHE 0.011 0.001 PHE U 62 TRP 0.027 0.002 TRP I 623 HIS 0.005 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00250 (21249) covalent geometry : angle 0.66763 (28869) SS BOND : bond 0.00278 ( 39) SS BOND : angle 1.06156 ( 78) hydrogen bonds : bond 0.03548 ( 729) hydrogen bonds : angle 5.10752 ( 2025) link_ALPHA1-2 : bond 0.00361 ( 6) link_ALPHA1-2 : angle 1.70884 ( 18) link_ALPHA1-3 : bond 0.00872 ( 18) link_ALPHA1-3 : angle 1.76376 ( 54) link_ALPHA1-6 : bond 0.00981 ( 15) link_ALPHA1-6 : angle 2.17555 ( 45) link_BETA1-4 : bond 0.00435 ( 54) link_BETA1-4 : angle 1.99179 ( 162) link_NAG-ASN : bond 0.00269 ( 60) link_NAG-ASN : angle 3.78788 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2566.99 seconds wall clock time: 45 minutes 51.34 seconds (2751.34 seconds total)