Starting phenix.real_space_refine on Sun Sep 13 05:08:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5v8m_8644/09_2026/5v8m_8644.cif Found real_map, /net/cci-nas-00/data/ceres_data/5v8m_8644/09_2026/5v8m_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5v8m_8644/09_2026/5v8m_8644.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5v8m_8644/09_2026/5v8m_8644.cif" model { file = "/net/cci-nas-00/data/ceres_data/5v8m_8644/09_2026/5v8m_8644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5v8m_8644/09_2026/5v8m_8644.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5v8m_8644/09_2026/5v8m_8644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5v8m_8644/09_2026/5v8m_8644.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 5.19, per 1000 atoms: 0.25 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: 2.65 Conformation dependent library (CDL) restraints added in 845.6 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: 0.98 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: 5.53 Time building geometry restraints manager: 3.30 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 - 16.06: 11026 16.06 - 32.12: 355 32.12 - 48.18: 85 48.18 - 64.24: 69 64.24 - 80.31: 6 Dihedral angle restraints: 11541 sinusoidal: 4689 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 11538 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.140 Find NCS groups from input model: 0.830 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 : 10.052 80.305 7002 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/Z covalent geometry : bond 0.01548 / 0.97 (21249) covalent geometry : angle 1.86044 / 1.16 (28869) SS BOND : bond 0.05067 / 2.67 ( 39) SS BOND : angle 2.92557 / 1.85 ( 78) hydrogen bonds : bond 0.16905 / 11.15 ( 729) hydrogen bonds : angle 8.97720 / 6.15 ( 2025) link_ALPHA1-2 : bond 0.02155 / 1.30 ( 6) link_ALPHA1-2 : angle 3.75042 / 2.36 ( 18) link_ALPHA1-3 : bond 0.03218 / 2.02 ( 18) link_ALPHA1-3 : angle 3.19944 / 2.23 ( 54) link_ALPHA1-6 : bond 0.02868 / 1.79 ( 15) link_ALPHA1-6 : angle 6.75404 / 4.66 ( 45) link_BETA1-4 : bond 0.03127 / 1.92 ( 54) link_BETA1-4 : angle 5.05798 / 3.42 ( 162) link_NAG-ASN : bond 0.02690 / 1.71 ( 60) link_NAG-ASN : angle 10.96745 / 7.76 ( 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 : 0.888 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: 0.8919 (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: 0.8249 (p) cc_final: 0.8045 (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: 0.8137 (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: 0.1625 time to fit residues: 95.8444 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 : 0.772 ------------------------------------------------------------------------------- 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... 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 = 0.3254 r_free = 0.3254 target = 0.059875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.050918 restraints weight = 112160.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.052372 restraints weight = 63720.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.053372 restraints weight = 42902.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.054070 restraints weight = 32387.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.054623 restraints weight = 26232.720| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21441 Z= 0.196 Angle : 0.988 19.217 29406 Z= 0.455 Chirality : 0.048 0.294 3657 Planarity : 0.006 0.078 3474 Dihedral : 5.977 31.878 2556 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.38 % Allowed : 1.01 % Favored : 98.61 % 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: 1.94 (0.18), residues: 2328 helix: 1.18 (0.27), residues: 372 sheet: 0.48 (0.18), residues: 732 loop : 2.16 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 585 TYR 0.018 0.002 TYR J 586 PHE 0.018 0.002 PHE U 62 TRP 0.022 0.002 TRP S 103 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (21249) covalent geometry : angle 0.85864 / 0.43 (28869) SS BOND : bond 0.00233 / 0.15 ( 39) SS BOND : angle 0.96565 / 0.66 ( 78) hydrogen bonds : bond 0.05411 / 3.58 ( 729) hydrogen bonds : angle 6.66453 / 4.62 ( 2025) link_ALPHA1-2 : bond 0.00123 / 0.06 ( 6) link_ALPHA1-2 : angle 1.82093 / 1.18 ( 18) link_ALPHA1-3 : bond 0.00544 / 0.33 ( 18) link_ALPHA1-3 : angle 1.70893 / 1.21 ( 54) link_ALPHA1-6 : bond 0.00596 / 0.33 ( 15) link_ALPHA1-6 : angle 1.76797 / 1.18 ( 45) link_BETA1-4 : bond 0.00792 / 0.55 ( 54) link_BETA1-4 : angle 2.40577 / 1.64 ( 162) link_NAG-ASN : bond 0.00578 / 0.34 ( 60) link_NAG-ASN : angle 5.80160 / 4.08 ( 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 319 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 311 time to evaluate : 0.828 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: A 150 MET cc_start: 0.8361 (mmm) cc_final: 0.7979 (mmm) REVERT: A 434 MET cc_start: 0.8419 (ppp) cc_final: 0.7819 (ppp) REVERT: B 530 MET cc_start: 0.7906 (ttm) cc_final: 0.7416 (ttm) REVERT: B 584 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8043 (tm-30) REVERT: B 610 TRP cc_start: 0.7251 (p-90) cc_final: 0.6856 (p-90) REVERT: B 633 LYS cc_start: 0.9269 (mttt) cc_final: 0.8881 (tppt) REVERT: H 5 LEU cc_start: 0.8895 (tp) cc_final: 0.8687 (tt) REVERT: H 23 GLU cc_start: 0.8016 (mp0) cc_final: 0.7760 (mp0) REVERT: H 43 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8259 (mp-120) REVERT: H 71 TRP cc_start: 0.8219 (p-90) cc_final: 0.7808 (p-90) REVERT: H 80 MET cc_start: 0.8645 (tmm) cc_final: 0.8298 (tmm) REVERT: H 100 TRP cc_start: 0.9421 (m-10) cc_final: 0.8884 (m-10) REVERT: L 33 LEU cc_start: 0.9575 (tp) cc_final: 0.9024 (tp) REVERT: L 34 ASN cc_start: 0.8724 (m-40) cc_final: 0.8418 (t0) REVERT: L 46 LEU cc_start: 0.8089 (tt) cc_final: 0.7044 (tt) REVERT: L 62 PHE cc_start: 0.9083 (m-10) cc_final: 0.8877 (m-80) REVERT: F 434 MET cc_start: 0.8523 (ptm) cc_final: 0.8248 (ptm) REVERT: I 530 MET cc_start: 0.8158 (ttm) cc_final: 0.7747 (ttm) REVERT: I 584 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8087 (tm-30) REVERT: I 610 TRP cc_start: 0.6470 (p-90) cc_final: 0.6241 (p-90) REVERT: I 626 MET cc_start: 0.7398 (ptp) cc_final: 0.7088 (ptt) REVERT: I 648 GLU cc_start: 0.8934 (tp30) cc_final: 0.8318 (tp30) REVERT: R 71 TRP cc_start: 0.7956 (p-90) cc_final: 0.7446 (p-90) REVERT: R 80 MET cc_start: 0.8711 (tmm) cc_final: 0.8429 (tmm) REVERT: R 100 TRP cc_start: 0.9438 (m-10) cc_final: 0.8630 (m-10) REVERT: T 33 LEU cc_start: 0.9561 (tp) cc_final: 0.9015 (tp) REVERT: T 34 ASN cc_start: 0.8389 (m-40) cc_final: 0.8078 (t0) REVERT: T 46 LEU cc_start: 0.8107 (tt) cc_final: 0.7227 (tt) REVERT: G 217 TYR cc_start: 0.7640 (m-80) cc_final: 0.7399 (m-80) REVERT: J 574 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8686 (mtmm) REVERT: J 584 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7968 (tm-30) REVERT: J 610 TRP cc_start: 0.7412 (p-90) cc_final: 0.6838 (p-90) REVERT: J 626 MET cc_start: 0.7481 (ptp) cc_final: 0.7201 (ptp) REVERT: J 634 GLU cc_start: 0.8640 (tt0) cc_final: 0.8426 (mt-10) REVERT: J 648 GLU cc_start: 0.8891 (tp30) cc_final: 0.8343 (tp30) REVERT: S 71 TRP cc_start: 0.8158 (p-90) cc_final: 0.7678 (p-90) REVERT: S 82 LYS cc_start: 0.8601 (mttt) cc_final: 0.8277 (mptt) REVERT: S 100 TRP cc_start: 0.9344 (m-10) cc_final: 0.8797 (m-10) REVERT: S 109 VAL cc_start: 0.9448 (t) cc_final: 0.9107 (t) REVERT: U 62 PHE cc_start: 0.9066 (m-10) cc_final: 0.8739 (m-80) outliers start: 8 outliers final: 2 residues processed: 319 average time/residue: 0.1459 time to fit residues: 71.6630 Evaluate side-chains 201 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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: 10.0000 chunk 104 optimal weight: 6.9990 chunk 210 optimal weight: 0.0370 chunk 93 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN B 618 ASN L 24 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 ASN R 59 ASN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 374 HIS ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 618 ASN S 28 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.057248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.048287 restraints weight = 115604.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049599 restraints weight = 66737.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.050526 restraints weight = 46191.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.051144 restraints weight = 35428.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.051632 restraints weight = 29381.016| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21441 Z= 0.224 Angle : 0.911 21.534 29406 Z= 0.422 Chirality : 0.054 1.173 3657 Planarity : 0.005 0.040 3474 Dihedral : 5.784 29.897 2556 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.19 % Allowed : 1.29 % Favored : 98.52 % 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: 1.29 (0.17), residues: 2328 helix: 1.26 (0.27), residues: 366 sheet: 0.24 (0.17), residues: 726 loop : 1.37 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 585 TYR 0.021 0.002 TYR U 49 PHE 0.029 0.002 PHE R 73 TRP 0.018 0.002 TRP S 103 HIS 0.005 0.001 HIS F 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 (21249) covalent geometry : angle 0.81463 / 0.40 (28869) SS BOND : bond 0.00275 / 0.15 ( 39) SS BOND : angle 0.99625 / 0.65 ( 78) hydrogen bonds : bond 0.04628 / 3.05 ( 729) hydrogen bonds : angle 5.90140 / 4.13 ( 2025) link_ALPHA1-2 : bond 0.00156 / 0.07 ( 6) link_ALPHA1-2 : angle 1.93896 / 1.20 ( 18) link_ALPHA1-3 : bond 0.00403 / 0.25 ( 18) link_ALPHA1-3 : angle 1.61866 / 1.14 ( 54) link_ALPHA1-6 : bond 0.00546 / 0.33 ( 15) link_ALPHA1-6 : angle 1.93970 / 1.32 ( 45) link_BETA1-4 : bond 0.00652 / 0.44 ( 54) link_BETA1-4 : angle 2.16490 / 1.52 ( 162) link_NAG-ASN : bond 0.00602 / 0.34 ( 60) link_NAG-ASN : angle 4.71749 / 3.28 ( 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 : 0.762 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: A 104 MET cc_start: 0.8880 (tpp) cc_final: 0.8445 (tpp) REVERT: A 150 MET cc_start: 0.8508 (mmm) cc_final: 0.8135 (mmm) REVERT: A 377 ASN cc_start: 0.8522 (t0) cc_final: 0.8322 (t0) REVERT: A 434 MET cc_start: 0.8728 (ppp) cc_final: 0.8037 (ppp) REVERT: B 584 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8118 (tm-30) REVERT: B 626 MET cc_start: 0.7195 (ptm) cc_final: 0.6939 (ptm) REVERT: B 633 LYS cc_start: 0.9483 (mttt) cc_final: 0.9282 (mtpt) REVERT: H 80 MET cc_start: 0.8733 (tmm) cc_final: 0.8512 (tmm) REVERT: L 33 LEU cc_start: 0.9499 (tp) cc_final: 0.9186 (tp) REVERT: L 34 ASN cc_start: 0.9299 (m-40) cc_final: 0.8881 (m-40) REVERT: L 62 PHE cc_start: 0.9219 (m-10) cc_final: 0.8995 (m-80) REVERT: F 95 MET cc_start: 0.7936 (ttp) cc_final: 0.7616 (ttm) REVERT: F 434 MET cc_start: 0.8800 (ptm) cc_final: 0.8447 (ptm) REVERT: I 530 MET cc_start: 0.8091 (ttm) cc_final: 0.7630 (ttm) REVERT: I 584 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8077 (tm-30) REVERT: I 610 TRP cc_start: 0.6789 (p-90) cc_final: 0.6407 (p-90) REVERT: I 626 MET cc_start: 0.7299 (ptp) cc_final: 0.6925 (ptt) REVERT: I 633 LYS cc_start: 0.9070 (mtpt) cc_final: 0.8853 (tppp) REVERT: R 82 LYS cc_start: 0.8498 (mttt) cc_final: 0.8145 (mmtt) REVERT: T 33 LEU cc_start: 0.9599 (tp) cc_final: 0.9212 (tp) REVERT: T 34 ASN cc_start: 0.9199 (m-40) cc_final: 0.8885 (m-40) REVERT: T 53 LYS cc_start: 0.9429 (mtmm) cc_final: 0.9061 (ptmt) REVERT: G 150 MET cc_start: 0.8450 (mmm) cc_final: 0.8216 (mmm) REVERT: G 217 TYR cc_start: 0.7868 (m-80) cc_final: 0.7570 (m-10) REVERT: G 434 MET cc_start: 0.9068 (ptm) cc_final: 0.8743 (ppp) REVERT: J 574 LYS cc_start: 0.8922 (mtpt) cc_final: 0.8698 (mtmm) REVERT: J 584 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8097 (tm-30) REVERT: J 610 TRP cc_start: 0.7347 (p-90) cc_final: 0.6413 (p-90) REVERT: J 633 LYS cc_start: 0.9177 (mtpt) cc_final: 0.8813 (tppp) REVERT: S 82 LYS cc_start: 0.8568 (mttt) cc_final: 0.8272 (mmtt) outliers start: 4 outliers final: 0 residues processed: 264 average time/residue: 0.1477 time to fit residues: 59.8834 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 : 0.767 ------------------------------------------------------------------------------- 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: 9.9990 chunk 112 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 161 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN B 651 ASN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 ASN I 640 GLN ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.054951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.046108 restraints weight = 116688.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.047375 restraints weight = 67876.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.048167 restraints weight = 46980.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.048834 restraints weight = 36942.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.049280 restraints weight = 30442.989| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 21441 Z= 0.302 Angle : 0.927 18.353 29406 Z= 0.431 Chirality : 0.051 0.858 3657 Planarity : 0.005 0.037 3474 Dihedral : 5.863 31.198 2556 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.19 % Allowed : 2.20 % Favored : 97.61 % 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: 0.64 (0.17), residues: 2328 helix: 0.91 (0.26), residues: 387 sheet: -0.08 (0.17), residues: 726 loop : 0.80 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 298 TYR 0.016 0.002 TYR L 36 PHE 0.019 0.002 PHE H 73 TRP 0.021 0.002 TRP B 631 HIS 0.009 0.002 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.30 (21249) covalent geometry : angle 0.84739 / 0.41 (28869) SS BOND : bond 0.00263 / 0.16 ( 39) SS BOND : angle 1.00331 / 0.68 ( 78) hydrogen bonds : bond 0.04720 / 3.07 ( 729) hydrogen bonds : angle 5.82866 / 4.12 ( 2025) link_ALPHA1-2 : bond 0.00186 / 0.10 ( 6) link_ALPHA1-2 : angle 2.05911 / 1.17 ( 18) link_ALPHA1-3 : bond 0.00410 / 0.26 ( 18) link_ALPHA1-3 : angle 1.61905 / 1.13 ( 54) link_ALPHA1-6 : bond 0.00582 / 0.36 ( 15) link_ALPHA1-6 : angle 2.04589 / 1.37 ( 45) link_BETA1-4 : bond 0.00435 / 0.31 ( 54) link_BETA1-4 : angle 2.09954 / 1.44 ( 162) link_NAG-ASN : bond 0.00584 / 0.36 ( 60) link_NAG-ASN : angle 4.29122 / 2.96 ( 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 215 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.9045 (mm) REVERT: B 548 ILE cc_start: 0.7601 (tp) cc_final: 0.7357 (tp) REVERT: B 584 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8226 (tm-30) REVERT: B 610 TRP cc_start: 0.7583 (p-90) cc_final: 0.7087 (p-90) REVERT: B 633 LYS cc_start: 0.9488 (mttt) cc_final: 0.9216 (mtpt) REVERT: H 80 MET cc_start: 0.8861 (tmm) cc_final: 0.8616 (tmm) REVERT: H 82 LYS cc_start: 0.8759 (mttt) cc_final: 0.8475 (mmtt) REVERT: L 33 LEU cc_start: 0.9693 (tp) cc_final: 0.9145 (tp) REVERT: L 34 ASN cc_start: 0.9288 (m-40) cc_final: 0.8766 (t0) REVERT: L 42 LYS cc_start: 0.9326 (mtmt) cc_final: 0.9106 (mtmm) REVERT: L 46 LEU cc_start: 0.8240 (tt) cc_final: 0.7985 (tt) REVERT: L 62 PHE cc_start: 0.9234 (m-10) cc_final: 0.8927 (m-80) REVERT: L 87 PHE cc_start: 0.7413 (m-10) cc_final: 0.7128 (m-10) REVERT: F 95 MET cc_start: 0.8118 (ttp) cc_final: 0.7540 (ttm) REVERT: F 434 MET cc_start: 0.8998 (ptm) cc_final: 0.8669 (ptm) REVERT: I 548 ILE cc_start: 0.7695 (tp) cc_final: 0.7491 (tp) REVERT: I 584 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8306 (tm-30) REVERT: I 610 TRP cc_start: 0.7565 (p-90) cc_final: 0.7005 (p-90) REVERT: T 33 LEU cc_start: 0.9662 (tp) cc_final: 0.9152 (tp) REVERT: T 34 ASN cc_start: 0.9221 (m-40) cc_final: 0.8768 (t0) REVERT: T 46 LEU cc_start: 0.8435 (tt) cc_final: 0.7701 (tt) REVERT: T 62 PHE cc_start: 0.9284 (m-80) cc_final: 0.9055 (m-80) REVERT: J 574 LYS cc_start: 0.9003 (mtpt) cc_final: 0.8742 (mtmm) REVERT: J 584 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8251 (tm-30) REVERT: J 610 TRP cc_start: 0.7409 (p-90) cc_final: 0.6522 (p-90) REVERT: J 626 MET cc_start: 0.8149 (ptp) cc_final: 0.7776 (ptp) REVERT: J 633 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8919 (tppp) REVERT: S 71 TRP cc_start: 0.8317 (p-90) cc_final: 0.7832 (p-90) REVERT: U 42 LYS cc_start: 0.9279 (mtmm) cc_final: 0.8984 (ptmm) outliers start: 4 outliers final: 1 residues processed: 215 average time/residue: 0.1353 time to fit residues: 45.5021 Evaluate side-chains 157 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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: 2.9990 chunk 128 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN H 108 GLN F 293 GLN ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN R 108 GLN G 293 GLN ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 ASN U 24 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.056644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.047833 restraints weight = 113025.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.049146 restraints weight = 65031.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.050047 restraints weight = 44563.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.050692 restraints weight = 34087.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.051177 restraints weight = 28106.555| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21441 Z= 0.130 Angle : 0.783 18.258 29406 Z= 0.361 Chirality : 0.048 0.744 3657 Planarity : 0.004 0.035 3474 Dihedral : 5.452 32.541 2556 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.19 % Allowed : 1.34 % Favored : 98.47 % 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: 1.02 (0.18), residues: 2328 helix: 1.59 (0.28), residues: 363 sheet: 0.17 (0.17), residues: 792 loop : 0.97 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 298 TYR 0.026 0.001 TYR T 49 PHE 0.017 0.001 PHE U 62 TRP 0.011 0.002 TRP S 103 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (21249) covalent geometry : angle 0.68683 / 0.34 (28869) SS BOND : bond 0.00244 / 0.15 ( 39) SS BOND : angle 0.66499 / 0.47 ( 78) hydrogen bonds : bond 0.04154 / 2.76 ( 729) hydrogen bonds : angle 5.41421 / 3.81 ( 2025) link_ALPHA1-2 : bond 0.00280 / 0.15 ( 6) link_ALPHA1-2 : angle 1.69098 / 1.07 ( 18) link_ALPHA1-3 : bond 0.00585 / 0.36 ( 18) link_ALPHA1-3 : angle 1.49517 / 1.01 ( 54) link_ALPHA1-6 : bond 0.00537 / 0.29 ( 15) link_ALPHA1-6 : angle 1.76050 / 1.20 ( 45) link_BETA1-4 : bond 0.00353 / 0.22 ( 54) link_BETA1-4 : angle 2.03874 / 1.41 ( 162) link_NAG-ASN : bond 0.00261 / 0.16 ( 60) link_NAG-ASN : angle 4.32602 / 3.04 ( 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 242 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 238 time to evaluate : 0.588 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: A 150 MET cc_start: 0.8302 (mmm) cc_final: 0.7768 (mmm) REVERT: B 548 ILE cc_start: 0.7546 (tp) cc_final: 0.7324 (tp) REVERT: B 571 TRP cc_start: 0.7746 (m-10) cc_final: 0.7467 (m-10) REVERT: B 584 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8254 (tm-30) REVERT: B 626 MET cc_start: 0.7289 (ptm) cc_final: 0.6864 (ptp) REVERT: H 71 TRP cc_start: 0.8227 (p-90) cc_final: 0.7768 (p-90) REVERT: H 80 MET cc_start: 0.8935 (tmm) cc_final: 0.8595 (tmm) REVERT: H 82 LYS cc_start: 0.8721 (mttt) cc_final: 0.8464 (mmtt) REVERT: L 62 PHE cc_start: 0.9103 (m-10) cc_final: 0.8720 (m-80) REVERT: L 87 PHE cc_start: 0.7397 (m-10) cc_final: 0.7132 (m-10) REVERT: F 95 MET cc_start: 0.7843 (ttp) cc_final: 0.7577 (ttm) REVERT: F 150 MET cc_start: 0.8421 (mmm) cc_final: 0.7954 (mmm) REVERT: F 434 MET cc_start: 0.8921 (ptm) cc_final: 0.8592 (ptm) REVERT: I 584 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8278 (tm-30) REVERT: I 610 TRP cc_start: 0.7301 (p-90) cc_final: 0.6765 (p-90) REVERT: R 71 TRP cc_start: 0.8200 (p-90) cc_final: 0.7829 (p-90) REVERT: R 80 MET cc_start: 0.8988 (tmm) cc_final: 0.8673 (tmm) REVERT: T 33 LEU cc_start: 0.9641 (tp) cc_final: 0.9161 (tp) REVERT: T 34 ASN cc_start: 0.9210 (m-40) cc_final: 0.8577 (t0) REVERT: T 46 LEU cc_start: 0.7937 (tt) cc_final: 0.7313 (tt) REVERT: G 107 ASP cc_start: 0.8608 (t0) cc_final: 0.8363 (t0) REVERT: J 530 MET cc_start: 0.8786 (mmm) cc_final: 0.8491 (mmm) REVERT: J 569 THR cc_start: 0.8265 (m) cc_final: 0.8028 (t) REVERT: J 574 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8716 (mttp) REVERT: J 584 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8222 (tm-30) REVERT: J 586 TYR cc_start: 0.8973 (t80) cc_final: 0.8672 (t80) REVERT: J 610 TRP cc_start: 0.7226 (p-90) cc_final: 0.6512 (p-90) REVERT: J 633 LYS cc_start: 0.9156 (mtpt) cc_final: 0.8921 (tppp) REVERT: S 23 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7986 (mp0) REVERT: S 31 ASP cc_start: 0.8051 (t0) cc_final: 0.7808 (t0) REVERT: S 32 TYR cc_start: 0.9078 (m-80) cc_final: 0.8433 (m-80) REVERT: S 71 TRP cc_start: 0.8282 (p-90) cc_final: 0.7846 (p-90) REVERT: U 42 LYS cc_start: 0.9354 (mtmm) cc_final: 0.9000 (ptmm) REVERT: U 46 LEU cc_start: 0.8776 (pt) cc_final: 0.8410 (tt) outliers start: 4 outliers final: 1 residues processed: 242 average time/residue: 0.1376 time to fit residues: 52.4035 Evaluate side-chains 168 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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: 10.0000 chunk 50 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 203 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN F 130 GLN F 203 GLN F 425 ASN ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN G 94 ASN G 99 ASN G 130 GLN G 203 GLN ** G 377 ASN ** 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** U 26 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.054252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.045412 restraints weight = 118254.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.046664 restraints weight = 69632.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.047511 restraints weight = 48339.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.048123 restraints weight = 37567.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.048561 restraints weight = 31325.264| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 21441 Z= 0.313 Angle : 0.937 16.319 29406 Z= 0.433 Chirality : 0.051 0.757 3657 Planarity : 0.005 0.091 3474 Dihedral : 5.780 29.841 2556 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.14 % Allowed : 1.48 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.17), residues: 2328 helix: 1.00 (0.27), residues: 366 sheet: -0.11 (0.17), residues: 759 loop : 0.46 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG T 65 TYR 0.022 0.002 TYR A 217 PHE 0.022 0.002 PHE F 53 TRP 0.031 0.003 TRP J 571 HIS 0.009 0.002 HIS G 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.31 (21249) covalent geometry : angle 0.85909 / 0.42 (28869) SS BOND : bond 0.00380 / 0.27 ( 39) SS BOND : angle 0.98237 / 0.66 ( 78) hydrogen bonds : bond 0.04591 / 2.98 ( 729) hydrogen bonds : angle 5.65543 / 4.02 ( 2025) link_ALPHA1-2 : bond 0.00259 / 0.14 ( 6) link_ALPHA1-2 : angle 2.10702 / 1.18 ( 18) link_ALPHA1-3 : bond 0.00462 / 0.29 ( 18) link_ALPHA1-3 : angle 1.70398 / 1.19 ( 54) link_ALPHA1-6 : bond 0.00596 / 0.37 ( 15) link_ALPHA1-6 : angle 2.18740 / 1.47 ( 45) link_BETA1-4 : bond 0.00417 / 0.29 ( 54) link_BETA1-4 : angle 2.10267 / 1.43 ( 162) link_NAG-ASN : bond 0.00683 / 0.39 ( 60) link_NAG-ASN : angle 4.25724 / 2.95 ( 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 197 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.749 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: A 150 MET cc_start: 0.8402 (mmm) cc_final: 0.7906 (mmm) REVERT: B 530 MET cc_start: 0.8696 (mmp) cc_final: 0.8061 (mmp) REVERT: B 546 SER cc_start: 0.8748 (m) cc_final: 0.8276 (p) REVERT: B 584 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8285 (tm-30) REVERT: B 610 TRP cc_start: 0.7304 (p-90) cc_final: 0.6675 (p-90) REVERT: B 626 MET cc_start: 0.7544 (ptm) cc_final: 0.7118 (ptp) REVERT: B 633 LYS cc_start: 0.9316 (mmmt) cc_final: 0.8928 (mtpt) REVERT: H 45 LEU cc_start: 0.9251 (mt) cc_final: 0.9001 (mt) REVERT: L 33 LEU cc_start: 0.9636 (tp) cc_final: 0.9144 (tp) REVERT: L 34 ASN cc_start: 0.9385 (m-40) cc_final: 0.8834 (t0) REVERT: L 46 LEU cc_start: 0.8573 (tt) cc_final: 0.8268 (tt) REVERT: L 87 PHE cc_start: 0.7131 (m-10) cc_final: 0.6794 (m-10) REVERT: F 95 MET cc_start: 0.8039 (ttp) cc_final: 0.7466 (ttm) REVERT: F 150 MET cc_start: 0.8617 (mmm) cc_final: 0.8325 (mmm) REVERT: F 434 MET cc_start: 0.8908 (ptm) cc_final: 0.8623 (ptm) REVERT: I 546 SER cc_start: 0.8850 (m) cc_final: 0.8294 (p) REVERT: I 584 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8285 (tm-30) REVERT: I 610 TRP cc_start: 0.7389 (p-90) cc_final: 0.6503 (p-90) REVERT: I 626 MET cc_start: 0.7866 (ptp) cc_final: 0.7642 (ptt) REVERT: R 71 TRP cc_start: 0.8319 (p-90) cc_final: 0.7875 (p-90) REVERT: T 33 LEU cc_start: 0.9602 (tp) cc_final: 0.9298 (tp) REVERT: T 34 ASN cc_start: 0.9265 (m-40) cc_final: 0.8906 (m-40) REVERT: G 434 MET cc_start: 0.8813 (ptm) cc_final: 0.8536 (ptm) REVERT: J 530 MET cc_start: 0.8890 (mmm) cc_final: 0.8622 (mmm) REVERT: J 569 THR cc_start: 0.8512 (m) cc_final: 0.8299 (t) REVERT: J 584 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8243 (tm-30) REVERT: J 610 TRP cc_start: 0.7386 (p-90) cc_final: 0.6427 (p-90) REVERT: J 633 LYS cc_start: 0.9202 (mtpt) cc_final: 0.8991 (tppp) REVERT: S 71 TRP cc_start: 0.8418 (p-90) cc_final: 0.7963 (p-90) REVERT: U 33 LEU cc_start: 0.9573 (tp) cc_final: 0.9344 (tp) outliers start: 3 outliers final: 0 residues processed: 197 average time/residue: 0.1348 time to fit residues: 42.0857 Evaluate side-chains 145 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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: 2.9990 chunk 188 optimal weight: 0.0010 chunk 113 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 202 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN G 99 ASN ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.055771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.046792 restraints weight = 114356.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.048134 restraints weight = 64365.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.049065 restraints weight = 43553.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.049733 restraints weight = 33081.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.050160 restraints weight = 27010.834| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21441 Z= 0.141 Angle : 0.778 17.056 29406 Z= 0.357 Chirality : 0.047 0.678 3657 Planarity : 0.004 0.038 3474 Dihedral : 5.382 28.304 2556 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.05 % Allowed : 1.15 % 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: 0.76 (0.18), residues: 2328 helix: 1.40 (0.28), residues: 366 sheet: 0.24 (0.18), residues: 738 loop : 0.56 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 61 TYR 0.015 0.002 TYR L 36 PHE 0.011 0.001 PHE F 53 TRP 0.050 0.002 TRP J 571 HIS 0.005 0.001 HIS F 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (21249) covalent geometry : angle 0.68173 / 0.34 (28869) SS BOND : bond 0.00329 / 0.23 ( 39) SS BOND : angle 0.95047 / 0.68 ( 78) hydrogen bonds : bond 0.03997 / 2.64 ( 729) hydrogen bonds : angle 5.30344 / 3.76 ( 2025) link_ALPHA1-2 : bond 0.00240 / 0.12 ( 6) link_ALPHA1-2 : angle 1.70110 / 1.05 ( 18) link_ALPHA1-3 : bond 0.00565 / 0.35 ( 18) link_ALPHA1-3 : angle 1.51631 / 1.04 ( 54) link_ALPHA1-6 : bond 0.00559 / 0.32 ( 15) link_ALPHA1-6 : angle 1.82028 / 1.25 ( 45) link_BETA1-4 : bond 0.00312 / 0.20 ( 54) link_BETA1-4 : angle 1.99248 / 1.38 ( 162) link_NAG-ASN : bond 0.00299 / 0.15 ( 60) link_NAG-ASN : angle 4.31436 / 3.00 ( 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 216 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 0.765 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: A 104 MET cc_start: 0.9231 (tpp) cc_final: 0.8802 (tpp) REVERT: A 150 MET cc_start: 0.8357 (mmm) cc_final: 0.7939 (mmm) REVERT: A 217 TYR cc_start: 0.8600 (m-80) cc_final: 0.7735 (m-80) REVERT: B 546 SER cc_start: 0.8621 (m) cc_final: 0.8156 (p) REVERT: B 548 ILE cc_start: 0.7558 (tp) cc_final: 0.7319 (tp) REVERT: B 584 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8342 (tm-30) REVERT: B 633 LYS cc_start: 0.9135 (mtpp) cc_final: 0.8693 (mmmm) REVERT: H 45 LEU cc_start: 0.9352 (mt) cc_final: 0.9092 (mt) REVERT: H 71 TRP cc_start: 0.8416 (p-90) cc_final: 0.7953 (p-90) REVERT: H 80 MET cc_start: 0.8956 (tmm) cc_final: 0.8670 (tmm) REVERT: H 82 LEU cc_start: 0.9250 (mt) cc_final: 0.9030 (mt) REVERT: L 33 LEU cc_start: 0.9644 (tp) cc_final: 0.9268 (tp) REVERT: L 34 ASN cc_start: 0.9285 (m-40) cc_final: 0.8738 (t0) REVERT: L 42 LYS cc_start: 0.9290 (mtmm) cc_final: 0.9024 (ptmm) REVERT: L 46 LEU cc_start: 0.8246 (tt) cc_final: 0.7915 (tt) REVERT: L 47 LEU cc_start: 0.9179 (mm) cc_final: 0.8274 (tp) REVERT: F 95 MET cc_start: 0.7710 (ttp) cc_final: 0.7413 (ttm) REVERT: F 150 MET cc_start: 0.8558 (mmm) cc_final: 0.8267 (mmm) REVERT: I 530 MET cc_start: 0.8270 (mmm) cc_final: 0.7930 (mmm) REVERT: I 546 SER cc_start: 0.8842 (m) cc_final: 0.8220 (p) REVERT: I 584 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8302 (tm-30) REVERT: I 610 TRP cc_start: 0.7280 (p-90) cc_final: 0.6581 (p-90) REVERT: R 71 TRP cc_start: 0.8259 (p-90) cc_final: 0.7917 (p-90) REVERT: R 80 MET cc_start: 0.8987 (tmm) cc_final: 0.8729 (tmm) REVERT: T 33 LEU cc_start: 0.9637 (tp) cc_final: 0.9228 (tp) REVERT: T 34 ASN cc_start: 0.9141 (m-40) cc_final: 0.8740 (t0) REVERT: T 36 TYR cc_start: 0.8430 (m-80) cc_final: 0.7843 (m-80) REVERT: T 42 LYS cc_start: 0.9358 (mtmt) cc_final: 0.9108 (ptmm) REVERT: T 46 LEU cc_start: 0.8392 (tt) cc_final: 0.7448 (tt) REVERT: J 530 MET cc_start: 0.8803 (mmm) cc_final: 0.8515 (mmm) REVERT: J 584 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8207 (tm-30) REVERT: J 610 TRP cc_start: 0.7161 (p-90) cc_final: 0.6324 (p-90) REVERT: J 633 LYS cc_start: 0.9153 (mtpt) cc_final: 0.8927 (tppp) REVERT: S 32 TYR cc_start: 0.8847 (m-80) cc_final: 0.8259 (m-80) REVERT: S 71 TRP cc_start: 0.8335 (p-90) cc_final: 0.8005 (p-90) REVERT: U 42 LYS cc_start: 0.9422 (mtmm) cc_final: 0.9093 (ptmm) REVERT: U 46 LEU cc_start: 0.8879 (pt) cc_final: 0.8451 (tt) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.1331 time to fit residues: 45.6839 Evaluate side-chains 163 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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: 10.0000 chunk 76 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 chunk 167 optimal weight: 0.2980 chunk 82 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 175 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 212 optimal weight: 0.4980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN G 99 ASN ** G 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.056396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.047532 restraints weight = 112750.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.048861 restraints weight = 64707.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.049764 restraints weight = 44200.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.050419 restraints weight = 33804.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.050906 restraints weight = 27847.996| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21441 Z= 0.129 Angle : 0.750 16.535 29406 Z= 0.348 Chirality : 0.046 0.620 3657 Planarity : 0.004 0.035 3474 Dihedral : 5.236 27.320 2556 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.10 % Allowed : 0.43 % Favored : 99.47 % 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: 0.77 (0.18), residues: 2328 helix: 1.57 (0.28), residues: 366 sheet: 0.23 (0.18), residues: 777 loop : 0.53 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 61 TYR 0.016 0.001 TYR L 36 PHE 0.014 0.001 PHE S 73 TRP 0.051 0.002 TRP J 571 HIS 0.004 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (21249) covalent geometry : angle 0.66231 / 0.33 (28869) SS BOND : bond 0.00384 / 0.20 ( 39) SS BOND : angle 0.88689 / 0.63 ( 78) hydrogen bonds : bond 0.03799 / 2.53 ( 729) hydrogen bonds : angle 5.20245 / 3.69 ( 2025) link_ALPHA1-2 : bond 0.00251 / 0.13 ( 6) link_ALPHA1-2 : angle 1.63808 / 1.01 ( 18) link_ALPHA1-3 : bond 0.00566 / 0.35 ( 18) link_ALPHA1-3 : angle 1.49507 / 1.02 ( 54) link_ALPHA1-6 : bond 0.00551 / 0.31 ( 15) link_ALPHA1-6 : angle 1.72311 / 1.19 ( 45) link_BETA1-4 : bond 0.00320 / 0.21 ( 54) link_BETA1-4 : angle 1.82765 / 1.26 ( 162) link_NAG-ASN : bond 0.00280 / 0.19 ( 60) link_NAG-ASN : angle 4.06358 / 2.80 ( 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 227 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 225 time to evaluate : 0.742 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: A 150 MET cc_start: 0.8353 (mmm) cc_final: 0.7949 (mmm) REVERT: B 530 MET cc_start: 0.8329 (mmp) cc_final: 0.7909 (mmp) REVERT: B 546 SER cc_start: 0.8566 (m) cc_final: 0.8102 (p) REVERT: B 548 ILE cc_start: 0.7571 (tp) cc_final: 0.7295 (tp) REVERT: B 584 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8322 (tm-30) REVERT: H 71 TRP cc_start: 0.8393 (p-90) cc_final: 0.7929 (p-90) REVERT: H 80 MET cc_start: 0.8941 (tmm) cc_final: 0.8679 (tmm) REVERT: L 33 LEU cc_start: 0.9690 (tp) cc_final: 0.9291 (tp) REVERT: L 34 ASN cc_start: 0.9326 (m-40) cc_final: 0.8847 (m-40) REVERT: L 42 LYS cc_start: 0.9402 (mtmm) cc_final: 0.9088 (ptmm) REVERT: F 150 MET cc_start: 0.8655 (mmm) cc_final: 0.8336 (mmm) REVERT: I 546 SER cc_start: 0.8786 (m) cc_final: 0.8114 (p) REVERT: I 584 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8281 (tm-30) REVERT: I 610 TRP cc_start: 0.7213 (p-90) cc_final: 0.6668 (p-90) REVERT: I 626 MET cc_start: 0.7786 (ptp) cc_final: 0.7537 (ptt) REVERT: R 71 TRP cc_start: 0.8237 (p-90) cc_final: 0.7894 (p-90) REVERT: R 80 MET cc_start: 0.8960 (tmm) cc_final: 0.8729 (tmm) REVERT: T 33 LEU cc_start: 0.9633 (tp) cc_final: 0.9163 (tp) REVERT: T 34 ASN cc_start: 0.9160 (m-40) cc_final: 0.8728 (t0) REVERT: T 46 LEU cc_start: 0.8376 (tt) cc_final: 0.7566 (tt) REVERT: G 100 MET cc_start: 0.9393 (ttp) cc_final: 0.9172 (ttm) REVERT: G 150 MET cc_start: 0.8276 (mmm) cc_final: 0.7999 (mmm) REVERT: J 530 MET cc_start: 0.8901 (mmm) cc_final: 0.8647 (mmm) REVERT: J 584 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8195 (tm-30) REVERT: J 610 TRP cc_start: 0.7067 (p-90) cc_final: 0.6309 (p-90) REVERT: J 633 LYS cc_start: 0.9127 (mtpt) cc_final: 0.8857 (tppp) REVERT: S 71 TRP cc_start: 0.8283 (p-90) cc_final: 0.7946 (p-90) REVERT: S 105 SER cc_start: 0.9425 (t) cc_final: 0.9210 (m) REVERT: U 42 LYS cc_start: 0.9333 (mtmm) cc_final: 0.9018 (ptmm) REVERT: U 46 LEU cc_start: 0.8971 (pt) cc_final: 0.8559 (tt) outliers start: 2 outliers final: 0 residues processed: 227 average time/residue: 0.1348 time to fit residues: 48.6388 Evaluate side-chains 173 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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: 5.9990 chunk 40 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 207 optimal weight: 0.6980 chunk 179 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 186 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.056117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.047201 restraints weight = 114243.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.048513 restraints weight = 66432.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049432 restraints weight = 45822.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.050092 restraints weight = 35133.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.050535 restraints weight = 28951.845| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21441 Z= 0.154 Angle : 0.754 15.618 29406 Z= 0.351 Chirality : 0.046 0.602 3657 Planarity : 0.004 0.034 3474 Dihedral : 5.210 26.832 2556 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.05 % Allowed : 0.38 % Favored : 99.57 % 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: 0.78 (0.18), residues: 2328 helix: 1.53 (0.28), residues: 366 sheet: 0.28 (0.18), residues: 753 loop : 0.51 (0.19), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 61 TYR 0.029 0.001 TYR G 217 PHE 0.011 0.001 PHE G 233 TRP 0.053 0.002 TRP J 571 HIS 0.003 0.001 HIS G 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (21249) covalent geometry : angle 0.67492 / 0.33 (28869) SS BOND : bond 0.00478 / 0.20 ( 39) SS BOND : angle 1.28762 / 0.90 ( 78) hydrogen bonds : bond 0.03784 / 2.52 ( 729) hydrogen bonds : angle 5.19145 / 3.69 ( 2025) link_ALPHA1-2 : bond 0.00148 / 0.07 ( 6) link_ALPHA1-2 : angle 1.70343 / 1.03 ( 18) link_ALPHA1-3 : bond 0.00530 / 0.33 ( 18) link_ALPHA1-3 : angle 1.51864 / 1.05 ( 54) link_ALPHA1-6 : bond 0.00548 / 0.32 ( 15) link_ALPHA1-6 : angle 1.77680 / 1.22 ( 45) link_BETA1-4 : bond 0.00295 / 0.19 ( 54) link_BETA1-4 : angle 1.77434 / 1.22 ( 162) link_NAG-ASN : bond 0.00240 / 0.14 ( 60) link_NAG-ASN : angle 3.81762 / 2.67 ( 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 220 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8997 (t0) cc_final: 0.8789 (t0) REVERT: A 150 MET cc_start: 0.8343 (mmm) cc_final: 0.7900 (mmm) REVERT: B 546 SER cc_start: 0.8683 (m) cc_final: 0.8232 (p) REVERT: B 548 ILE cc_start: 0.7563 (tp) cc_final: 0.7297 (tp) REVERT: B 584 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8330 (tm-30) REVERT: H 45 LEU cc_start: 0.9360 (mt) cc_final: 0.9143 (mt) REVERT: H 71 TRP cc_start: 0.8446 (p-90) cc_final: 0.7957 (p-90) REVERT: H 80 MET cc_start: 0.8961 (tmm) cc_final: 0.8680 (tmm) REVERT: L 33 LEU cc_start: 0.9655 (tp) cc_final: 0.9178 (tp) REVERT: L 34 ASN cc_start: 0.9344 (m-40) cc_final: 0.8806 (t0) REVERT: L 42 LYS cc_start: 0.9391 (mtmm) cc_final: 0.9059 (ptmm) REVERT: L 46 LEU cc_start: 0.8408 (tt) cc_final: 0.8132 (tt) REVERT: F 150 MET cc_start: 0.8631 (mmm) cc_final: 0.8283 (mmm) REVERT: I 546 SER cc_start: 0.8881 (m) cc_final: 0.8232 (p) REVERT: I 584 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8339 (tm-30) REVERT: I 610 TRP cc_start: 0.7216 (p-90) cc_final: 0.6610 (p-90) REVERT: I 626 MET cc_start: 0.7948 (ptp) cc_final: 0.7737 (ptp) REVERT: R 71 TRP cc_start: 0.8285 (p-90) cc_final: 0.7922 (p-90) REVERT: R 80 MET cc_start: 0.8990 (tmm) cc_final: 0.8743 (tmm) REVERT: T 33 LEU cc_start: 0.9638 (tp) cc_final: 0.9133 (tp) REVERT: T 34 ASN cc_start: 0.9226 (m-40) cc_final: 0.8675 (t0) REVERT: T 36 TYR cc_start: 0.8358 (m-80) cc_final: 0.7773 (m-80) REVERT: T 46 LEU cc_start: 0.8419 (tt) cc_final: 0.7661 (tt) REVERT: G 150 MET cc_start: 0.8092 (mmm) cc_final: 0.7783 (mmm) REVERT: J 530 MET cc_start: 0.8989 (mmm) cc_final: 0.7976 (mtp) REVERT: J 584 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8265 (tm-30) REVERT: J 610 TRP cc_start: 0.7189 (p-90) cc_final: 0.6371 (p-90) REVERT: J 626 MET cc_start: 0.7533 (ptp) cc_final: 0.7222 (ptm) REVERT: S 31 ASP cc_start: 0.8109 (t0) cc_final: 0.7888 (t70) REVERT: S 32 TYR cc_start: 0.9030 (m-80) cc_final: 0.8585 (m-80) REVERT: S 71 TRP cc_start: 0.8323 (p-90) cc_final: 0.7992 (p-90) REVERT: U 42 LYS cc_start: 0.9340 (mtmm) cc_final: 0.9023 (ptmm) REVERT: U 46 LEU cc_start: 0.8901 (pt) cc_final: 0.8507 (tt) REVERT: U 69 GLN cc_start: 0.7936 (pm20) cc_final: 0.7711 (pm20) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.1348 time to fit residues: 47.3238 Evaluate side-chains 171 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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: 6.9990 chunk 95 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 575 GLN R 28 ASN S 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.056209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.047262 restraints weight = 114650.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.048571 restraints weight = 66369.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049491 restraints weight = 45769.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.050156 restraints weight = 35139.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.050646 restraints weight = 28866.685| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21441 Z= 0.137 Angle : 0.732 14.995 29406 Z= 0.344 Chirality : 0.045 0.564 3657 Planarity : 0.004 0.041 3474 Dihedral : 5.134 26.237 2556 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.05 % Allowed : 0.14 % 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: 0.84 (0.18), residues: 2328 helix: 1.67 (0.28), residues: 366 sheet: 0.31 (0.18), residues: 777 loop : 0.54 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 61 TYR 0.015 0.001 TYR G 217 PHE 0.013 0.001 PHE G 288 TRP 0.035 0.002 TRP I 628 HIS 0.004 0.001 HIS F 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (21249) covalent geometry : angle 0.65675 / 0.33 (28869) SS BOND : bond 0.00324 / 0.16 ( 39) SS BOND : angle 0.95141 / 0.63 ( 78) hydrogen bonds : bond 0.03740 / 2.47 ( 729) hydrogen bonds : angle 5.11542 / 3.62 ( 2025) link_ALPHA1-2 : bond 0.00201 / 0.10 ( 6) link_ALPHA1-2 : angle 1.65457 / 1.01 ( 18) link_ALPHA1-3 : bond 0.00546 / 0.34 ( 18) link_ALPHA1-3 : angle 1.51068 / 1.03 ( 54) link_ALPHA1-6 : bond 0.00544 / 0.31 ( 15) link_ALPHA1-6 : angle 1.73443 / 1.19 ( 45) link_BETA1-4 : bond 0.00307 / 0.20 ( 54) link_BETA1-4 : angle 1.72435 / 1.18 ( 162) link_NAG-ASN : bond 0.00227 / 0.13 ( 60) link_NAG-ASN : angle 3.69244 / 2.60 ( 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 225 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.777 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: A 104 MET cc_start: 0.9271 (tpp) cc_final: 0.8289 (tpt) REVERT: A 150 MET cc_start: 0.8354 (mmm) cc_final: 0.7919 (mmm) REVERT: A 217 TYR cc_start: 0.8616 (m-80) cc_final: 0.7412 (m-80) REVERT: B 546 SER cc_start: 0.8663 (m) cc_final: 0.8189 (p) REVERT: B 548 ILE cc_start: 0.7406 (tp) cc_final: 0.7083 (tp) REVERT: B 584 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8270 (tm-30) REVERT: H 71 TRP cc_start: 0.8424 (p-90) cc_final: 0.7960 (p-90) REVERT: H 80 MET cc_start: 0.8961 (tmm) cc_final: 0.8715 (tmm) REVERT: H 98 ASP cc_start: 0.8861 (p0) cc_final: 0.8242 (t0) REVERT: L 21 ILE cc_start: 0.8902 (pt) cc_final: 0.8679 (pt) REVERT: L 33 LEU cc_start: 0.9678 (tp) cc_final: 0.9259 (tp) REVERT: L 34 ASN cc_start: 0.9331 (m-40) cc_final: 0.8870 (m-40) REVERT: L 42 LYS cc_start: 0.9384 (mtmm) cc_final: 0.9057 (ptmm) REVERT: L 62 PHE cc_start: 0.9222 (m-80) cc_final: 0.8985 (m-80) REVERT: F 150 MET cc_start: 0.8631 (mmm) cc_final: 0.8301 (mmm) REVERT: I 530 MET cc_start: 0.8386 (mmp) cc_final: 0.7760 (mtp) REVERT: I 546 SER cc_start: 0.8866 (m) cc_final: 0.8209 (p) REVERT: I 584 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8292 (tm-30) REVERT: I 610 TRP cc_start: 0.7185 (p-90) cc_final: 0.6579 (p-90) REVERT: I 626 MET cc_start: 0.7505 (ptp) cc_final: 0.6896 (ptt) REVERT: R 71 TRP cc_start: 0.8260 (p-90) cc_final: 0.7911 (p-90) REVERT: R 80 MET cc_start: 0.9013 (tmm) cc_final: 0.8724 (tmm) REVERT: T 33 LEU cc_start: 0.9635 (tp) cc_final: 0.9145 (tp) REVERT: T 34 ASN cc_start: 0.9208 (m-40) cc_final: 0.8684 (t0) REVERT: T 36 TYR cc_start: 0.8433 (m-80) cc_final: 0.7427 (m-80) REVERT: T 42 LYS cc_start: 0.9338 (ptpp) cc_final: 0.8926 (pttp) REVERT: G 150 MET cc_start: 0.8163 (mmm) cc_final: 0.7883 (mmm) REVERT: J 584 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8257 (tm-30) REVERT: J 586 TYR cc_start: 0.8975 (t80) cc_final: 0.8768 (t80) REVERT: J 610 TRP cc_start: 0.7249 (p-90) cc_final: 0.6442 (p-90) REVERT: S 23 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8416 (mm-30) REVERT: S 71 TRP cc_start: 0.8316 (p-90) cc_final: 0.7986 (p-90) REVERT: U 42 LYS cc_start: 0.9324 (mtmm) cc_final: 0.9011 (ptmm) REVERT: U 46 LEU cc_start: 0.8928 (pt) cc_final: 0.8540 (tt) REVERT: U 69 GLN cc_start: 0.7952 (pm20) cc_final: 0.7725 (pm20) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.1394 time to fit residues: 49.8728 Evaluate side-chains 176 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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: 5.9990 chunk 45 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN F 99 ASN R 28 ASN S 1 GLN S 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.055529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.046625 restraints weight = 118499.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.047896 restraints weight = 70366.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.048775 restraints weight = 49284.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.049380 restraints weight = 38306.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.049822 restraints weight = 31966.075| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21441 Z= 0.220 Angle : 0.790 14.883 29406 Z= 0.370 Chirality : 0.046 0.580 3657 Planarity : 0.004 0.036 3474 Dihedral : 5.357 26.965 2556 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % 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: 0.66 (0.18), residues: 2328 helix: 1.49 (0.28), residues: 366 sheet: 0.25 (0.18), residues: 741 loop : 0.38 (0.19), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 61 TYR 0.021 0.002 TYR G 217 PHE 0.011 0.002 PHE S 91 TRP 0.034 0.002 TRP I 571 HIS 0.006 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 (21249) covalent geometry : angle 0.71960 / 0.36 (28869) SS BOND : bond 0.00276 / 0.16 ( 39) SS BOND : angle 1.08987 / 0.74 ( 78) hydrogen bonds : bond 0.03978 / 2.62 ( 729) hydrogen bonds : angle 5.27814 / 3.74 ( 2025) link_ALPHA1-2 : bond 0.00081 / 0.05 ( 6) link_ALPHA1-2 : angle 1.89174 / 1.09 ( 18) link_ALPHA1-3 : bond 0.00511 / 0.32 ( 18) link_ALPHA1-3 : angle 1.63063 / 1.14 ( 54) link_ALPHA1-6 : bond 0.00584 / 0.36 ( 15) link_ALPHA1-6 : angle 1.88916 / 1.27 ( 45) link_BETA1-4 : bond 0.00285 / 0.19 ( 54) link_BETA1-4 : angle 1.73393 / 1.19 ( 162) link_NAG-ASN : bond 0.00399 / 0.23 ( 60) link_NAG-ASN : angle 3.69337 / 2.60 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2451.15 seconds wall clock time: 43 minutes 58.32 seconds (2638.32 seconds total)