Starting phenix.real_space_refine on Thu Oct 22 18:20:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pds_71542/10_2026/9pds_71542.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pds_71542/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/9pds_71542/10_2026/9pds_71542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pds_71542/10_2026/9pds_71542.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pds_71542/10_2026/9pds_71542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pds_71542/10_2026/9pds_71542.map" } 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-2.3rc1-6221/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: 1.01, per 1000 atoms: 0.30 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: 0.34 Conformation dependent library (CDL) restraints added in 125.8 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: 0.07 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: 0.30 Time building geometry restraints manager: 0.43 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.540 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.980 ------------------------------------------------------------------------------- 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 : 0.134 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: 0.0898 time to fit residues: 7.0128 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 : 0.128 ------------------------------------------------------------------------------- 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: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4561 r_free = 0.4561 target = 0.173426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.149870 restraints weight = 4973.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.154445 restraints weight = 2656.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.157604 restraints weight = 1714.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.159602 restraints weight = 1230.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.161210 restraints weight = 965.757| |-----------------------------------------------------------------------------| r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3526 Z= 0.119 Angle : 0.978 11.192 4472 Z= 0.372 Chirality : 0.029 0.083 301 Planarity : 0.002 0.011 559 Dihedral : 52.073 179.875 391 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.65 % Allowed : 28.90 % Favored : 67.44 % 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: -3.48 (0.45), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.001 PHE F 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 3483) covalent geometry : angle 0.97789 / 0.37 ( 4472) hydrogen bonds : bond 0.02506 / 1.11 ( 21) hydrogen bonds : angle 6.22284 / 4.13 ( 57) Misc. bond : bond 0.00022 / 0.01 ( 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 60 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 3 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6274 (p90) REVERT: b 3 PHE cc_start: 0.7327 (m-80) cc_final: 0.7119 (m-80) REVERT: f 3 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7503 (m-10) REVERT: l 1 PHE cc_start: 0.6794 (OUTLIER) cc_final: 0.6218 (t80) REVERT: n 2 LYS cc_start: 0.7358 (tptt) cc_final: 0.6700 (tptt) REVERT: w 6 LYS cc_start: 0.7289 (mptt) cc_final: 0.7079 (mtpt) REVERT: o 2 LYS cc_start: 0.7237 (mptt) cc_final: 0.6855 (mptt) REVERT: o 6 LYS cc_start: 0.7664 (pttp) cc_final: 0.7421 (pttp) outliers start: 11 outliers final: 7 residues processed: 54 average time/residue: 0.1056 time to fit residues: 6.5740 Evaluate side-chains 55 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain l residue 1 PHE Chi-restraints excluded: chain l residue 3 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.122802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.100237 restraints weight = 6098.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.103352 restraints weight = 3426.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.105533 restraints weight = 2340.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.107002 restraints weight = 1805.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.108080 restraints weight = 1509.980| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.054 3526 Z= 0.495 Angle : 1.219 13.330 4472 Z= 0.527 Chirality : 0.049 0.172 301 Planarity : 0.005 0.037 559 Dihedral : 51.524 179.888 389 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.28 % Favored : 83.72 % Rotamer: Outliers : 7.97 % Allowed : 25.25 % Favored : 66.78 % 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: -4.50 (0.41), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.31), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.042 0.004 PHE g 7 Details of bonding type rmsd/Z covalent geometry : bond 0.01199 / 0.50 ( 3483) covalent geometry : angle 1.21944 / 0.53 ( 4472) hydrogen bonds : bond 0.03218 / 1.79 ( 21) hydrogen bonds : angle 4.60981 / 3.18 ( 57) Misc. bond : bond 0.00140 / 0.08 ( 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 70 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 8 GLU cc_start: 0.7804 (tt0) cc_final: 0.7196 (mt-10) REVERT: F 5 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8237 (t80) REVERT: G 6 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8139 (tttt) REVERT: H 3 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: T 2 LYS cc_start: 0.7794 (tptp) cc_final: 0.7446 (tptp) REVERT: J 5 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8209 (t80) REVERT: K 3 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.6209 (p90) REVERT: K 8 GLU cc_start: 0.6961 (pm20) cc_final: 0.6589 (pm20) REVERT: a 6 LYS cc_start: 0.7578 (tptp) cc_final: 0.6325 (mptt) REVERT: M 2 LYS cc_start: 0.8376 (mmtp) cc_final: 0.7875 (mmtp) REVERT: V 6 LYS cc_start: 0.7848 (mtmt) cc_final: 0.7596 (mtmm) REVERT: g 6 LYS cc_start: 0.8438 (tttt) cc_final: 0.8189 (ttmt) REVERT: i 6 LYS cc_start: 0.7885 (tptp) cc_final: 0.6401 (mptt) REVERT: e 3 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.6966 (p90) REVERT: f 3 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8248 (m-80) REVERT: k 2 LYS cc_start: 0.8068 (mmtt) cc_final: 0.7746 (mptt) REVERT: l 6 LYS cc_start: 0.8422 (ptmm) cc_final: 0.8187 (ptmm) REVERT: m 1 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.6314 (m-80) REVERT: n 2 LYS cc_start: 0.7921 (tptt) cc_final: 0.7540 (tptt) REVERT: o 6 LYS cc_start: 0.7634 (pttp) cc_final: 0.7410 (pttm) REVERT: u 2 LYS cc_start: 0.7889 (tptm) cc_final: 0.7670 (tptt) REVERT: u 6 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7937 (tttp) outliers start: 24 outliers final: 10 residues processed: 70 average time/residue: 0.1345 time to fit residues: 10.5052 Evaluate side-chains 50 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 32 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain V residue 5 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f 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 1 PHE Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain x residue 7 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.137289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.116202 restraints weight = 5506.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.119583 restraints weight = 2785.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.121781 restraints weight = 1791.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.123357 restraints weight = 1332.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.124492 restraints weight = 1073.440| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3526 Z= 0.124 Angle : 1.007 11.322 4472 Z= 0.388 Chirality : 0.031 0.083 301 Planarity : 0.002 0.014 559 Dihedral : 52.199 179.731 387 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 6.31 % Allowed : 25.91 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.42 (0.41), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.31), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.001 PHE e 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3483) covalent geometry : angle 1.00675 / 0.39 ( 4472) hydrogen bonds : bond 0.01635 / 0.77 ( 21) hydrogen bonds : angle 4.29302 / 3.16 ( 57) Misc. bond : bond 0.00027 / 0.02 ( 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 63 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 8 GLU cc_start: 0.7619 (tt0) cc_final: 0.6849 (mt-10) REVERT: F 2 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7702 (mtpt) REVERT: F 5 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7743 (t80) REVERT: F 7 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6041 (m-80) REVERT: H 3 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7538 (m-80) REVERT: T 2 LYS cc_start: 0.7089 (tptp) cc_final: 0.6617 (tptp) REVERT: K 3 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.5859 (p90) REVERT: M 2 LYS cc_start: 0.8324 (mmtp) cc_final: 0.7964 (mmtp) REVERT: g 6 LYS cc_start: 0.8246 (tttt) cc_final: 0.7950 (ttmt) REVERT: g 7 PHE cc_start: 0.5777 (OUTLIER) cc_final: 0.3059 (p90) REVERT: e 3 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6591 (p90) REVERT: k 2 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7846 (mptt) REVERT: l 1 PHE cc_start: 0.7894 (t80) cc_final: 0.7346 (t80) REVERT: s 8 GLU cc_start: 0.7289 (mp0) cc_final: 0.7088 (mp0) REVERT: n 2 LYS cc_start: 0.7732 (tptt) cc_final: 0.7322 (tptt) REVERT: u 6 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7856 (tttp) outliers start: 19 outliers final: 9 residues processed: 61 average time/residue: 0.1341 time to fit residues: 9.1830 Evaluate side-chains 53 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain l residue 3 PHE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain u residue 6 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.117053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.094969 restraints weight = 6259.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.097968 restraints weight = 3487.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.100001 restraints weight = 2366.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.101216 restraints weight = 1825.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.102267 restraints weight = 1547.802| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.7585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.047 3526 Z= 0.467 Angle : 1.197 13.974 4472 Z= 0.512 Chirality : 0.047 0.151 301 Planarity : 0.005 0.021 559 Dihedral : 50.920 179.968 387 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.89 % Favored : 84.11 % Rotamer: Outliers : 7.64 % Allowed : 24.92 % Favored : 67.44 % 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: -5.25 (0.35), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.27), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.033 0.003 PHE e 1 Details of bonding type rmsd/Z covalent geometry : bond 0.01148 / 0.47 ( 3483) covalent geometry : angle 1.19661 / 0.51 ( 4472) hydrogen bonds : bond 0.03080 / 1.50 ( 21) hydrogen bonds : angle 4.56989 / 3.18 ( 57) Misc. bond : bond 0.00097 / 0.06 ( 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 66 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 6 LYS cc_start: 0.7374 (mmtt) cc_final: 0.6809 (mttt) REVERT: H 3 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7743 (m-80) REVERT: T 2 LYS cc_start: 0.7790 (tptp) cc_final: 0.7460 (tptp) REVERT: T 6 LYS cc_start: 0.7970 (tptp) cc_final: 0.6663 (mptt) REVERT: U 8 GLU cc_start: 0.7857 (tt0) cc_final: 0.7225 (tm-30) REVERT: K 2 LYS cc_start: 0.8148 (mttt) cc_final: 0.7942 (mmmt) REVERT: K 3 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.5870 (p90) REVERT: K 6 LYS cc_start: 0.8438 (ptmt) cc_final: 0.7963 (ptmm) REVERT: L 3 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.8157 (m-10) REVERT: a 2 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7501 (tmmt) REVERT: a 6 LYS cc_start: 0.8025 (tptp) cc_final: 0.6766 (mptt) REVERT: g 6 LYS cc_start: 0.8584 (tttt) cc_final: 0.8210 (ttmt) REVERT: i 6 LYS cc_start: 0.8205 (tptp) cc_final: 0.6640 (mptt) REVERT: c 1 PHE cc_start: 0.6168 (OUTLIER) cc_final: 0.5687 (m-80) REVERT: e 3 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6684 (p90) REVERT: f 3 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: l 2 LYS cc_start: 0.7926 (tptt) cc_final: 0.7699 (tptt) REVERT: l 3 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7726 (t80) REVERT: l 6 LYS cc_start: 0.8272 (ptmm) cc_final: 0.7752 (ptmm) REVERT: n 2 LYS cc_start: 0.7903 (tptt) cc_final: 0.7458 (tptt) REVERT: o 6 LYS cc_start: 0.7494 (pttm) cc_final: 0.7053 (pttm) REVERT: u 2 LYS cc_start: 0.7869 (tptm) cc_final: 0.7477 (tptt) outliers start: 23 outliers final: 9 residues processed: 64 average time/residue: 0.1508 time to fit residues: 10.7078 Evaluate side-chains 57 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 7 PHE 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 X residue 3 PHE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f 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 7 PHE Chi-restraints excluded: chain x residue 7 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.131383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.110576 restraints weight = 5885.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.114060 restraints weight = 2797.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.116390 restraints weight = 1743.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.117956 restraints weight = 1265.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.119002 restraints weight = 1011.250| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.7123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3526 Z= 0.127 Angle : 1.007 11.299 4472 Z= 0.398 Chirality : 0.030 0.089 301 Planarity : 0.002 0.009 559 Dihedral : 51.532 179.968 387 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 6.31 % Allowed : 27.57 % Favored : 66.11 % 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: -4.99 (0.37), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.28), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.001 PHE e 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 3483) covalent geometry : angle 1.00653 / 0.40 ( 4472) hydrogen bonds : bond 0.01549 / 0.77 ( 21) hydrogen bonds : angle 3.90875 / 2.81 ( 57) Misc. bond : bond 0.00036 / 0.02 ( 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 65 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 8 GLU cc_start: 0.7728 (tt0) cc_final: 0.7051 (mt-10) REVERT: E 6 LYS cc_start: 0.7081 (mmtt) cc_final: 0.6515 (mttt) REVERT: G 6 LYS cc_start: 0.8697 (ttmt) cc_final: 0.7929 (tttt) REVERT: T 2 LYS cc_start: 0.7203 (tptp) cc_final: 0.6652 (tptp) REVERT: K 2 LYS cc_start: 0.7882 (mttt) cc_final: 0.7601 (mmmt) REVERT: K 3 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.5388 (p90) REVERT: K 6 LYS cc_start: 0.8171 (ptmt) cc_final: 0.7718 (ptmm) REVERT: L 6 LYS cc_start: 0.7487 (mmmm) cc_final: 0.6984 (mmtp) REVERT: X 6 LYS cc_start: 0.6744 (mtpt) cc_final: 0.6514 (mtmm) REVERT: g 6 LYS cc_start: 0.8486 (tttt) cc_final: 0.8241 (ttmt) REVERT: g 7 PHE cc_start: 0.6967 (OUTLIER) cc_final: 0.3462 (p90) REVERT: e 3 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6312 (p90) REVERT: k 2 LYS cc_start: 0.8347 (mmtp) cc_final: 0.8106 (mptt) REVERT: l 2 LYS cc_start: 0.7595 (tptt) cc_final: 0.7344 (tptt) REVERT: l 3 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7174 (t80) REVERT: n 2 LYS cc_start: 0.7646 (tptt) cc_final: 0.7271 (tptt) REVERT: n 6 LYS cc_start: 0.8221 (ptmm) cc_final: 0.7959 (tttp) outliers start: 19 outliers final: 11 residues processed: 64 average time/residue: 0.1242 time to fit residues: 8.9548 Evaluate side-chains 55 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain a residue 1 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f 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 7 PHE Chi-restraints excluded: chain x residue 7 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.114798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.093365 restraints weight = 6867.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.096289 restraints weight = 3717.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.098323 restraints weight = 2485.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.099695 restraints weight = 1890.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.100551 restraints weight = 1570.089| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.8294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.054 3526 Z= 0.535 Angle : 1.242 14.454 4472 Z= 0.539 Chirality : 0.048 0.159 301 Planarity : 0.005 0.032 559 Dihedral : 50.696 179.938 387 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.60 % Favored : 81.40 % Rotamer: Outliers : 6.64 % Allowed : 25.58 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.70 (0.34), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.34 (0.26), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.033 0.004 PHE o 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01307 / 0.54 ( 3483) covalent geometry : angle 1.24158 / 0.54 ( 4472) hydrogen bonds : bond 0.03064 / 1.61 ( 21) hydrogen bonds : angle 4.89813 / 3.26 ( 57) Misc. bond : bond 0.00125 / 0.07 ( 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 67 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 6 LYS cc_start: 0.7600 (mmtt) cc_final: 0.6938 (mttt) REVERT: G 6 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8447 (ttmt) REVERT: H 3 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7736 (m-80) REVERT: S 8 GLU cc_start: 0.7859 (tt0) cc_final: 0.7451 (tt0) REVERT: T 2 LYS cc_start: 0.7799 (tptp) cc_final: 0.7379 (tptp) REVERT: T 6 LYS cc_start: 0.8067 (tptp) cc_final: 0.6788 (mptt) REVERT: U 2 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7883 (tmtt) REVERT: K 2 LYS cc_start: 0.8238 (mttt) cc_final: 0.7919 (mmmt) REVERT: K 3 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.5882 (p90) REVERT: K 6 LYS cc_start: 0.8579 (ptmt) cc_final: 0.8054 (ptmm) REVERT: L 3 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8155 (m-10) REVERT: L 6 LYS cc_start: 0.8201 (mmmm) cc_final: 0.7735 (mmtp) REVERT: a 6 LYS cc_start: 0.8096 (tptp) cc_final: 0.6866 (mptt) REVERT: V 6 LYS cc_start: 0.7522 (mtmm) cc_final: 0.6977 (mtpp) REVERT: i 6 LYS cc_start: 0.8268 (tptp) cc_final: 0.6701 (mptt) REVERT: c 1 PHE cc_start: 0.6058 (OUTLIER) cc_final: 0.5527 (m-80) REVERT: e 3 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.6744 (p90) REVERT: f 3 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8337 (m-80) REVERT: k 2 LYS cc_start: 0.8009 (mmtp) cc_final: 0.7805 (mmtm) REVERT: l 3 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7758 (t80) REVERT: l 6 LYS cc_start: 0.8359 (ptmm) cc_final: 0.7999 (ptmm) REVERT: s 8 GLU cc_start: 0.7389 (mp0) cc_final: 0.6998 (mp0) REVERT: n 2 LYS cc_start: 0.7788 (tptt) cc_final: 0.7336 (tptt) REVERT: n 6 LYS cc_start: 0.8290 (ptmm) cc_final: 0.7883 (tttp) REVERT: u 2 LYS cc_start: 0.7901 (tptm) cc_final: 0.7461 (tptt) REVERT: y 6 LYS cc_start: 0.8053 (tttp) cc_final: 0.7834 (tttp) outliers start: 20 outliers final: 10 residues processed: 67 average time/residue: 0.1483 time to fit residues: 11.0851 Evaluate side-chains 62 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain I residue 1 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain c 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 l residue 3 PHE Chi-restraints excluded: chain l residue 5 PHE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain x residue 7 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.131322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.110264 restraints weight = 6390.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.113668 restraints weight = 2918.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.115992 restraints weight = 1793.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.117556 restraints weight = 1294.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.118668 restraints weight = 1031.299| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.7844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3526 Z= 0.133 Angle : 1.028 11.391 4472 Z= 0.414 Chirality : 0.031 0.090 301 Planarity : 0.002 0.012 559 Dihedral : 51.596 179.798 387 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.98 % Allowed : 26.25 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.20 (0.36), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.28), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.001 PHE e 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 3483) covalent geometry : angle 1.02821 / 0.41 ( 4472) hydrogen bonds : bond 0.01625 / 0.79 ( 21) hydrogen bonds : angle 3.97012 / 2.73 ( 57) Misc. bond : bond 0.00030 / 0.02 ( 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 63 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 6 LYS cc_start: 0.7134 (mmtt) cc_final: 0.6256 (mttt) REVERT: G 6 LYS cc_start: 0.8677 (ttmt) cc_final: 0.7951 (tttt) REVERT: H 3 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7462 (m-80) REVERT: S 8 GLU cc_start: 0.7086 (tt0) cc_final: 0.6609 (tt0) REVERT: T 2 LYS cc_start: 0.7103 (tptp) cc_final: 0.6576 (tptp) REVERT: K 2 LYS cc_start: 0.7970 (mttt) cc_final: 0.7543 (mmmt) REVERT: K 3 PHE cc_start: 0.6803 (OUTLIER) cc_final: 0.5293 (p90) REVERT: K 6 LYS cc_start: 0.8228 (ptmt) cc_final: 0.7579 (ptmm) REVERT: L 6 LYS cc_start: 0.7696 (mmmm) cc_final: 0.7129 (mttp) REVERT: X 6 LYS cc_start: 0.6466 (mtpt) cc_final: 0.6257 (mtmm) REVERT: e 3 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6179 (p90) REVERT: k 2 LYS cc_start: 0.8205 (mmtp) cc_final: 0.7838 (mptt) REVERT: l 2 LYS cc_start: 0.7444 (tptt) cc_final: 0.7229 (tptt) REVERT: n 2 LYS cc_start: 0.7565 (tptt) cc_final: 0.7168 (tptt) REVERT: n 6 LYS cc_start: 0.8161 (ptmm) cc_final: 0.7647 (tttp) REVERT: y 6 LYS cc_start: 0.7874 (tttp) cc_final: 0.7612 (tttp) outliers start: 15 outliers final: 11 residues processed: 62 average time/residue: 0.1384 time to fit residues: 9.5839 Evaluate side-chains 57 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain a residue 1 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain i residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain l residue 5 PHE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain x residue 7 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.114123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.092719 restraints weight = 7039.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.095588 restraints weight = 3798.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.097572 restraints weight = 2540.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.098794 restraints weight = 1936.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.099733 restraints weight = 1627.349| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.8702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.053 3526 Z= 0.533 Angle : 1.234 13.807 4472 Z= 0.535 Chirality : 0.047 0.163 301 Planarity : 0.005 0.028 559 Dihedral : 50.753 179.777 387 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.60 % Favored : 81.40 % Rotamer: Outliers : 5.32 % Allowed : 25.25 % Favored : 69.44 % 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: -5.84 (0.33), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.25), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.032 0.004 PHE o 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01308 / 0.54 ( 3483) covalent geometry : angle 1.23374 / 0.54 ( 4472) hydrogen bonds : bond 0.02596 / 1.39 ( 21) hydrogen bonds : angle 5.07810 / 3.38 ( 57) Misc. bond : bond 0.00102 / 0.06 ( 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 62 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 6 LYS cc_start: 0.7611 (mmtt) cc_final: 0.6889 (mttt) REVERT: H 3 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: S 8 GLU cc_start: 0.7746 (tt0) cc_final: 0.7331 (tt0) REVERT: T 2 LYS cc_start: 0.7852 (tptp) cc_final: 0.7367 (tptp) REVERT: T 6 LYS cc_start: 0.8068 (tptp) cc_final: 0.6800 (mptt) REVERT: U 2 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7741 (tmtt) REVERT: J 8 GLU cc_start: 0.7648 (pm20) cc_final: 0.7425 (pm20) REVERT: K 2 LYS cc_start: 0.8196 (mttt) cc_final: 0.7842 (mmmt) REVERT: K 3 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.5875 (p90) REVERT: K 6 LYS cc_start: 0.8635 (ptmt) cc_final: 0.8056 (ptmm) REVERT: L 3 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.8201 (m-10) REVERT: L 6 LYS cc_start: 0.8207 (mmmm) cc_final: 0.7835 (mmtp) REVERT: a 2 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7441 (tmmt) REVERT: a 6 LYS cc_start: 0.8089 (tptp) cc_final: 0.6917 (mptt) REVERT: i 6 LYS cc_start: 0.8284 (tptp) cc_final: 0.6691 (mptt) REVERT: e 3 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.6935 (p90) REVERT: f 3 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: k 2 LYS cc_start: 0.7844 (mmtp) cc_final: 0.7551 (mmtm) REVERT: l 6 LYS cc_start: 0.8428 (ptmm) cc_final: 0.7762 (ptmm) REVERT: n 2 LYS cc_start: 0.7753 (tptt) cc_final: 0.7295 (tptt) REVERT: u 2 LYS cc_start: 0.7838 (tptm) cc_final: 0.7470 (tptt) outliers start: 16 outliers final: 10 residues processed: 61 average time/residue: 0.1499 time to fit residues: 10.1157 Evaluate side-chains 59 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain I residue 1 PHE 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 X residue 3 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain l residue 5 PHE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain x residue 7 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.130417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.109914 restraints weight = 6611.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.113236 restraints weight = 3104.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.115483 restraints weight = 1934.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.117096 restraints weight = 1396.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.118075 restraints weight = 1106.077| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.8256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3526 Z= 0.133 Angle : 1.047 11.369 4472 Z= 0.423 Chirality : 0.031 0.087 301 Planarity : 0.002 0.013 559 Dihedral : 51.568 179.848 387 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.65 % Allowed : 25.91 % Favored : 69.44 % 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: -5.39 (0.35), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.27), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.001 PHE e 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 3483) covalent geometry : angle 1.04670 / 0.42 ( 4472) hydrogen bonds : bond 0.01399 / 0.68 ( 21) hydrogen bonds : angle 4.07790 / 2.78 ( 57) Misc. bond : bond 0.00029 / 0.02 ( 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 62 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 6 LYS cc_start: 0.7206 (mmtt) cc_final: 0.6498 (mttt) REVERT: H 3 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: S 8 GLU cc_start: 0.6927 (tt0) cc_final: 0.6555 (tt0) REVERT: T 2 LYS cc_start: 0.7195 (tptp) cc_final: 0.6668 (tptp) REVERT: K 2 LYS cc_start: 0.7979 (mttt) cc_final: 0.7635 (mmmt) REVERT: K 3 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.5302 (p90) REVERT: K 6 LYS cc_start: 0.8297 (ptmt) cc_final: 0.7673 (ptmm) REVERT: L 6 LYS cc_start: 0.7796 (mmmm) cc_final: 0.7291 (mttp) REVERT: a 6 LYS cc_start: 0.7095 (tptp) cc_final: 0.5808 (mptt) REVERT: e 3 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6426 (p90) REVERT: k 2 LYS cc_start: 0.8150 (mmtp) cc_final: 0.7824 (mptt) REVERT: l 2 LYS cc_start: 0.7718 (tptt) cc_final: 0.7107 (tptt) REVERT: l 6 LYS cc_start: 0.8280 (ptmm) cc_final: 0.7555 (ptmm) REVERT: n 2 LYS cc_start: 0.7601 (tptt) cc_final: 0.7199 (tptt) REVERT: n 6 LYS cc_start: 0.8215 (ptmm) cc_final: 0.7669 (tttp) REVERT: u 2 LYS cc_start: 0.7681 (tptm) cc_final: 0.7361 (tptt) REVERT: y 6 LYS cc_start: 0.8012 (tttp) cc_final: 0.7709 (tttp) outliers start: 14 outliers final: 10 residues processed: 61 average time/residue: 0.1415 time to fit residues: 9.5926 Evaluate side-chains 58 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain a residue 1 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain l residue 5 PHE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain x residue 7 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.115648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.094695 restraints weight = 7849.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.097400 restraints weight = 4037.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.099245 restraints weight = 2610.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.100448 restraints weight = 1972.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.101097 restraints weight = 1618.271| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.8891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.054 3526 Z= 0.526 Angle : 1.234 13.777 4472 Z= 0.535 Chirality : 0.047 0.160 301 Planarity : 0.005 0.030 559 Dihedral : 50.706 179.989 387 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.60 % Favored : 81.40 % Rotamer: Outliers : 4.32 % Allowed : 26.25 % Favored : 69.44 % 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: -5.91 (0.33), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.50 (0.25), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.031 0.004 PHE o 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01294 / 0.53 ( 3483) covalent geometry : angle 1.23357 / 0.53 ( 4472) hydrogen bonds : bond 0.02626 / 1.43 ( 21) hydrogen bonds : angle 5.11949 / 3.40 ( 57) Misc. bond : bond 0.00105 / 0.06 ( 43) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 530.66 seconds wall clock time: 9 minutes 52.03 seconds (592.03 seconds total)