Starting phenix.real_space_refine on Wed Mar 5 21:46:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oh2_16876/03_2025/8oh2_16876.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oh2_16876/03_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_16876/03_2025/8oh2_16876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oh2_16876/03_2025/8oh2_16876.map" model { file = "/net/cci-nas-00/data/ceres_data/8oh2_16876/03_2025/8oh2_16876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oh2_16876/03_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-5624/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: 3.39, per 1000 atoms: 0.92 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: 1.01 Conformation dependent library (CDL) restraints added in 403.6 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: 0.47 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: 0.74 Time building geometry restraints manager: 1.18 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: 2.120 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.270 Find NCS groups from input model: 0.220 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:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.490 ------------------------------------------------------------------------------- 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 : 0.485 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: 0.7330 time to fit residues: 94.4177 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 : 0.497 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.102341 restraints weight = 4416.903| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.68 r_work: 0.3611 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 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 : 0.493 Fit side-chains REVERT: G 353 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8539 (tttt) REVERT: I 358 ASP cc_start: 0.8543 (m-30) cc_final: 0.8327 (m-30) REVERT: J 353 LYS cc_start: 0.8347 (ttmt) cc_final: 0.8027 (ttpp) REVERT: P 353 LYS cc_start: 0.8826 (ttpt) cc_final: 0.8325 (ttmm) REVERT: S 353 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8540 (tttt) REVERT: W 356 SER cc_start: 0.8792 (t) cc_final: 0.8555 (p) REVERT: e 353 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8546 (tttt) outliers start: 15 outliers final: 8 residues processed: 106 average time/residue: 0.7044 time to fit residues: 78.5843 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 : 0.538 ------------------------------------------------------------------------------- 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: 0.5980 chunk 3 optimal weight: 0.0670 chunk 27 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 30.0000 chunk 11 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.0770 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.154546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.125546 restraints weight = 4619.104| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.42 r_work: 0.3762 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.013 3636 Z= 0.061 Angle : 0.453 7.275 4860 Z= 0.208 Chirality : 0.048 0.124 612 Planarity : 0.001 0.006 612 Dihedral : 15.017 59.998 504 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.69 % Allowed : 21.99 % 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: -2.21 (0.33), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.25), 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 113 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.493 Fit side-chains REVERT: A 353 LYS cc_start: 0.8714 (ttmp) cc_final: 0.8414 (tttt) REVERT: D 353 LYS cc_start: 0.8685 (ttpt) cc_final: 0.8290 (ttmm) REVERT: G 353 LYS cc_start: 0.8800 (ttmt) cc_final: 0.8464 (tttt) REVERT: I 358 ASP cc_start: 0.8343 (m-30) cc_final: 0.8087 (m-30) REVERT: J 353 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8082 (ttpt) REVERT: P 353 LYS cc_start: 0.8816 (ttpt) cc_final: 0.8280 (ttmm) REVERT: S 353 LYS cc_start: 0.8811 (ttmt) cc_final: 0.8467 (tttt) REVERT: W 353 LYS cc_start: 0.8654 (tttt) cc_final: 0.8428 (ttmt) REVERT: e 353 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8409 (tttt) outliers start: 3 outliers final: 1 residues processed: 111 average time/residue: 0.6404 time to fit residues: 74.9719 Evaluate side-chains 102 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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: 7.9990 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.132636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.102582 restraints weight = 4485.280| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.71 r_work: 0.3627 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3636 Z= 0.221 Angle : 0.548 8.197 4860 Z= 0.256 Chirality : 0.047 0.117 612 Planarity : 0.001 0.004 612 Dihedral : 15.243 59.946 504 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.31 % Allowed : 22.45 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.32), 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 0.003 0.001 HIS d 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 98 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.495 Fit side-chains REVERT: G 353 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8537 (tttt) REVERT: I 358 ASP cc_start: 0.8550 (m-30) cc_final: 0.8242 (m-30) REVERT: J 353 LYS cc_start: 0.8343 (ttmt) cc_final: 0.8000 (ttpp) REVERT: P 353 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8295 (ttmm) REVERT: S 353 LYS cc_start: 0.8912 (ttmt) cc_final: 0.8520 (tttt) REVERT: W 356 SER cc_start: 0.8795 (t) cc_final: 0.8517 (p) REVERT: e 353 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8541 (tttt) outliers start: 10 outliers final: 6 residues processed: 94 average time/residue: 0.7595 time to fit residues: 74.7867 Evaluate side-chains 91 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 c 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: 0.0070 chunk 12 optimal weight: 0.0670 chunk 3 optimal weight: 0.0040 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 overall best weight: 0.5950 ------------------------------------------------------------------------------- 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 = 0.153612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.124218 restraints weight = 4769.595| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.46 r_work: 0.3743 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2997 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= 0.063 Angle : 0.472 7.908 4860 Z= 0.213 Chirality : 0.048 0.119 612 Planarity : 0.001 0.004 612 Dihedral : 14.958 59.988 504 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.31 % Allowed : 22.92 % Favored : 74.77 % 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: -1.96 (0.35), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS Y 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 110 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.502 Fit side-chains REVERT: G 353 LYS cc_start: 0.8821 (ttmt) cc_final: 0.8483 (tttt) REVERT: J 353 LYS cc_start: 0.8319 (ttmt) cc_final: 0.7961 (ttpp) REVERT: P 353 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8259 (ttmm) REVERT: S 353 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8468 (tttt) REVERT: W 353 LYS cc_start: 0.8687 (tttt) cc_final: 0.8442 (ttmt) REVERT: W 356 SER cc_start: 0.8646 (t) cc_final: 0.8361 (p) REVERT: e 353 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8420 (tttt) outliers start: 10 outliers final: 6 residues processed: 105 average time/residue: 0.6366 time to fit residues: 70.5337 Evaluate side-chains 98 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 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: 0.0030 chunk 29 optimal weight: 30.0000 chunk 11 optimal weight: 8.9990 chunk 9 optimal weight: 0.0000 chunk 8 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 overall best weight: 5.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS N 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.131094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.100857 restraints weight = 4496.934| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.73 r_work: 0.3594 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3636 Z= 0.346 Angle : 0.623 8.825 4860 Z= 0.295 Chirality : 0.047 0.116 612 Planarity : 0.002 0.006 612 Dihedral : 15.246 59.490 504 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.32 (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 B 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 100 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.496 Fit side-chains REVERT: G 353 LYS cc_start: 0.8953 (ttmt) cc_final: 0.8579 (tttt) REVERT: J 353 LYS cc_start: 0.8367 (ttmt) cc_final: 0.8025 (ttpp) REVERT: S 353 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8585 (tttt) REVERT: W 356 SER cc_start: 0.8866 (t) cc_final: 0.8609 (p) REVERT: d 357 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7442 (tt) REVERT: e 353 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8555 (tttt) outliers start: 15 outliers final: 9 residues processed: 95 average time/residue: 0.6982 time to fit residues: 69.7707 Evaluate side-chains 95 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 K residue 362 HIS 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 d residue 357 LEU 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: 7.9990 chunk 33 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.131825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.101381 restraints weight = 4557.621| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.76 r_work: 0.3607 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3636 Z= 0.291 Angle : 0.604 8.955 4860 Z= 0.284 Chirality : 0.047 0.119 612 Planarity : 0.002 0.005 612 Dihedral : 15.127 59.499 504 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 3.01 % Allowed : 22.45 % Favored : 74.54 % 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: -2.36 (0.33), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 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: 13 poor density : 87 time to evaluate : 0.547 Fit side-chains REVERT: G 353 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8576 (tttt) REVERT: J 353 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8035 (ttpp) REVERT: P 353 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8317 (ttmm) REVERT: S 353 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8552 (tttt) REVERT: W 356 SER cc_start: 0.8826 (t) cc_final: 0.8587 (p) REVERT: d 357 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7406 (tt) REVERT: e 353 LYS cc_start: 0.8963 (ttmt) cc_final: 0.8579 (tttt) outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 0.7097 time to fit residues: 70.0853 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 : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain K residue 362 HIS 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 c residue 353 LYS Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain d residue 357 LEU 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: 9.9990 chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.131876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.101475 restraints weight = 4789.447| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.77 r_work: 0.3612 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3636 Z= 0.281 Angle : 0.589 9.091 4860 Z= 0.280 Chirality : 0.047 0.120 612 Planarity : 0.001 0.005 612 Dihedral : 15.101 59.954 504 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 2.31 % Allowed : 23.15 % Favored : 74.54 % 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: -2.37 (0.33), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 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 91 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.509 Fit side-chains REVERT: G 353 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8559 (tttt) REVERT: J 353 LYS cc_start: 0.8378 (ttmt) cc_final: 0.8033 (ttpp) REVERT: P 353 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8356 (ttmm) REVERT: S 353 LYS cc_start: 0.8920 (ttmt) cc_final: 0.8562 (tttt) REVERT: W 356 SER cc_start: 0.8811 (t) cc_final: 0.8596 (p) REVERT: e 353 LYS cc_start: 0.8925 (ttmt) cc_final: 0.8567 (tttt) outliers start: 10 outliers final: 9 residues processed: 86 average time/residue: 0.7009 time to fit residues: 63.4694 Evaluate side-chains 91 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain K residue 362 HIS Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain U residue 356 SER 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: 8.9990 chunk 31 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.134847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.104422 restraints weight = 4807.351| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.76 r_work: 0.3668 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3636 Z= 0.104 Angle : 0.511 9.012 4860 Z= 0.233 Chirality : 0.047 0.118 612 Planarity : 0.001 0.004 612 Dihedral : 14.897 59.990 504 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.31 % Allowed : 23.38 % 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: -2.13 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS d 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 104 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.449 Fit side-chains REVERT: G 353 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8533 (tttt) REVERT: J 353 LYS cc_start: 0.8373 (ttmt) cc_final: 0.8031 (ttpp) REVERT: P 353 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8371 (ttmm) REVERT: S 353 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8522 (tttt) REVERT: W 356 SER cc_start: 0.8726 (t) cc_final: 0.8473 (p) REVERT: e 353 LYS cc_start: 0.8862 (ttmt) cc_final: 0.8519 (tttt) outliers start: 10 outliers final: 8 residues processed: 99 average time/residue: 0.6858 time to fit residues: 71.6706 Evaluate side-chains 98 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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: 30.0000 chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.131217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.100590 restraints weight = 4894.086| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.78 r_work: 0.3593 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3636 Z= 0.341 Angle : 0.628 9.459 4860 Z= 0.298 Chirality : 0.047 0.120 612 Planarity : 0.002 0.005 612 Dihedral : 15.099 59.779 504 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 2.31 % Allowed : 23.61 % Favored : 74.07 % 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 : -1.77 (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 96 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.457 Fit side-chains REVERT: G 353 LYS cc_start: 0.8911 (ttmt) cc_final: 0.8564 (tttt) REVERT: J 353 LYS cc_start: 0.8367 (ttmt) cc_final: 0.8020 (ttpp) REVERT: S 353 LYS cc_start: 0.8957 (ttmt) cc_final: 0.8601 (tttt) REVERT: W 356 SER cc_start: 0.8860 (t) cc_final: 0.8613 (p) REVERT: e 353 LYS cc_start: 0.8944 (ttmt) cc_final: 0.8578 (tttt) outliers start: 10 outliers final: 9 residues processed: 92 average time/residue: 0.6790 time to fit residues: 65.7516 Evaluate side-chains 95 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 T residue 357 LEU Chi-restraints excluded: chain U residue 356 SER 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: 8.9990 chunk 11 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 29 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.133308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.102802 restraints weight = 4777.066| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.76 r_work: 0.3637 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3636 Z= 0.155 Angle : 0.546 9.092 4860 Z= 0.249 Chirality : 0.047 0.119 612 Planarity : 0.001 0.004 612 Dihedral : 14.972 59.917 504 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.85 % Allowed : 23.84 % 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: -2.20 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3193.44 seconds wall clock time: 55 minutes 20.80 seconds (3320.80 seconds total)