Starting phenix.real_space_refine on Tue Aug 4 13:35:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pds_71542/08_2026/9pds_71542.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pds_71542/08_2026/9pds_71542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pds_71542/08_2026/9pds_71542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pds_71542/08_2026/9pds_71542.map" model { file = "/net/cci-nas-00/data/ceres_data/9pds_71542/08_2026/9pds_71542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pds_71542/08_2026/9pds_71542.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.022 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 2451 2.51 5 N 473 2.21 5 O 473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3397 Number of models: 1 Model: "" Number of chains: 86 Chain: "O" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "Q" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "E" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "R" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "I" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "Z" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "M" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "V" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "g" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "i" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "c" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "e" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "p" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "k" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "r" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "m" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "v" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "o" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "u" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "z" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "x" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.95, per 1000 atoms: 0.28 Number of scatterers: 3397 At special positions: 0 Unit cell: (83, 84.66, 75.53, 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 473 8.00 N 473 7.00 C 2451 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=43, symmetry=0 Number of additional bonds: simple=43, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 81.1 milliseconds 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 602 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 3 sheets defined 0.0% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'O' and resid 3 through 6 removed outlier: 8.613A pdb=" N LYS t 6 " --> pdb=" O PHE S 3 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE S 5 " --> pdb=" O LYS t 6 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY Z 4 " --> pdb=" O PHE t 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 5 through 6 removed outlier: 7.583A pdb=" N PHE Q 5 " --> pdb=" O LYS T 6 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE T 5 " --> pdb=" O LYS U 6 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE U 5 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE a 5 " --> pdb=" O LYS b 6 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE b 5 " --> pdb=" O LYS i 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'p' and resid 2 through 7 removed outlier: 6.269A pdb=" N PHE p 3 " --> pdb=" O GLY q 4 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LYS q 6 " --> pdb=" O PHE p 3 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE p 5 " --> pdb=" O LYS q 6 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS v 6 " --> pdb=" O PHE s 5 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE v 3 " --> pdb=" O GLY w 4 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LYS w 6 " --> pdb=" O PHE v 3 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE v 5 " --> pdb=" O LYS w 6 " (cutoff:3.500A) 21 hydrogen bonds defined for protein. 57 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: 0.37 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 344 1.26 - 1.33: 255 1.33 - 1.40: 1207 1.40 - 1.48: 387 1.48 - 1.55: 1290 Bond restraints: 3483 Sorted by residual: bond pdb=" C ACE b 0 " pdb=" N PHE b 1 " ideal model delta sigma weight residual 1.329 1.464 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C ACE U 0 " pdb=" N PHE U 1 " ideal model delta sigma weight residual 1.329 1.464 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C ACE t 0 " pdb=" N PHE t 1 " ideal model delta sigma weight residual 1.329 1.464 -0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" C ACE Q 0 " pdb=" N PHE Q 1 " ideal model delta sigma weight residual 1.329 1.464 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C ACE z 0 " pdb=" N PHE z 1 " ideal model delta sigma weight residual 1.329 1.464 -0.135 2.00e-02 2.50e+03 4.53e+01 ... (remaining 3478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 4047 1.61 - 3.21: 233 3.21 - 4.82: 104 4.82 - 6.42: 64 6.42 - 8.03: 24 Bond angle restraints: 4472 Sorted by residual: angle pdb=" CA PHE y 1 " pdb=" CB PHE y 1 " pdb=" CG PHE y 1 " ideal model delta sigma weight residual 113.80 108.27 5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" CA PHE g 1 " pdb=" CB PHE g 1 " pdb=" CG PHE g 1 " ideal model delta sigma weight residual 113.80 109.07 4.73 1.00e+00 1.00e+00 2.24e+01 angle pdb=" CA PHE R 1 " pdb=" CB PHE R 1 " pdb=" CG PHE R 1 " ideal model delta sigma weight residual 113.80 109.27 4.53 1.00e+00 1.00e+00 2.05e+01 angle pdb=" CA PHE Z 1 " pdb=" CB PHE Z 1 " pdb=" CG PHE Z 1 " ideal model delta sigma weight residual 113.80 109.39 4.41 1.00e+00 1.00e+00 1.94e+01 angle pdb=" CA PHE j 1 " pdb=" CB PHE j 1 " pdb=" CG PHE j 1 " ideal model delta sigma weight residual 113.80 109.42 4.38 1.00e+00 1.00e+00 1.92e+01 ... (remaining 4467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 1645 36.00 - 72.00: 126 72.00 - 108.00: 3 108.00 - 144.00: 0 144.00 - 180.00: 32 Dihedral angle restraints: 1806 sinusoidal: 903 harmonic: 903 Sorted by residual: dihedral pdb=" CH3 ACE M 0 " pdb=" C ACE M 0 " pdb=" N PHE M 1 " pdb=" CA PHE M 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.00 -180.00 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE v 0 " pdb=" C ACE v 0 " pdb=" N PHE v 1 " pdb=" CA PHE v 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.01 -179.99 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE p 0 " pdb=" C ACE p 0 " pdb=" N PHE p 1 " pdb=" CA PHE p 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.01 -179.99 1 5.00e+00 4.00e-02 7.68e+02 ... (remaining 1803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 266 0.036 - 0.072: 28 0.072 - 0.107: 0 0.107 - 0.143: 0 0.143 - 0.178: 7 Chirality restraints: 301 Sorted by residual: chirality pdb=" CA GLU u 8 " pdb=" N GLU u 8 " pdb=" C GLU u 8 " pdb=" CB GLU u 8 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA GLU n 8 " pdb=" N GLU n 8 " pdb=" C GLU n 8 " pdb=" CB GLU n 8 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA GLU y 8 " pdb=" N GLU y 8 " pdb=" C GLU y 8 " pdb=" CB GLU y 8 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 298 not shown) Planarity restraints: 559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 3 " 0.004 2.00e-02 2.50e+03 4.30e-03 3.23e-01 pdb=" CG PHE G 3 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE G 3 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE G 3 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE G 3 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 3 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE G 3 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE T 3 " 0.005 2.00e-02 2.50e+03 4.25e-03 3.16e-01 pdb=" CG PHE T 3 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE T 3 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE T 3 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE T 3 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE T 3 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE T 3 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE o 5 " -0.005 2.00e-02 2.50e+03 3.65e-03 2.34e-01 pdb=" CG PHE o 5 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE o 5 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE o 5 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE o 5 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE o 5 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE o 5 " -0.001 2.00e-02 2.50e+03 ... (remaining 556 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 1360 2.88 - 3.38: 2172 3.38 - 3.89: 5125 3.89 - 4.39: 5764 4.39 - 4.90: 10112 Nonbonded interactions: 24533 Sorted by model distance: nonbonded pdb=" O PHE v 7 " pdb=" N NH2 w 9 " model vdw 2.370 3.120 nonbonded pdb=" NZ LYS u 2 " pdb=" O PHE u 3 " model vdw 2.372 3.120 nonbonded pdb=" N NH2 Z 9 " pdb=" O PHE t 7 " model vdw 2.381 3.120 nonbonded pdb=" OE1 GLU Z 8 " pdb=" NZ LYS t 6 " model vdw 2.416 3.120 nonbonded pdb=" OE1 GLU E 8 " pdb=" NZ LYS F 2 " model vdw 2.471 3.120 ... (remaining 24528 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 '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 'O' 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 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'g' 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.860 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 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 : 0.017 0.135 3526 Z= 0.976 Angle : 1.289 8.028 4472 Z= 0.663 Chirality : 0.032 0.178 301 Planarity : 0.001 0.005 559 Dihedral : 35.651 179.997 1204 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 1.16 % Allowed : 13.95 % Favored : 84.88 % Rotamer: Outliers : 6.64 % Allowed : 27.57 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.45), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE G 3 Details of bonding type rmsd/Z covalent geometry : bond 0.01626 / 0.80 ( 3483) covalent geometry : angle 1.28924 / 0.66 ( 4472) hydrogen bonds : bond 0.26384 / 14.53 ( 21) hydrogen bonds : angle 10.79601 / 6.93 ( 57) Misc. bond : bond 0.05069 / 2.94 ( 43) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 LYS cc_start: 0.7530 (ptpp) cc_final: 0.7279 (mtpt) REVERT: X 1 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6788 (p90) REVERT: l 1 PHE cc_start: 0.6665 (OUTLIER) cc_final: 0.6243 (t80) REVERT: o 2 LYS cc_start: 0.7674 (mptt) cc_final: 0.7155 (mptt) outliers start: 20 outliers final: 0 residues processed: 66 average time/residue: 0.0845 time to fit residues: 6.5903 Evaluate side-chains 45 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 1 PHE Chi-restraints excluded: chain l residue 1 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.088575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.070935 restraints weight = 8994.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.072972 restraints weight = 5312.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074341 restraints weight = 3747.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075277 restraints weight = 2950.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.075870 restraints weight = 2490.706| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 1.0092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.318 3526 Z= 3.264 Angle : 3.276 30.605 4472 Z= 1.629 Chirality : 0.196 0.818 301 Planarity : 0.022 0.149 559 Dihedral : 33.311 179.686 391 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 90.05 Ramachandran Plot: Outliers : 4.65 % Allowed : 31.78 % Favored : 63.57 % Rotamer: Outliers : 11.63 % Allowed : 28.90 % Favored : 59.47 % Cbeta Deviations : 4.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.66 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.74 (0.39), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.13 (0.30), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.115 0.015 PHE b 1 Details of bonding type rmsd/Z covalent geometry : bond 0.07948 / 3.28 ( 3483) covalent geometry : angle 3.27600 / 1.63 ( 4472) hydrogen bonds : bond 0.18645 / 9.85 ( 21) hydrogen bonds : angle 10.41114 / 6.76 ( 57) Misc. bond : bond 0.00705 / 0.39 ( 43) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 2 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8358 (tmtt) REVERT: E 6 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7773 (ttmm) REVERT: F 2 LYS cc_start: 0.8715 (ptpp) cc_final: 0.8376 (mtpp) REVERT: G 6 LYS cc_start: 0.9066 (ttmt) cc_final: 0.8568 (tttt) REVERT: H 8 GLU cc_start: 0.7778 (mp0) cc_final: 0.7147 (mp0) REVERT: S 8 GLU cc_start: 0.8238 (tt0) cc_final: 0.7987 (tt0) REVERT: U 2 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8073 (tmtt) REVERT: I 6 LYS cc_start: 0.8285 (mmtt) cc_final: 0.8026 (mmtm) REVERT: K 6 LYS cc_start: 0.9032 (ttmt) cc_final: 0.8466 (tttt) REVERT: L 3 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8435 (m-80) REVERT: Z 2 LYS cc_start: 0.8826 (tttm) cc_final: 0.8155 (ttmt) REVERT: a 2 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8008 (tmmt) REVERT: W 2 LYS cc_start: 0.7816 (mmmt) cc_final: 0.7513 (mmmm) REVERT: g 3 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8621 (m-80) REVERT: g 6 LYS cc_start: 0.8406 (mptt) cc_final: 0.7969 (ttmt) REVERT: i 2 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.7528 (tmtt) REVERT: j 8 GLU cc_start: 0.8052 (tt0) cc_final: 0.7839 (tt0) REVERT: c 3 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8343 (m-10) REVERT: c 6 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8084 (pptt) REVERT: e 6 LYS cc_start: 0.8911 (ttmt) cc_final: 0.8348 (tttt) REVERT: f 3 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8651 (m-80) REVERT: q 6 LYS cc_start: 0.8372 (mptt) cc_final: 0.8118 (mtpt) REVERT: s 6 LYS cc_start: 0.8382 (mptt) cc_final: 0.8001 (ttmm) REVERT: m 6 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8131 (mtpp) REVERT: n 2 LYS cc_start: 0.8215 (tptt) cc_final: 0.7517 (tptt) REVERT: o 6 LYS cc_start: 0.8230 (pttp) cc_final: 0.7988 (pttm) REVERT: u 2 LYS cc_start: 0.8268 (tptp) cc_final: 0.7856 (tptt) REVERT: z 2 LYS cc_start: 0.8812 (tttm) cc_final: 0.8550 (tttp) REVERT: z 8 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7930 (mt-10) REVERT: x 2 LYS cc_start: 0.8351 (mptt) cc_final: 0.8082 (mptt) outliers start: 35 outliers final: 23 residues processed: 116 average time/residue: 0.1208 time to fit residues: 15.4594 Evaluate side-chains 102 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain H residue 1 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain g residue 3 PHE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain k residue 3 PHE Chi-restraints excluded: chain l residue 3 PHE Chi-restraints excluded: chain l residue 5 PHE Chi-restraints excluded: chain m residue 3 PHE Chi-restraints excluded: chain u residue 1 PHE Chi-restraints excluded: chain z residue 6 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.086263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.069578 restraints weight = 8885.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071385 restraints weight = 5307.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.072663 restraints weight = 3786.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.073527 restraints weight = 2976.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.074066 restraints weight = 2513.421| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 1.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.290 3526 Z= 3.221 Angle : 3.108 29.682 4472 Z= 1.581 Chirality : 0.172 0.485 301 Planarity : 0.018 0.064 559 Dihedral : 25.811 179.559 387 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 98.54 Ramachandran Plot: Outliers : 4.65 % Allowed : 50.39 % Favored : 44.96 % Rotamer: Outliers : 22.26 % Allowed : 22.59 % Favored : 55.15 % Cbeta Deviations : 5.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.99 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.17 (0.31), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.22 (0.23), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.104 0.014 PHE W 3 Details of bonding type rmsd/Z covalent geometry : bond 0.07875 / 3.24 ( 3483) covalent geometry : angle 3.10801 / 1.58 ( 4472) hydrogen bonds : bond 0.20513 / 10.91 ( 21) hydrogen bonds : angle 10.76976 / 7.19 ( 57) Misc. bond : bond 0.00702 / 0.38 ( 43) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 86 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 6 LYS cc_start: 0.8041 (mmtt) cc_final: 0.7590 (mptt) REVERT: F 2 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8412 (mtpp) REVERT: G 2 LYS cc_start: 0.3543 (mmmt) cc_final: 0.2009 (tppt) REVERT: G 6 LYS cc_start: 0.9104 (ttmt) cc_final: 0.8661 (tttt) REVERT: H 6 LYS cc_start: 0.8208 (mmmt) cc_final: 0.7958 (mttt) REVERT: R 3 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: S 6 LYS cc_start: 0.7924 (mptt) cc_final: 0.7628 (mttp) REVERT: U 2 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8282 (tmtt) REVERT: I 6 LYS cc_start: 0.8210 (mmtt) cc_final: 0.6744 (mptt) REVERT: I 8 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8408 (mp0) REVERT: K 2 LYS cc_start: 0.8480 (mttt) cc_final: 0.8272 (mmmt) REVERT: K 6 LYS cc_start: 0.9056 (ttmt) cc_final: 0.8482 (tttt) REVERT: Z 2 LYS cc_start: 0.8874 (tttm) cc_final: 0.8319 (tttt) REVERT: a 2 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8024 (tmtt) REVERT: a 6 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8490 (tptm) REVERT: W 6 LYS cc_start: 0.9135 (ttmt) cc_final: 0.8655 (tttt) REVERT: i 2 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7436 (tmtt) REVERT: c 6 LYS cc_start: 0.8618 (mmtt) cc_final: 0.7869 (pptt) REVERT: e 6 LYS cc_start: 0.9033 (ttmt) cc_final: 0.8482 (tttt) REVERT: f 3 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8591 (m-80) REVERT: p 8 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: q 6 LYS cc_start: 0.8266 (mptt) cc_final: 0.8034 (mtpt) REVERT: k 2 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7416 (mmmt) REVERT: s 6 LYS cc_start: 0.8554 (mptt) cc_final: 0.8140 (ttmm) REVERT: s 8 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7394 (mt-10) REVERT: n 2 LYS cc_start: 0.8294 (tptt) cc_final: 0.7635 (tptt) REVERT: u 3 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8279 (t80) outliers start: 67 outliers final: 44 residues processed: 141 average time/residue: 0.1235 time to fit residues: 19.2283 Evaluate side-chains 134 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 81 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain H residue 1 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain T residue 6 LYS Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain k residue 2 LYS Chi-restraints excluded: chain k residue 3 PHE Chi-restraints excluded: chain k residue 5 PHE Chi-restraints excluded: chain l residue 3 PHE Chi-restraints excluded: chain l residue 5 PHE Chi-restraints excluded: chain m residue 3 PHE Chi-restraints excluded: chain m residue 5 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain o residue 3 PHE Chi-restraints excluded: chain o residue 5 PHE Chi-restraints excluded: chain u residue 3 PHE Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain x residue 3 PHE Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain y residue 8 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.073058 restraints weight = 8826.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.074783 restraints weight = 5526.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076005 restraints weight = 4027.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.076851 restraints weight = 3208.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077450 restraints weight = 2728.760| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 1.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.302 3526 Z= 3.200 Angle : 3.047 18.505 4472 Z= 1.579 Chirality : 0.167 0.500 301 Planarity : 0.018 0.050 559 Dihedral : 24.414 179.092 387 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 98.04 Ramachandran Plot: Outliers : 3.10 % Allowed : 55.43 % Favored : 41.47 % Rotamer: Outliers : 23.26 % Allowed : 27.24 % Favored : 49.50 % Cbeta Deviations : 6.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.66 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.50 (0.28), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.47 (0.22), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.104 0.014 PHE m 1 Details of bonding type rmsd/Z covalent geometry : bond 0.07852 / 3.22 ( 3483) covalent geometry : angle 3.04699 / 1.58 ( 4472) hydrogen bonds : bond 0.21591 / 11.52 ( 21) hydrogen bonds : angle 10.70387 / 7.17 ( 57) Misc. bond : bond 0.00678 / 0.37 ( 43) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 82 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 6 LYS cc_start: 0.9046 (ttmt) cc_final: 0.8657 (tttt) REVERT: R 3 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: U 2 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8474 (tmtt) REVERT: I 6 LYS cc_start: 0.8147 (mmtt) cc_final: 0.6862 (mptt) REVERT: K 6 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8624 (tttt) REVERT: Z 2 LYS cc_start: 0.8959 (tttm) cc_final: 0.8495 (tttt) REVERT: a 2 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8456 (tmtt) REVERT: M 6 LYS cc_start: 0.8314 (mmmm) cc_final: 0.8088 (mptt) REVERT: W 6 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8912 (tttt) REVERT: i 2 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7417 (tmtt) REVERT: c 3 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8636 (m-10) REVERT: c 6 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8003 (pptt) REVERT: e 6 LYS cc_start: 0.9144 (ttmt) cc_final: 0.8670 (tttt) REVERT: f 3 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8527 (m-80) REVERT: p 6 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8442 (tttt) REVERT: p 8 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: q 6 LYS cc_start: 0.8376 (mptt) cc_final: 0.8094 (mtpt) REVERT: k 2 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.7365 (mmmt) REVERT: k 6 LYS cc_start: 0.8608 (mtpp) cc_final: 0.8217 (mtmm) REVERT: l 3 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7884 (t80) REVERT: r 3 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8585 (m-80) REVERT: s 6 LYS cc_start: 0.8699 (mptt) cc_final: 0.8321 (ttmm) REVERT: m 6 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8210 (mtmm) REVERT: n 2 LYS cc_start: 0.8423 (tptt) cc_final: 0.7558 (tptt) REVERT: u 3 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8466 (t80) outliers start: 70 outliers final: 46 residues processed: 142 average time/residue: 0.1288 time to fit residues: 20.2797 Evaluate side-chains 135 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 79 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain H residue 1 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain T residue 6 LYS Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain L residue 1 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain b residue 8 GLU Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 1 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 7 PHE Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain k residue 2 LYS Chi-restraints excluded: chain k residue 3 PHE Chi-restraints excluded: chain k residue 5 PHE Chi-restraints excluded: chain l residue 3 PHE Chi-restraints excluded: chain r residue 3 PHE Chi-restraints excluded: chain m residue 3 PHE Chi-restraints excluded: chain m residue 5 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain v residue 5 PHE Chi-restraints excluded: chain o residue 3 PHE Chi-restraints excluded: chain o residue 5 PHE Chi-restraints excluded: chain u residue 3 PHE Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain x residue 3 PHE Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain y residue 8 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.083503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.066509 restraints weight = 10755.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.068585 restraints weight = 5980.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.069993 restraints weight = 4083.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.070926 restraints weight = 3131.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.071625 restraints weight = 2612.015| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 1.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.311 3526 Z= 3.191 Angle : 3.003 17.664 4472 Z= 1.561 Chirality : 0.167 0.506 301 Planarity : 0.017 0.050 559 Dihedral : 24.287 179.268 387 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 99.41 Ramachandran Plot: Outliers : 2.33 % Allowed : 59.30 % Favored : 38.37 % Rotamer: Outliers : 24.58 % Allowed : 29.90 % Favored : 45.51 % Cbeta Deviations : 5.98 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.66 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.62 (0.29), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.57 (0.22), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.105 0.014 PHE x 1 Details of bonding type rmsd/Z covalent geometry : bond 0.07837 / 3.21 ( 3483) covalent geometry : angle 3.00252 / 1.56 ( 4472) hydrogen bonds : bond 0.22261 / 11.87 ( 21) hydrogen bonds : angle 10.75793 / 7.18 ( 57) Misc. bond : bond 0.00687 / 0.37 ( 43) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 83 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 7 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8117 (t80) REVERT: G 6 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8646 (tttt) REVERT: R 3 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8105 (m-80) REVERT: R 8 GLU cc_start: 0.8836 (tt0) cc_final: 0.8560 (tt0) REVERT: U 2 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8245 (tmtt) REVERT: I 6 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7024 (mptt) REVERT: I 8 GLU cc_start: 0.8329 (mp0) cc_final: 0.8033 (mp0) REVERT: K 2 LYS cc_start: 0.8084 (mmmt) cc_final: 0.7541 (mmtt) REVERT: K 6 LYS cc_start: 0.9130 (ttmt) cc_final: 0.8563 (tttt) REVERT: L 6 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8342 (mmmm) REVERT: Z 2 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8229 (tttt) REVERT: a 2 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8290 (tmtt) REVERT: a 6 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8495 (tptm) REVERT: M 6 LYS cc_start: 0.8308 (mmmm) cc_final: 0.8018 (mptt) REVERT: W 2 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7558 (mmmt) REVERT: W 6 LYS cc_start: 0.9123 (ttmt) cc_final: 0.8786 (tttt) REVERT: g 6 LYS cc_start: 0.8298 (mptt) cc_final: 0.7545 (ttmt) REVERT: g 7 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8401 (m-80) REVERT: i 2 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7220 (tmtt) REVERT: c 3 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8678 (m-10) REVERT: c 6 LYS cc_start: 0.8614 (mmtt) cc_final: 0.7940 (pptt) REVERT: e 6 LYS cc_start: 0.9142 (ttmt) cc_final: 0.8609 (tttt) REVERT: f 3 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: p 6 LYS cc_start: 0.8897 (ttmt) cc_final: 0.8499 (tttt) REVERT: q 6 LYS cc_start: 0.8299 (mptt) cc_final: 0.8030 (mtpt) REVERT: k 2 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7382 (mmmt) REVERT: k 6 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8245 (mtmm) REVERT: l 3 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7986 (t80) REVERT: r 3 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8560 (m-80) REVERT: s 6 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8269 (ttmm) REVERT: m 6 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8055 (mtmm) REVERT: n 2 LYS cc_start: 0.8273 (tptt) cc_final: 0.7392 (tptt) outliers start: 74 outliers final: 50 residues processed: 145 average time/residue: 0.0916 time to fit residues: 14.8008 Evaluate side-chains 143 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 79 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain H residue 1 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain T residue 1 PHE Chi-restraints excluded: chain T residue 6 LYS Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain L residue 1 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain V residue 8 GLU Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 1 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 7 PHE Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain k residue 2 LYS Chi-restraints excluded: chain k residue 3 PHE Chi-restraints excluded: chain k residue 5 PHE Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain l residue 3 PHE Chi-restraints excluded: chain r residue 2 LYS Chi-restraints excluded: chain r residue 3 PHE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain t residue 8 GLU Chi-restraints excluded: chain m residue 3 PHE Chi-restraints excluded: chain m residue 5 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain v residue 5 PHE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain o residue 3 PHE Chi-restraints excluded: chain o residue 5 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain x residue 3 PHE Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain y residue 8 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.083188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.066228 restraints weight = 10613.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068264 restraints weight = 5958.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.069647 restraints weight = 4093.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070615 restraints weight = 3149.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071269 restraints weight = 2614.674| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 1.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.309 3526 Z= 3.183 Angle : 2.988 18.406 4472 Z= 1.553 Chirality : 0.166 0.515 301 Planarity : 0.017 0.052 559 Dihedral : 24.519 179.285 387 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 101.08 Ramachandran Plot: Outliers : 1.94 % Allowed : 59.69 % Favored : 38.37 % Rotamer: Outliers : 28.57 % Allowed : 28.24 % Favored : 43.19 % Cbeta Deviations : 6.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.67 (0.29), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.60 (0.22), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.109 0.014 PHE x 1 Details of bonding type rmsd/Z covalent geometry : bond 0.07819 / 3.20 ( 3483) covalent geometry : angle 2.98797 / 1.55 ( 4472) hydrogen bonds : bond 0.22653 / 12.04 ( 21) hydrogen bonds : angle 10.99696 / 7.38 ( 57) Misc. bond : bond 0.00675 / 0.37 ( 43) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 82 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 7 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8380 (t80) REVERT: G 6 LYS cc_start: 0.9033 (ttmt) cc_final: 0.8636 (tttt) REVERT: R 3 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: U 2 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8248 (tmtt) REVERT: I 3 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8339 (m-10) REVERT: I 6 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.6660 (mmtt) REVERT: I 8 GLU cc_start: 0.8343 (mp0) cc_final: 0.7975 (mp0) REVERT: K 2 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7268 (mmmt) REVERT: K 6 LYS cc_start: 0.9194 (ttmt) cc_final: 0.8664 (tttt) REVERT: Z 2 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8228 (tttt) REVERT: a 2 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8308 (tmtt) REVERT: a 6 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8516 (tptm) REVERT: M 6 LYS cc_start: 0.8327 (mmmm) cc_final: 0.8073 (mptt) REVERT: W 6 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8794 (tttt) REVERT: g 6 LYS cc_start: 0.8279 (mptt) cc_final: 0.7457 (ttmt) REVERT: i 2 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7248 (tmtt) REVERT: c 3 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8638 (m-10) REVERT: c 6 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8049 (pptt) REVERT: e 6 LYS cc_start: 0.9113 (ttmt) cc_final: 0.8554 (tttt) REVERT: f 3 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8468 (m-80) REVERT: p 8 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: q 6 LYS cc_start: 0.8389 (mptt) cc_final: 0.8007 (mtpp) REVERT: k 1 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: k 2 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7419 (mmmt) REVERT: k 6 LYS cc_start: 0.8591 (mtpp) cc_final: 0.7681 (mtmm) REVERT: r 3 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8568 (m-80) REVERT: s 6 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8252 (ttmm) REVERT: m 6 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8072 (mtmm) REVERT: n 2 LYS cc_start: 0.8267 (tptt) cc_final: 0.7390 (tptt) REVERT: v 6 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8207 (ttmt) REVERT: w 6 LYS cc_start: 0.9141 (mptt) cc_final: 0.8857 (mptt) REVERT: u 3 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8287 (t80) outliers start: 86 outliers final: 56 residues processed: 151 average time/residue: 0.0991 time to fit residues: 16.7187 Evaluate side-chains 154 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 80 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain H residue 1 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain T residue 1 PHE Chi-restraints excluded: chain T residue 6 LYS Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain I residue 3 PHE Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain L residue 1 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain V residue 8 GLU Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 1 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 7 PHE Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain k residue 1 PHE Chi-restraints excluded: chain k residue 2 LYS Chi-restraints excluded: chain k residue 3 PHE Chi-restraints excluded: chain k residue 5 PHE Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain r residue 2 LYS Chi-restraints excluded: chain r residue 3 PHE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain t residue 8 GLU Chi-restraints excluded: chain m residue 3 PHE Chi-restraints excluded: chain m residue 5 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain v residue 5 PHE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain w residue 2 LYS Chi-restraints excluded: chain o residue 3 PHE Chi-restraints excluded: chain o residue 5 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain u residue 3 PHE Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain x residue 3 PHE Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain y residue 8 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.087573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.071243 restraints weight = 9328.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073039 restraints weight = 5738.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.074277 restraints weight = 4126.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075109 restraints weight = 3278.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.075522 restraints weight = 2787.394| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 1.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.305 3526 Z= 3.181 Angle : 2.985 17.993 4472 Z= 1.551 Chirality : 0.166 0.515 301 Planarity : 0.017 0.052 559 Dihedral : 24.487 179.327 387 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 101.54 Ramachandran Plot: Outliers : 2.33 % Allowed : 58.53 % Favored : 39.15 % Rotamer: Outliers : 28.24 % Allowed : 29.24 % Favored : 42.52 % Cbeta Deviations : 6.64 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.72 (0.28), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.64 (0.21), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.110 0.014 PHE x 1 Details of bonding type rmsd/Z covalent geometry : bond 0.07816 / 3.20 ( 3483) covalent geometry : angle 2.98461 / 1.55 ( 4472) hydrogen bonds : bond 0.23049 / 12.27 ( 21) hydrogen bonds : angle 11.21912 / 7.56 ( 57) Misc. bond : bond 0.00680 / 0.37 ( 43) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 84 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 2 LYS cc_start: 0.8856 (tttp) cc_final: 0.8416 (ttmt) REVERT: E 7 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8539 (t80) REVERT: G 6 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8659 (tttt) REVERT: R 3 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8085 (m-80) REVERT: U 2 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8423 (tmtt) REVERT: I 3 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8345 (m-10) REVERT: I 6 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7374 (mmtt) REVERT: K 2 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7335 (mmmt) REVERT: K 6 LYS cc_start: 0.9248 (ttmt) cc_final: 0.8762 (tttt) REVERT: Z 2 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8388 (tttt) REVERT: a 2 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8417 (tmtt) REVERT: a 6 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8655 (tptm) REVERT: W 6 LYS cc_start: 0.9166 (ttmt) cc_final: 0.8728 (tttt) REVERT: g 6 LYS cc_start: 0.8361 (mptt) cc_final: 0.7613 (ttmt) REVERT: i 2 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7383 (tmtt) REVERT: c 3 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8613 (m-10) REVERT: c 6 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8136 (pptt) REVERT: e 6 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8617 (tttt) REVERT: f 3 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8520 (m-80) REVERT: p 8 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: q 6 LYS cc_start: 0.8567 (mptt) cc_final: 0.8246 (mtpp) REVERT: k 1 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: k 2 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.7522 (mmmt) REVERT: l 2 LYS cc_start: 0.8494 (tptt) cc_final: 0.7967 (tptt) REVERT: r 3 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8615 (m-80) REVERT: s 6 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8401 (ttmm) REVERT: m 6 LYS cc_start: 0.8649 (mtpp) cc_final: 0.8224 (mtmm) REVERT: n 2 LYS cc_start: 0.8360 (tptt) cc_final: 0.7533 (tptt) REVERT: v 6 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8384 (ttmt) REVERT: v 7 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.9002 (m-80) REVERT: w 6 LYS cc_start: 0.9207 (mptt) cc_final: 0.8928 (mptt) REVERT: u 2 LYS cc_start: 0.8432 (tptt) cc_final: 0.8231 (tptt) REVERT: u 3 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8264 (t80) outliers start: 85 outliers final: 58 residues processed: 153 average time/residue: 0.1083 time to fit residues: 18.4482 Evaluate side-chains 159 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 82 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain H residue 1 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain T residue 1 PHE Chi-restraints excluded: chain T residue 6 LYS Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain I residue 3 PHE Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain L residue 1 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain V residue 8 GLU Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 1 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 7 PHE Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain k residue 1 PHE Chi-restraints excluded: chain k residue 2 LYS Chi-restraints excluded: chain k residue 3 PHE Chi-restraints excluded: chain k residue 5 PHE Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain r residue 2 LYS Chi-restraints excluded: chain r residue 3 PHE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain t residue 8 GLU Chi-restraints excluded: chain m residue 3 PHE Chi-restraints excluded: chain m residue 5 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain v residue 5 PHE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain v residue 7 PHE Chi-restraints excluded: chain w residue 2 LYS Chi-restraints excluded: chain o residue 3 PHE Chi-restraints excluded: chain o residue 5 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain u residue 3 PHE Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain x residue 3 PHE Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain y residue 8 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.087747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071524 restraints weight = 9147.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.073280 restraints weight = 5712.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.074500 restraints weight = 4143.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.075328 restraints weight = 3303.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.075906 restraints weight = 2816.148| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 1.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.305 3526 Z= 3.181 Angle : 2.987 17.764 4472 Z= 1.553 Chirality : 0.167 0.512 301 Planarity : 0.017 0.052 559 Dihedral : 24.484 179.357 387 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 101.23 Ramachandran Plot: Outliers : 2.33 % Allowed : 58.14 % Favored : 39.53 % Rotamer: Outliers : 29.24 % Allowed : 28.24 % Favored : 42.52 % Cbeta Deviations : 6.64 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.66 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.82 (0.27), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.72 (0.20), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.108 0.013 PHE x 1 Details of bonding type rmsd/Z covalent geometry : bond 0.07816 / 3.20 ( 3483) covalent geometry : angle 2.98714 / 1.55 ( 4472) hydrogen bonds : bond 0.23299 / 12.36 ( 21) hydrogen bonds : angle 11.41472 / 7.71 ( 57) Misc. bond : bond 0.00681 / 0.37 ( 43) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 82 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 2 LYS cc_start: 0.8873 (tttp) cc_final: 0.8408 (ttmt) REVERT: E 7 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8548 (t80) REVERT: G 6 LYS cc_start: 0.9012 (ttmt) cc_final: 0.8672 (tttt) REVERT: R 3 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8079 (m-80) REVERT: U 2 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8441 (tmtt) REVERT: I 3 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8340 (m-10) REVERT: I 6 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7412 (mmtt) REVERT: K 2 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7343 (mmmt) REVERT: K 6 LYS cc_start: 0.9229 (ttmt) cc_final: 0.8723 (tttt) REVERT: Z 2 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8378 (tttt) REVERT: a 2 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8418 (tmtt) REVERT: a 6 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8654 (tptm) REVERT: W 6 LYS cc_start: 0.9164 (ttmt) cc_final: 0.8891 (tttt) REVERT: g 6 LYS cc_start: 0.8360 (mptt) cc_final: 0.7604 (ttmt) REVERT: i 2 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.7388 (tmtt) REVERT: c 3 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8610 (m-10) REVERT: c 6 LYS cc_start: 0.8584 (mmtt) cc_final: 0.8137 (pptt) REVERT: e 6 LYS cc_start: 0.9132 (ttmt) cc_final: 0.8585 (tttt) REVERT: f 3 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: p 8 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: q 6 LYS cc_start: 0.8554 (mptt) cc_final: 0.8262 (mtpp) REVERT: k 1 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: k 2 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7508 (mmmt) REVERT: l 2 LYS cc_start: 0.8605 (tptt) cc_final: 0.8110 (tptt) REVERT: r 3 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8600 (m-80) REVERT: s 6 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8530 (mttp) REVERT: m 6 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8265 (mtmm) REVERT: n 2 LYS cc_start: 0.8375 (tptt) cc_final: 0.7544 (tptt) REVERT: v 6 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8405 (ttmt) REVERT: v 7 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.8996 (m-80) REVERT: w 6 LYS cc_start: 0.9205 (mptt) cc_final: 0.8923 (mptt) REVERT: u 2 LYS cc_start: 0.8414 (tptt) cc_final: 0.8166 (tptt) REVERT: u 3 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8269 (t80) outliers start: 88 outliers final: 61 residues processed: 152 average time/residue: 0.1343 time to fit residues: 22.7341 Evaluate side-chains 161 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 81 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain H residue 1 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain T residue 1 PHE Chi-restraints excluded: chain T residue 6 LYS Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain I residue 3 PHE Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain L residue 1 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain V residue 8 GLU Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 1 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 7 PHE Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain k residue 1 PHE Chi-restraints excluded: chain k residue 2 LYS Chi-restraints excluded: chain k residue 3 PHE Chi-restraints excluded: chain k residue 5 PHE Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain r residue 2 LYS Chi-restraints excluded: chain r residue 3 PHE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 8 GLU Chi-restraints excluded: chain t residue 8 GLU Chi-restraints excluded: chain m residue 5 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain v residue 5 PHE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain v residue 7 PHE Chi-restraints excluded: chain w residue 2 LYS Chi-restraints excluded: chain o residue 3 PHE Chi-restraints excluded: chain o residue 5 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain u residue 3 PHE Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain x residue 1 PHE Chi-restraints excluded: chain x residue 3 PHE Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain y residue 8 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.087636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.071041 restraints weight = 9862.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.072906 restraints weight = 5916.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.074211 restraints weight = 4207.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.075096 restraints weight = 3308.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.075587 restraints weight = 2789.570| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 1.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.303 3526 Z= 3.182 Angle : 3.001 17.832 4472 Z= 1.559 Chirality : 0.166 0.512 301 Planarity : 0.017 0.051 559 Dihedral : 24.495 179.440 387 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 100.32 Ramachandran Plot: Outliers : 1.94 % Allowed : 58.91 % Favored : 39.15 % Rotamer: Outliers : 29.57 % Allowed : 28.90 % Favored : 41.53 % Cbeta Deviations : 6.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.66 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.84 (0.26), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.73 (0.20), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.107 0.013 PHE x 1 Details of bonding type rmsd/Z covalent geometry : bond 0.07819 / 3.20 ( 3483) covalent geometry : angle 3.00110 / 1.56 ( 4472) hydrogen bonds : bond 0.23479 / 12.43 ( 21) hydrogen bonds : angle 11.61360 / 7.85 ( 57) Misc. bond : bond 0.00682 / 0.37 ( 43) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 83 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 2 LYS cc_start: 0.8890 (tttp) cc_final: 0.8426 (ttmt) REVERT: E 7 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8542 (t80) REVERT: G 6 LYS cc_start: 0.9003 (ttmt) cc_final: 0.8675 (tttt) REVERT: R 3 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: U 2 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8414 (tmtt) REVERT: I 3 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8308 (m-10) REVERT: I 6 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7411 (mmtt) REVERT: K 2 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7371 (mmmt) REVERT: K 6 LYS cc_start: 0.9235 (ttmt) cc_final: 0.8733 (tttt) REVERT: Z 2 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8359 (tttt) REVERT: a 2 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8375 (tmtt) REVERT: a 6 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8603 (tptm) REVERT: a 7 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8900 (m-80) REVERT: W 6 LYS cc_start: 0.9160 (ttmt) cc_final: 0.8844 (tttt) REVERT: g 6 LYS cc_start: 0.8346 (mptt) cc_final: 0.7576 (ttmt) REVERT: i 2 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.7314 (tmtt) REVERT: c 3 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8610 (m-10) REVERT: c 6 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8123 (pptt) REVERT: e 6 LYS cc_start: 0.9148 (ttmt) cc_final: 0.8631 (tttt) REVERT: f 3 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8518 (m-80) REVERT: p 8 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: q 6 LYS cc_start: 0.8557 (mptt) cc_final: 0.8227 (mtpp) REVERT: k 1 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: k 2 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7509 (mmmt) REVERT: r 3 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8579 (m-80) REVERT: s 6 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8457 (mttp) REVERT: m 6 LYS cc_start: 0.8660 (mtpp) cc_final: 0.8251 (mtmm) REVERT: n 2 LYS cc_start: 0.8353 (tptt) cc_final: 0.7519 (tptt) REVERT: v 6 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8387 (ttmt) REVERT: v 7 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8992 (m-80) REVERT: w 6 LYS cc_start: 0.9202 (mptt) cc_final: 0.8915 (mptt) REVERT: u 2 LYS cc_start: 0.8406 (tptt) cc_final: 0.8129 (tptt) REVERT: u 3 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8251 (t80) outliers start: 89 outliers final: 61 residues processed: 154 average time/residue: 0.1149 time to fit residues: 19.7458 Evaluate side-chains 164 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 83 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain H residue 1 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain T residue 1 PHE Chi-restraints excluded: chain T residue 6 LYS Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain I residue 3 PHE Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain L residue 1 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain a residue 7 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain V residue 8 GLU Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 1 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 7 PHE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain k residue 1 PHE Chi-restraints excluded: chain k residue 2 LYS Chi-restraints excluded: chain k residue 3 PHE Chi-restraints excluded: chain k residue 5 PHE Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain r residue 2 LYS Chi-restraints excluded: chain r residue 3 PHE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 8 GLU Chi-restraints excluded: chain m residue 5 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain v residue 5 PHE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain v residue 7 PHE Chi-restraints excluded: chain w residue 2 LYS Chi-restraints excluded: chain o residue 3 PHE Chi-restraints excluded: chain o residue 5 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain u residue 3 PHE Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain x residue 1 PHE Chi-restraints excluded: chain x residue 3 PHE Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain y residue 8 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.087376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071124 restraints weight = 9512.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.072913 restraints weight = 5837.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.074156 restraints weight = 4198.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.074989 restraints weight = 3330.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.075580 restraints weight = 2837.123| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 1.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.304 3526 Z= 3.182 Angle : 3.004 17.823 4472 Z= 1.560 Chirality : 0.167 0.512 301 Planarity : 0.017 0.051 559 Dihedral : 24.426 179.505 387 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 99.86 Ramachandran Plot: Outliers : 2.33 % Allowed : 58.53 % Favored : 39.15 % Rotamer: Outliers : 27.24 % Allowed : 30.23 % Favored : 42.52 % Cbeta Deviations : 6.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.66 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.82 (0.27), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.72 (0.20), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.107 0.013 PHE x 1 Details of bonding type rmsd/Z covalent geometry : bond 0.07818 / 3.20 ( 3483) covalent geometry : angle 3.00379 / 1.56 ( 4472) hydrogen bonds : bond 0.23569 / 12.45 ( 21) hydrogen bonds : angle 11.76662 / 7.94 ( 57) Misc. bond : bond 0.00685 / 0.37 ( 43) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 84 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 2 LYS cc_start: 0.8893 (tttp) cc_final: 0.8439 (ttmt) REVERT: E 7 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8597 (t80) REVERT: G 6 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8683 (tttt) REVERT: R 3 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8006 (m-80) REVERT: U 2 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8444 (tmtt) REVERT: I 3 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8305 (m-10) REVERT: I 6 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7445 (mmtt) REVERT: K 6 LYS cc_start: 0.9233 (ttmt) cc_final: 0.8743 (tttt) REVERT: Z 2 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8381 (tttt) REVERT: a 2 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8393 (tmtt) REVERT: a 6 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8620 (tptm) REVERT: a 7 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8892 (m-80) REVERT: W 6 LYS cc_start: 0.9169 (ttmt) cc_final: 0.8866 (tttt) REVERT: g 6 LYS cc_start: 0.8364 (mptt) cc_final: 0.7608 (ttmt) REVERT: i 2 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.7340 (tmtt) REVERT: c 3 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8602 (m-10) REVERT: c 6 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8154 (pptt) REVERT: f 3 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: p 8 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: q 6 LYS cc_start: 0.8572 (mptt) cc_final: 0.8256 (mtpp) REVERT: k 1 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: k 2 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7511 (mmmt) REVERT: r 3 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8614 (m-80) REVERT: s 6 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8490 (mttp) REVERT: m 6 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8311 (mtmm) REVERT: n 2 LYS cc_start: 0.8371 (tptt) cc_final: 0.7549 (tptt) REVERT: v 7 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8999 (m-80) REVERT: w 6 LYS cc_start: 0.9210 (mptt) cc_final: 0.8931 (mptt) REVERT: u 2 LYS cc_start: 0.8424 (tptt) cc_final: 0.8144 (tptt) REVERT: u 3 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8329 (t80) outliers start: 82 outliers final: 61 residues processed: 149 average time/residue: 0.0848 time to fit residues: 14.0829 Evaluate side-chains 162 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 83 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain H residue 1 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain T residue 1 PHE Chi-restraints excluded: chain T residue 6 LYS Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain I residue 3 PHE Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain L residue 1 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain a residue 7 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain V residue 8 GLU Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 1 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 7 PHE Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain k residue 1 PHE Chi-restraints excluded: chain k residue 2 LYS Chi-restraints excluded: chain k residue 3 PHE Chi-restraints excluded: chain k residue 5 PHE Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain r residue 2 LYS Chi-restraints excluded: chain r residue 3 PHE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain m residue 5 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain v residue 5 PHE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain v residue 7 PHE Chi-restraints excluded: chain w residue 2 LYS Chi-restraints excluded: chain o residue 3 PHE Chi-restraints excluded: chain o residue 5 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain u residue 3 PHE Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain x residue 1 PHE Chi-restraints excluded: chain x residue 3 PHE Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain y residue 8 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.086280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.070117 restraints weight = 9293.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.071963 restraints weight = 5523.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.073241 restraints weight = 3918.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.074061 restraints weight = 3066.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.074720 restraints weight = 2597.725| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 1.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.304 3526 Z= 3.181 Angle : 3.006 17.805 4472 Z= 1.562 Chirality : 0.167 0.510 301 Planarity : 0.017 0.051 559 Dihedral : 24.440 179.436 387 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 99.56 Ramachandran Plot: Outliers : 1.94 % Allowed : 58.53 % Favored : 39.53 % Rotamer: Outliers : 25.91 % Allowed : 32.23 % Favored : 41.86 % Cbeta Deviations : 6.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.66 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.83 (0.27), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.72 (0.20), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.107 0.013 PHE x 1 Details of bonding type rmsd/Z covalent geometry : bond 0.07818 / 3.20 ( 3483) covalent geometry : angle 3.00620 / 1.56 ( 4472) hydrogen bonds : bond 0.23610 / 12.41 ( 21) hydrogen bonds : angle 11.62887 / 7.89 ( 57) Misc. bond : bond 0.00687 / 0.37 ( 43) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 612.80 seconds wall clock time: 11 minutes 22.76 seconds (682.76 seconds total)