Starting phenix.real_space_refine on Tue Feb 11 02:37:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oh2_16876/02_2025/8oh2_16876.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oh2_16876/02_2025/8oh2_16876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oh2_16876/02_2025/8oh2_16876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oh2_16876/02_2025/8oh2_16876.map" model { file = "/net/cci-nas-00/data/ceres_data/8oh2_16876/02_2025/8oh2_16876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oh2_16876/02_2025/8oh2_16876.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 3 Type Number sf(0) Gaussians C 2232 2.51 5 N 684 2.21 5 O 786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3702 Number of models: 1 Model: "" Number of chains: 102 Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 12} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.10, per 1000 atoms: 0.84 Number of scatterers: 3702 At special positions: 0 Unit cell: (153.9, 93.1, 35.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 786 8.00 N 684 7.00 C 2232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=36, symmetry=0 Number of additional bonds: simple=36, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 360.2 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 864 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 63.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 361 removed outlier: 9.195A pdb=" N SER A 352 " --> pdb=" O LYS M 353 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N GLY M 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 354 " --> pdb=" O GLY M 355 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N LEU M 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N SER A 356 " --> pdb=" O LEU M 357 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ASN M 359 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP A 358 " --> pdb=" O ASN M 359 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N THR M 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 360 " --> pdb=" O THR M 361 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N SER M 352 " --> pdb=" O LYS Y 353 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N GLY Y 355 " --> pdb=" O SER M 352 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE M 354 " --> pdb=" O GLY Y 355 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LEU Y 357 " --> pdb=" O ILE M 354 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N SER M 356 " --> pdb=" O LEU Y 357 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN Y 359 " --> pdb=" O SER M 356 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASP M 358 " --> pdb=" O ASN Y 359 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR Y 361 " --> pdb=" O ASP M 358 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE M 360 " --> pdb=" O THR Y 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 351 through 361 removed outlier: 9.318A pdb=" N SER B 352 " --> pdb=" O LYS N 353 " (cutoff:3.500A) removed outlier: 10.651A pdb=" N GLY N 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE B 354 " --> pdb=" O GLY N 355 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N LEU N 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER B 356 " --> pdb=" O LEU N 357 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ASN N 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP B 358 " --> pdb=" O ASN N 359 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N THR N 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE B 360 " --> pdb=" O THR N 361 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLN N 351 " --> pdb=" O SER Z 352 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE Z 354 " --> pdb=" O GLN N 351 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS N 353 " --> pdb=" O ILE Z 354 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N SER Z 356 " --> pdb=" O LYS N 353 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLY N 355 " --> pdb=" O SER Z 356 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N ASP Z 358 " --> pdb=" O GLY N 355 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N LEU N 357 " --> pdb=" O ASP Z 358 " (cutoff:3.500A) removed outlier: 9.616A pdb=" N ILE Z 360 " --> pdb=" O LEU N 357 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ASN N 359 " --> pdb=" O ILE Z 360 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 353 through 361 removed outlier: 6.506A pdb=" N ILE C 354 " --> pdb=" O GLY O 355 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU O 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N SER C 356 " --> pdb=" O LEU O 357 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ASN O 359 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP C 358 " --> pdb=" O ASN O 359 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR O 361 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 360 " --> pdb=" O THR O 361 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE O 354 " --> pdb=" O GLY a 355 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU a 357 " --> pdb=" O ILE O 354 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER O 356 " --> pdb=" O LEU a 357 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASN a 359 " --> pdb=" O SER O 356 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP O 358 " --> pdb=" O ASN a 359 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR a 361 " --> pdb=" O ASP O 358 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE O 360 " --> pdb=" O THR a 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 351 through 361 removed outlier: 9.196A pdb=" N SER D 352 " --> pdb=" O LYS P 353 " (cutoff:3.500A) removed outlier: 10.409A pdb=" N GLY P 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE D 354 " --> pdb=" O GLY P 355 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N LEU P 357 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER D 356 " --> pdb=" O LEU P 357 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN P 359 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP D 358 " --> pdb=" O ASN P 359 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR P 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE D 360 " --> pdb=" O THR P 361 " (cutoff:3.500A) removed outlier: 10.572A pdb=" N GLY b 355 " --> pdb=" O SER P 352 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE P 354 " --> pdb=" O GLY b 355 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU b 357 " --> pdb=" O ILE P 354 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER P 356 " --> pdb=" O LEU b 357 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN b 359 " --> pdb=" O SER P 356 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP P 358 " --> pdb=" O ASN b 359 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N THR b 361 " --> pdb=" O ASP P 358 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE P 360 " --> pdb=" O THR b 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 351 through 361 removed outlier: 6.215A pdb=" N GLN E 351 " --> pdb=" O SER Q 352 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE Q 354 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LYS E 353 " --> pdb=" O ILE Q 354 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER Q 356 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY E 355 " --> pdb=" O SER Q 356 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N ASP Q 358 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N LEU E 357 " --> pdb=" O ASP Q 358 " (cutoff:3.500A) removed outlier: 9.788A pdb=" N ILE Q 360 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N ASN E 359 " --> pdb=" O ILE Q 360 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY c 355 " --> pdb=" O ILE Q 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 353 through 361 removed outlier: 6.651A pdb=" N ILE F 354 " --> pdb=" O GLY R 355 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU R 357 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER F 356 " --> pdb=" O LEU R 357 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASN R 359 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP F 358 " --> pdb=" O ASN R 359 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR R 361 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE F 360 " --> pdb=" O THR R 361 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE R 354 " --> pdb=" O GLY d 355 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU d 357 " --> pdb=" O ILE R 354 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER R 356 " --> pdb=" O LEU d 357 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ASN d 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP R 358 " --> pdb=" O ASN d 359 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N THR d 361 " --> pdb=" O ASP R 358 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE R 360 " --> pdb=" O THR d 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 351 through 361 removed outlier: 6.373A pdb=" N GLN G 351 " --> pdb=" O SER S 352 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE S 354 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS G 353 " --> pdb=" O ILE S 354 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N SER S 356 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLY G 355 " --> pdb=" O SER S 356 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N ASP S 358 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N LEU G 357 " --> pdb=" O ASP S 358 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N ILE S 360 " --> pdb=" O LEU G 357 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N ASN G 359 " --> pdb=" O ILE S 360 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N SER S 352 " --> pdb=" O LYS e 353 " (cutoff:3.500A) removed outlier: 10.520A pdb=" N GLY e 355 " --> pdb=" O SER S 352 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE S 354 " --> pdb=" O GLY e 355 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LEU e 357 " --> pdb=" O ILE S 354 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER S 356 " --> pdb=" O LEU e 357 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASN e 359 " --> pdb=" O SER S 356 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP S 358 " --> pdb=" O ASN e 359 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR e 361 " --> pdb=" O ASP S 358 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE S 360 " --> pdb=" O THR e 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 351 through 361 removed outlier: 6.164A pdb=" N GLN H 351 " --> pdb=" O SER T 352 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE T 354 " --> pdb=" O GLN H 351 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LYS H 353 " --> pdb=" O ILE T 354 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N SER T 356 " --> pdb=" O LYS H 353 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLY H 355 " --> pdb=" O SER T 356 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N ASP T 358 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N LEU H 357 " --> pdb=" O ASP T 358 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N ILE T 360 " --> pdb=" O LEU H 357 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N ASN H 359 " --> pdb=" O ILE T 360 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN T 351 " --> pdb=" O SER f 352 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE f 354 " --> pdb=" O GLN T 351 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS T 353 " --> pdb=" O ILE f 354 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N SER f 356 " --> pdb=" O LYS T 353 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLY T 355 " --> pdb=" O SER f 356 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N ASP f 358 " --> pdb=" O GLY T 355 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N LEU T 357 " --> pdb=" O ASP f 358 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N ILE f 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N ASN T 359 " --> pdb=" O ILE f 360 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'I' and resid 353 through 361 removed outlier: 6.360A pdb=" N ILE I 354 " --> pdb=" O GLY U 355 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU U 357 " --> pdb=" O ILE I 354 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER I 356 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASN U 359 " --> pdb=" O SER I 356 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP I 358 " --> pdb=" O ASN U 359 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR U 361 " --> pdb=" O ASP I 358 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE I 360 " --> pdb=" O THR U 361 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE U 354 " --> pdb=" O GLY g 355 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU g 357 " --> pdb=" O ILE U 354 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER U 356 " --> pdb=" O LEU g 357 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ASN g 359 " --> pdb=" O SER U 356 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP U 358 " --> pdb=" O ASN g 359 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR g 361 " --> pdb=" O ASP U 358 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE U 360 " --> pdb=" O THR g 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 354 through 361 removed outlier: 6.692A pdb=" N ILE J 354 " --> pdb=" O GLY V 355 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU V 357 " --> pdb=" O ILE J 354 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER J 356 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ASN V 359 " --> pdb=" O SER J 356 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP J 358 " --> pdb=" O ASN V 359 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N THR V 361 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE J 360 " --> pdb=" O THR V 361 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N LEU h 357 " --> pdb=" O ILE V 354 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER V 356 " --> pdb=" O LEU h 357 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASN h 359 " --> pdb=" O SER V 356 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP V 358 " --> pdb=" O ASN h 359 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR h 361 " --> pdb=" O ASP V 358 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE V 360 " --> pdb=" O THR h 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 354 through 361 removed outlier: 6.535A pdb=" N ILE K 354 " --> pdb=" O GLY W 355 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N LEU W 357 " --> pdb=" O ILE K 354 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER K 356 " --> pdb=" O LEU W 357 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ASN W 359 " --> pdb=" O SER K 356 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASP K 358 " --> pdb=" O ASN W 359 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR W 361 " --> pdb=" O ASP K 358 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE K 360 " --> pdb=" O THR W 361 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N LEU i 357 " --> pdb=" O ILE W 354 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER W 356 " --> pdb=" O LEU i 357 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASN i 359 " --> pdb=" O SER W 356 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP W 358 " --> pdb=" O ASN i 359 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR i 361 " --> pdb=" O ASP W 358 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE W 360 " --> pdb=" O THR i 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 353 through 354 removed outlier: 6.310A pdb=" N LYS L 353 " --> pdb=" O ILE X 354 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS X 353 " --> pdb=" O ILE j 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'L' and resid 357 through 361 removed outlier: 6.467A pdb=" N ASP L 358 " --> pdb=" O ASN X 359 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N THR X 361 " --> pdb=" O ASP L 358 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE L 360 " --> pdb=" O THR X 361 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP X 358 " --> pdb=" O ASN j 359 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR j 361 " --> pdb=" O ASP X 358 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE X 360 " --> pdb=" O THR j 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 6 hydrogen bonds defined for protein. 18 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: 0.73 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 648 1.28 - 1.35: 612 1.35 - 1.41: 153 1.41 - 1.48: 531 1.48 - 1.54: 1692 Bond restraints: 3636 Sorted by residual: bond pdb=" C ACE d 349 " pdb=" O ACE d 349 " ideal model delta sigma weight residual 1.199 1.226 -0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C ACE X 349 " pdb=" O ACE X 349 " ideal model delta sigma weight residual 1.199 1.225 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C ACE L 349 " pdb=" O ACE L 349 " ideal model delta sigma weight residual 1.199 1.225 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C ACE j 349 " pdb=" O ACE j 349 " ideal model delta sigma weight residual 1.199 1.225 -0.026 2.00e-02 2.50e+03 1.72e+00 bond pdb=" C ACE R 349 " pdb=" O ACE R 349 " ideal model delta sigma weight residual 1.199 1.225 -0.026 2.00e-02 2.50e+03 1.70e+00 ... (remaining 3631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 4388 0.91 - 1.81: 383 1.81 - 2.72: 54 2.72 - 3.63: 23 3.63 - 4.54: 12 Bond angle restraints: 4860 Sorted by residual: angle pdb=" C ILE O 354 " pdb=" N GLY O 355 " pdb=" CA GLY O 355 " ideal model delta sigma weight residual 119.94 121.47 -1.53 1.09e+00 8.42e-01 1.98e+00 angle pdb=" C ILE a 354 " pdb=" N GLY a 355 " pdb=" CA GLY a 355 " ideal model delta sigma weight residual 119.94 121.46 -1.52 1.09e+00 8.42e-01 1.96e+00 angle pdb=" C ILE U 354 " pdb=" N GLY U 355 " pdb=" CA GLY U 355 " ideal model delta sigma weight residual 119.94 121.45 -1.51 1.09e+00 8.42e-01 1.92e+00 angle pdb=" C ILE C 354 " pdb=" N GLY C 355 " pdb=" CA GLY C 355 " ideal model delta sigma weight residual 119.94 121.45 -1.51 1.09e+00 8.42e-01 1.91e+00 angle pdb=" C ILE g 354 " pdb=" N GLY g 355 " pdb=" CA GLY g 355 " ideal model delta sigma weight residual 119.94 121.43 -1.49 1.09e+00 8.42e-01 1.88e+00 ... (remaining 4855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.13: 1896 11.13 - 22.27: 198 22.27 - 33.40: 36 33.40 - 44.53: 36 44.53 - 55.66: 30 Dihedral angle restraints: 2196 sinusoidal: 900 harmonic: 1296 Sorted by residual: dihedral pdb=" CA ASN b 359 " pdb=" C ASN b 359 " pdb=" N ILE b 360 " pdb=" CA ILE b 360 " ideal model delta harmonic sigma weight residual 180.00 -162.85 -17.15 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ASN h 359 " pdb=" C ASN h 359 " pdb=" N ILE h 360 " pdb=" CA ILE h 360 " ideal model delta harmonic sigma weight residual -180.00 -162.87 -17.13 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASN P 359 " pdb=" C ASN P 359 " pdb=" N ILE P 360 " pdb=" CA ILE P 360 " ideal model delta harmonic sigma weight residual -180.00 -162.87 -17.13 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 2193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 258 0.021 - 0.042: 162 0.042 - 0.062: 104 0.062 - 0.083: 16 0.083 - 0.104: 72 Chirality restraints: 612 Sorted by residual: chirality pdb=" CA ILE Q 354 " pdb=" N ILE Q 354 " pdb=" C ILE Q 354 " pdb=" CB ILE Q 354 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.69e-01 chirality pdb=" CA ILE e 354 " pdb=" N ILE e 354 " pdb=" C ILE e 354 " pdb=" CB ILE e 354 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.67e-01 chirality pdb=" CA ILE E 354 " pdb=" N ILE E 354 " pdb=" C ILE E 354 " pdb=" CB ILE E 354 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.65e-01 ... (remaining 609 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN U 351 " -0.002 2.00e-02 2.50e+03 3.89e-03 1.51e-01 pdb=" C GLN U 351 " 0.007 2.00e-02 2.50e+03 pdb=" O GLN U 351 " -0.003 2.00e-02 2.50e+03 pdb=" N SER U 352 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN a 351 " 0.002 2.00e-02 2.50e+03 3.75e-03 1.41e-01 pdb=" C GLN a 351 " -0.006 2.00e-02 2.50e+03 pdb=" O GLN a 351 " 0.002 2.00e-02 2.50e+03 pdb=" N SER a 352 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN g 351 " -0.002 2.00e-02 2.50e+03 3.68e-03 1.35e-01 pdb=" C GLN g 351 " 0.006 2.00e-02 2.50e+03 pdb=" O GLN g 351 " -0.002 2.00e-02 2.50e+03 pdb=" N SER g 352 " -0.002 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 191 2.75 - 3.29: 2985 3.29 - 3.83: 6226 3.83 - 4.36: 6686 4.36 - 4.90: 12113 Nonbonded interactions: 28201 Sorted by model distance: nonbonded pdb=" NE2 HIS I 362 " pdb=" O HOH I 401 " model vdw 2.219 3.120 nonbonded pdb=" NE2 HIS g 362 " pdb=" O HOH g 401 " model vdw 2.230 3.120 nonbonded pdb=" NE2 HIS U 362 " pdb=" O HOH U 401 " model vdw 2.240 3.120 nonbonded pdb=" O HIS C 362 " pdb=" N NH2 O 363 " model vdw 2.310 3.120 nonbonded pdb=" NE2 HIS O 362 " pdb=" O HOH O 401 " model vdw 2.341 3.120 ... (remaining 28196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.250 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.007 0.034 3636 Z= 0.486 Angle : 0.622 4.537 4860 Z= 0.307 Chirality : 0.044 0.104 612 Planarity : 0.001 0.004 612 Dihedral : 13.000 55.661 1332 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.25), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.19), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS d 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.445 Fit side-chains REVERT: G 353 LYS cc_start: 0.8591 (ttmt) cc_final: 0.8266 (tttt) REVERT: J 353 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7932 (ttpt) REVERT: K 353 LYS cc_start: 0.8336 (tttt) cc_final: 0.8126 (mtpp) REVERT: N 362 HIS cc_start: 0.7792 (t70) cc_final: 0.7580 (t70) REVERT: S 353 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8302 (tttt) REVERT: V 353 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7566 (mtpp) REVERT: X 360 ILE cc_start: 0.8251 (mt) cc_final: 0.7942 (OUTLIER) REVERT: b 353 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8127 (ttmm) REVERT: e 353 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8166 (tttt) REVERT: j 360 ILE cc_start: 0.8327 (mt) cc_final: 0.8075 (mm) outliers start: 0 outliers final: 1 residues processed: 123 average time/residue: 0.7404 time to fit residues: 95.3014 Evaluate side-chains 94 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 351 GLN T 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.132418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.102341 restraints weight = 4416.901| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.67 r_work: 0.3611 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3636 Z= 0.253 Angle : 0.585 9.262 4860 Z= 0.274 Chirality : 0.048 0.121 612 Planarity : 0.002 0.012 612 Dihedral : 15.312 59.799 504 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.47 % Allowed : 16.44 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.28), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.22), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS Q 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.463 Fit side-chains REVERT: G 353 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8541 (tttt) REVERT: I 358 ASP cc_start: 0.8547 (m-30) cc_final: 0.8328 (m-30) REVERT: J 353 LYS cc_start: 0.8349 (ttmt) cc_final: 0.8026 (ttpp) REVERT: P 353 LYS cc_start: 0.8826 (ttpt) cc_final: 0.8323 (ttmm) REVERT: S 353 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8540 (tttt) REVERT: W 356 SER cc_start: 0.8794 (t) cc_final: 0.8554 (p) REVERT: e 353 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8547 (tttt) outliers start: 15 outliers final: 8 residues processed: 106 average time/residue: 0.7077 time to fit residues: 78.7831 Evaluate side-chains 96 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain f residue 356 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 32 optimal weight: 0.0970 chunk 3 optimal weight: 0.0070 chunk 27 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 17 optimal weight: 30.0000 chunk 11 optimal weight: 0.1980 chunk 28 optimal weight: 0.0030 chunk 26 optimal weight: 0.0670 overall best weight: 0.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 359 ASN c 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.157907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.129077 restraints weight = 4590.287| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.42 r_work: 0.3818 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 3636 Z= 0.061 Angle : 0.454 7.536 4860 Z= 0.207 Chirality : 0.048 0.120 612 Planarity : 0.001 0.006 612 Dihedral : 14.917 59.353 504 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.93 % Allowed : 21.76 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS Y 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.462 Fit side-chains REVERT: A 353 LYS cc_start: 0.8687 (ttmp) cc_final: 0.8381 (ttmt) REVERT: D 353 LYS cc_start: 0.8646 (ttpt) cc_final: 0.8253 (ttmm) REVERT: G 353 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8463 (tttt) REVERT: H 353 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8473 (ptpt) REVERT: J 353 LYS cc_start: 0.8281 (ttmt) cc_final: 0.8040 (ttpt) REVERT: P 353 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8251 (ttmm) REVERT: S 353 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8449 (tttt) REVERT: e 353 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8333 (tttt) outliers start: 4 outliers final: 1 residues processed: 123 average time/residue: 0.5984 time to fit residues: 77.7765 Evaluate side-chains 109 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 361 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 359 ASN W 362 HIS f 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.130684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.100194 restraints weight = 4482.360| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.78 r_work: 0.3586 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 3636 Z= 0.473 Angle : 0.693 8.913 4860 Z= 0.335 Chirality : 0.049 0.125 612 Planarity : 0.002 0.007 612 Dihedral : 15.285 59.602 504 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.94 % Allowed : 22.22 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.32), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.24), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS j 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.499 Fit side-chains REVERT: G 353 LYS cc_start: 0.8958 (ttmt) cc_final: 0.8594 (tttt) REVERT: J 353 LYS cc_start: 0.8369 (ttmt) cc_final: 0.8022 (ttpp) REVERT: K 356 SER cc_start: 0.9031 (t) cc_final: 0.8766 (p) REVERT: S 353 LYS cc_start: 0.8973 (ttmt) cc_final: 0.8607 (tttt) REVERT: W 356 SER cc_start: 0.8863 (t) cc_final: 0.8622 (p) REVERT: e 353 LYS cc_start: 0.8971 (ttmt) cc_final: 0.8594 (tttt) outliers start: 17 outliers final: 11 residues processed: 98 average time/residue: 0.7558 time to fit residues: 77.5813 Evaluate side-chains 96 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain b residue 361 THR Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain d residue 361 THR Chi-restraints excluded: chain f residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS H 362 HIS N 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.131767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.101321 restraints weight = 4850.023| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.79 r_work: 0.3608 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3636 Z= 0.306 Angle : 0.588 8.713 4860 Z= 0.284 Chirality : 0.047 0.119 612 Planarity : 0.002 0.005 612 Dihedral : 15.127 59.747 504 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 3.47 % Allowed : 22.22 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.32), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.24), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.492 Fit side-chains REVERT: G 353 LYS cc_start: 0.8940 (ttmt) cc_final: 0.8584 (tttt) REVERT: J 353 LYS cc_start: 0.8384 (ttmt) cc_final: 0.7998 (ttpp) REVERT: K 356 SER cc_start: 0.8990 (t) cc_final: 0.8723 (p) REVERT: S 353 LYS cc_start: 0.8925 (ttmt) cc_final: 0.8553 (tttt) REVERT: W 356 SER cc_start: 0.8849 (t) cc_final: 0.8588 (p) REVERT: e 353 LYS cc_start: 0.8951 (ttmt) cc_final: 0.8586 (tttt) outliers start: 15 outliers final: 11 residues processed: 101 average time/residue: 0.7116 time to fit residues: 75.5300 Evaluate side-chains 99 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain b residue 361 THR Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain f residue 356 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 0.0970 chunk 29 optimal weight: 0.0770 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 34 optimal weight: 0.0370 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 overall best weight: 2.0418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.134030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.103657 restraints weight = 4485.796| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.72 r_work: 0.3658 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3636 Z= 0.138 Angle : 0.512 8.359 4860 Z= 0.239 Chirality : 0.047 0.120 612 Planarity : 0.001 0.004 612 Dihedral : 14.960 59.731 504 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.78 % Allowed : 23.61 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS j 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.489 Fit side-chains REVERT: G 353 LYS cc_start: 0.8875 (ttmt) cc_final: 0.8524 (tttt) REVERT: J 353 LYS cc_start: 0.8371 (ttmt) cc_final: 0.7996 (ttpp) REVERT: K 356 SER cc_start: 0.8942 (t) cc_final: 0.8660 (p) REVERT: P 353 LYS cc_start: 0.8805 (ttpt) cc_final: 0.8357 (ttmm) REVERT: S 353 LYS cc_start: 0.8879 (ttmt) cc_final: 0.8496 (tttt) REVERT: W 356 SER cc_start: 0.8797 (t) cc_final: 0.8506 (p) REVERT: e 353 LYS cc_start: 0.8882 (ttmt) cc_final: 0.8518 (tttt) outliers start: 12 outliers final: 9 residues processed: 100 average time/residue: 0.7167 time to fit residues: 75.3082 Evaluate side-chains 98 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain b residue 361 THR Chi-restraints excluded: chain c residue 353 LYS Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain d residue 361 THR Chi-restraints excluded: chain f residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 30.0000 chunk 33 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.130624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.100028 restraints weight = 4719.378| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.76 r_work: 0.3586 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 3636 Z= 0.467 Angle : 0.673 9.434 4860 Z= 0.331 Chirality : 0.049 0.123 612 Planarity : 0.002 0.006 612 Dihedral : 15.148 59.872 504 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.94 % Allowed : 22.92 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.32), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.24), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS j 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.464 Fit side-chains REVERT: G 353 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8600 (tttt) REVERT: J 353 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8019 (ttpp) REVERT: K 356 SER cc_start: 0.8980 (t) cc_final: 0.8721 (p) REVERT: S 353 LYS cc_start: 0.8941 (ttmt) cc_final: 0.8597 (tttt) REVERT: W 356 SER cc_start: 0.8862 (t) cc_final: 0.8631 (p) REVERT: e 353 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8588 (tttt) outliers start: 17 outliers final: 15 residues processed: 92 average time/residue: 0.7037 time to fit residues: 68.0739 Evaluate side-chains 98 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 361 THR Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain b residue 361 THR Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain d residue 361 THR Chi-restraints excluded: chain f residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 30.0000 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.133069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.102484 restraints weight = 4709.590| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.76 r_work: 0.3636 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3636 Z= 0.196 Angle : 0.548 8.999 4860 Z= 0.259 Chirality : 0.047 0.120 612 Planarity : 0.001 0.004 612 Dihedral : 15.005 59.258 504 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 2.78 % Allowed : 24.31 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.33), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS j 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.459 Fit side-chains REVERT: G 353 LYS cc_start: 0.8912 (ttmt) cc_final: 0.8568 (tttt) REVERT: J 353 LYS cc_start: 0.8346 (ttmt) cc_final: 0.7986 (ttpp) REVERT: K 356 SER cc_start: 0.8962 (t) cc_final: 0.8693 (p) REVERT: P 353 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8309 (ttmm) REVERT: S 353 LYS cc_start: 0.8914 (ttmt) cc_final: 0.8571 (tttt) REVERT: W 356 SER cc_start: 0.8833 (t) cc_final: 0.8563 (p) REVERT: e 353 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8543 (tttt) outliers start: 12 outliers final: 10 residues processed: 92 average time/residue: 0.7170 time to fit residues: 69.2541 Evaluate side-chains 92 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain b residue 361 THR Chi-restraints excluded: chain c residue 353 LYS Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain d residue 361 THR Chi-restraints excluded: chain f residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 10.0000 chunk 21 optimal weight: 0.3980 chunk 31 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 0.0050 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.157354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.126032 restraints weight = 4868.779| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.45 r_work: 0.3712 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 3636 Z= 0.093 Angle : 0.493 8.945 4860 Z= 0.226 Chirality : 0.047 0.117 612 Planarity : 0.001 0.006 612 Dihedral : 14.796 59.722 504 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.31 % Allowed : 24.77 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.35), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS j 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.459 Fit side-chains REVERT: A 353 LYS cc_start: 0.8722 (ttmp) cc_final: 0.8421 (tttt) REVERT: G 353 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8493 (tttt) REVERT: J 353 LYS cc_start: 0.8312 (ttmt) cc_final: 0.7947 (ttpp) REVERT: K 356 SER cc_start: 0.8831 (t) cc_final: 0.8482 (p) REVERT: P 353 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8326 (ttmm) REVERT: S 353 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8459 (tttt) REVERT: W 356 SER cc_start: 0.8709 (t) cc_final: 0.8442 (p) REVERT: e 353 LYS cc_start: 0.8793 (ttmt) cc_final: 0.8455 (tttt) outliers start: 10 outliers final: 8 residues processed: 101 average time/residue: 0.7012 time to fit residues: 74.4803 Evaluate side-chains 104 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain b residue 361 THR Chi-restraints excluded: chain c residue 353 LYS Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain d residue 361 THR Chi-restraints excluded: chain f residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 40.0000 chunk 13 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.131419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.100704 restraints weight = 4967.124| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.80 r_work: 0.3604 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3636 Z= 0.378 Angle : 0.628 9.388 4860 Z= 0.304 Chirality : 0.048 0.121 612 Planarity : 0.002 0.005 612 Dihedral : 15.091 59.815 504 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.31 % Allowed : 25.00 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.33), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS j 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.494 Fit side-chains REVERT: G 353 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8592 (tttt) REVERT: J 353 LYS cc_start: 0.8360 (ttmt) cc_final: 0.8021 (ttpp) REVERT: K 356 SER cc_start: 0.8960 (t) cc_final: 0.8699 (p) REVERT: S 353 LYS cc_start: 0.8956 (ttmt) cc_final: 0.8599 (tttt) REVERT: W 356 SER cc_start: 0.8856 (t) cc_final: 0.8612 (p) REVERT: e 353 LYS cc_start: 0.8951 (ttmt) cc_final: 0.8584 (tttt) outliers start: 10 outliers final: 9 residues processed: 88 average time/residue: 0.7363 time to fit residues: 68.1437 Evaluate side-chains 92 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain b residue 361 THR Chi-restraints excluded: chain c residue 353 LYS Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain d residue 361 THR Chi-restraints excluded: chain f residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 5 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 0.0060 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.130621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.100304 restraints weight = 4833.644| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.74 r_work: 0.3619 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3636 Z= 0.271 Angle : 0.589 9.226 4860 Z= 0.278 Chirality : 0.047 0.121 612 Planarity : 0.001 0.006 612 Dihedral : 15.042 59.720 504 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.55 % Allowed : 25.23 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.33), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS j 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3156.53 seconds wall clock time: 56 minutes 46.55 seconds (3406.55 seconds total)