Starting phenix.real_space_refine on Fri Mar 6 01:29:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xnh_67051/03_2026/9xnh_67051.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xnh_67051/03_2026/9xnh_67051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xnh_67051/03_2026/9xnh_67051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xnh_67051/03_2026/9xnh_67051.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xnh_67051/03_2026/9xnh_67051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xnh_67051/03_2026/9xnh_67051.map" } resolution = 3.66 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 154 5.16 5 C 17006 2.51 5 N 4466 2.21 5 O 5170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26796 Number of models: 1 Model: "" Number of chains: 1 Chain: "I" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1218 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 11, 'TRANS': 172} Restraints were copied for chains: J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d Time building chain proxies: 2.38, per 1000 atoms: 0.09 Number of scatterers: 26796 At special positions: 0 Unit cell: (86.211, 86.211, 322.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 154 16.00 O 5170 8.00 N 4466 7.00 C 17006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 69 " distance=2.03 Simple disulfide: pdb=" SG CYS I 153 " - pdb=" SG CYS I 170 " distance=2.03 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 69 " distance=2.03 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 69 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 69 " distance=2.03 Simple disulfide: pdb=" SG CYS M 43 " - pdb=" SG CYS M 69 " distance=2.03 Simple disulfide: pdb=" SG CYS N 43 " - pdb=" SG CYS N 69 " distance=2.03 Simple disulfide: pdb=" SG CYS O 43 " - pdb=" SG CYS O 69 " distance=2.03 Simple disulfide: pdb=" SG CYS P 43 " - pdb=" SG CYS P 69 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 43 " - pdb=" SG CYS Q 69 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 69 " distance=2.03 Simple disulfide: pdb=" SG CYS S 43 " - pdb=" SG CYS S 69 " distance=2.03 Simple disulfide: pdb=" SG CYS T 43 " - pdb=" SG CYS T 69 " distance=2.03 Simple disulfide: pdb=" SG CYS U 43 " - pdb=" SG CYS U 69 " distance=2.03 Simple disulfide: pdb=" SG CYS V 43 " - pdb=" SG CYS V 69 " distance=2.03 Simple disulfide: pdb=" SG CYS W 43 " - pdb=" SG CYS W 69 " distance=2.03 Simple disulfide: pdb=" SG CYS X 43 " - pdb=" SG CYS X 69 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 43 " - pdb=" SG CYS Y 69 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 43 " - pdb=" SG CYS Z 69 " distance=2.03 Simple disulfide: pdb=" SG CYS a 43 " - pdb=" SG CYS a 69 " distance=2.03 Simple disulfide: pdb=" SG CYS b 43 " - pdb=" SG CYS b 69 " distance=2.03 Simple disulfide: pdb=" SG CYS c 43 " - pdb=" SG CYS c 69 " distance=2.03 Simple disulfide: pdb=" SG CYS d 43 " - pdb=" SG CYS d 69 " distance=2.03 Simple disulfide: pdb=" SG CYS J 153 " - pdb=" SG CYS J 170 " distance=2.03 Simple disulfide: pdb=" SG CYS K 153 " - pdb=" SG CYS K 170 " distance=2.03 Simple disulfide: pdb=" SG CYS L 153 " - pdb=" SG CYS L 170 " distance=2.03 Simple disulfide: pdb=" SG CYS M 153 " - pdb=" SG CYS M 170 " distance=2.03 Simple disulfide: pdb=" SG CYS N 153 " - pdb=" SG CYS N 170 " distance=2.03 Simple disulfide: pdb=" SG CYS O 153 " - pdb=" SG CYS O 170 " distance=2.03 Simple disulfide: pdb=" SG CYS P 153 " - pdb=" SG CYS P 170 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 153 " - pdb=" SG CYS Q 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 153 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS S 153 " - pdb=" SG CYS S 170 " distance=2.03 Simple disulfide: pdb=" SG CYS T 153 " - pdb=" SG CYS T 170 " distance=2.03 Simple disulfide: pdb=" SG CYS U 153 " - pdb=" SG CYS U 170 " distance=2.03 Simple disulfide: pdb=" SG CYS V 153 " - pdb=" SG CYS V 170 " distance=2.03 Simple disulfide: pdb=" SG CYS W 153 " - pdb=" SG CYS W 170 " distance=2.03 Simple disulfide: pdb=" SG CYS X 153 " - pdb=" SG CYS X 170 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 153 " - pdb=" SG CYS Y 170 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 153 " - pdb=" SG CYS Z 170 " distance=2.03 Simple disulfide: pdb=" SG CYS a 153 " - pdb=" SG CYS a 170 " distance=2.03 Simple disulfide: pdb=" SG CYS b 153 " - pdb=" SG CYS b 170 " distance=2.03 Simple disulfide: pdb=" SG CYS c 153 " - pdb=" SG CYS c 170 " distance=2.03 Simple disulfide: pdb=" SG CYS d 153 " - pdb=" SG CYS d 170 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.3 seconds 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7128 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 44 sheets defined 35.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'I' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA I 6 " --> pdb=" O THR I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET I 28 " --> pdb=" O TYR I 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA I 31 " --> pdb=" O TYR I 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR I 35 " --> pdb=" O ALA I 31 " (cutoff:3.500A) Proline residue: I 36 - end of helix removed outlier: 4.528A pdb=" N THR I 45 " --> pdb=" O ALA I 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA I 46 " --> pdb=" O ALA I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 112 Processing helix chain 'I' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA I 142 " --> pdb=" O VAL I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 165 Processing helix chain 'J' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA J 6 " --> pdb=" O THR J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET J 28 " --> pdb=" O TYR J 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA J 31 " --> pdb=" O TYR J 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR J 35 " --> pdb=" O ALA J 31 " (cutoff:3.500A) Proline residue: J 36 - end of helix removed outlier: 4.528A pdb=" N THR J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA J 46 " --> pdb=" O ALA J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 112 Processing helix chain 'J' and resid 136 through 143 removed outlier: 3.518A pdb=" N ALA J 142 " --> pdb=" O VAL J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 Processing helix chain 'K' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA K 6 " --> pdb=" O THR K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET K 28 " --> pdb=" O TYR K 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA K 31 " --> pdb=" O TYR K 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR K 35 " --> pdb=" O ALA K 31 " (cutoff:3.500A) Proline residue: K 36 - end of helix removed outlier: 4.529A pdb=" N THR K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA K 46 " --> pdb=" O ALA K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 112 Processing helix chain 'K' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA K 142 " --> pdb=" O VAL K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 165 Processing helix chain 'L' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA L 6 " --> pdb=" O THR L 2 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA L 31 " --> pdb=" O TYR L 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR L 35 " --> pdb=" O ALA L 31 " (cutoff:3.500A) Proline residue: L 36 - end of helix removed outlier: 4.528A pdb=" N THR L 45 " --> pdb=" O ALA L 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA L 46 " --> pdb=" O ALA L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 112 Processing helix chain 'L' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA L 142 " --> pdb=" O VAL L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 165 Processing helix chain 'M' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA M 6 " --> pdb=" O THR M 2 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET M 28 " --> pdb=" O TYR M 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA M 31 " --> pdb=" O TYR M 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR M 35 " --> pdb=" O ALA M 31 " (cutoff:3.500A) Proline residue: M 36 - end of helix removed outlier: 4.528A pdb=" N THR M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 112 Processing helix chain 'M' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA M 142 " --> pdb=" O VAL M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 165 Processing helix chain 'N' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA N 6 " --> pdb=" O THR N 2 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET N 28 " --> pdb=" O TYR N 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA N 31 " --> pdb=" O TYR N 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR N 35 " --> pdb=" O ALA N 31 " (cutoff:3.500A) Proline residue: N 36 - end of helix removed outlier: 4.529A pdb=" N THR N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA N 46 " --> pdb=" O ALA N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 112 Processing helix chain 'N' and resid 136 through 143 removed outlier: 3.518A pdb=" N ALA N 142 " --> pdb=" O VAL N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 165 Processing helix chain 'O' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA O 6 " --> pdb=" O THR O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET O 28 " --> pdb=" O TYR O 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA O 31 " --> pdb=" O TYR O 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR O 35 " --> pdb=" O ALA O 31 " (cutoff:3.500A) Proline residue: O 36 - end of helix removed outlier: 4.528A pdb=" N THR O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA O 46 " --> pdb=" O ALA O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 112 Processing helix chain 'O' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA O 142 " --> pdb=" O VAL O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 161 through 165 Processing helix chain 'P' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA P 6 " --> pdb=" O THR P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET P 28 " --> pdb=" O TYR P 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA P 31 " --> pdb=" O TYR P 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR P 35 " --> pdb=" O ALA P 31 " (cutoff:3.500A) Proline residue: P 36 - end of helix removed outlier: 4.529A pdb=" N THR P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA P 46 " --> pdb=" O ALA P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 Processing helix chain 'P' and resid 136 through 143 removed outlier: 3.518A pdb=" N ALA P 142 " --> pdb=" O VAL P 138 " (cutoff:3.500A) Processing helix chain 'P' and resid 161 through 165 Processing helix chain 'Q' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA Q 6 " --> pdb=" O THR Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET Q 28 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA Q 31 " --> pdb=" O TYR Q 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR Q 35 " --> pdb=" O ALA Q 31 " (cutoff:3.500A) Proline residue: Q 36 - end of helix removed outlier: 4.529A pdb=" N THR Q 45 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 112 Processing helix chain 'Q' and resid 136 through 143 removed outlier: 3.518A pdb=" N ALA Q 142 " --> pdb=" O VAL Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 161 through 165 Processing helix chain 'R' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA R 6 " --> pdb=" O THR R 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET R 28 " --> pdb=" O TYR R 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA R 31 " --> pdb=" O TYR R 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR R 35 " --> pdb=" O ALA R 31 " (cutoff:3.500A) Proline residue: R 36 - end of helix removed outlier: 4.529A pdb=" N THR R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 112 Processing helix chain 'R' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA R 142 " --> pdb=" O VAL R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 165 Processing helix chain 'S' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA S 6 " --> pdb=" O THR S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET S 28 " --> pdb=" O TYR S 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA S 31 " --> pdb=" O TYR S 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR S 35 " --> pdb=" O ALA S 31 " (cutoff:3.500A) Proline residue: S 36 - end of helix removed outlier: 4.528A pdb=" N THR S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 112 Processing helix chain 'S' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA S 142 " --> pdb=" O VAL S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 161 through 165 Processing helix chain 'T' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA T 6 " --> pdb=" O THR T 2 " (cutoff:3.500A) Processing helix chain 'T' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET T 28 " --> pdb=" O TYR T 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA T 31 " --> pdb=" O TYR T 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR T 35 " --> pdb=" O ALA T 31 " (cutoff:3.500A) Proline residue: T 36 - end of helix removed outlier: 4.529A pdb=" N THR T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA T 46 " --> pdb=" O ALA T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 108 through 112 Processing helix chain 'T' and resid 136 through 143 removed outlier: 3.518A pdb=" N ALA T 142 " --> pdb=" O VAL T 138 " (cutoff:3.500A) Processing helix chain 'T' and resid 161 through 165 Processing helix chain 'U' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA U 6 " --> pdb=" O THR U 2 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET U 28 " --> pdb=" O TYR U 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA U 31 " --> pdb=" O TYR U 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR U 35 " --> pdb=" O ALA U 31 " (cutoff:3.500A) Proline residue: U 36 - end of helix removed outlier: 4.528A pdb=" N THR U 45 " --> pdb=" O ALA U 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA U 46 " --> pdb=" O ALA U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 108 through 112 Processing helix chain 'U' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA U 142 " --> pdb=" O VAL U 138 " (cutoff:3.500A) Processing helix chain 'U' and resid 161 through 165 Processing helix chain 'V' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA V 6 " --> pdb=" O THR V 2 " (cutoff:3.500A) Processing helix chain 'V' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET V 28 " --> pdb=" O TYR V 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA V 31 " --> pdb=" O TYR V 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR V 35 " --> pdb=" O ALA V 31 " (cutoff:3.500A) Proline residue: V 36 - end of helix removed outlier: 4.528A pdb=" N THR V 45 " --> pdb=" O ALA V 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA V 46 " --> pdb=" O ALA V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 108 through 112 Processing helix chain 'V' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA V 142 " --> pdb=" O VAL V 138 " (cutoff:3.500A) Processing helix chain 'V' and resid 161 through 165 Processing helix chain 'W' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA W 6 " --> pdb=" O THR W 2 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET W 28 " --> pdb=" O TYR W 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA W 31 " --> pdb=" O TYR W 27 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR W 35 " --> pdb=" O ALA W 31 " (cutoff:3.500A) Proline residue: W 36 - end of helix removed outlier: 4.529A pdb=" N THR W 45 " --> pdb=" O ALA W 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA W 46 " --> pdb=" O ALA W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 112 Processing helix chain 'W' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA W 142 " --> pdb=" O VAL W 138 " (cutoff:3.500A) Processing helix chain 'W' and resid 161 through 165 Processing helix chain 'X' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA X 6 " --> pdb=" O THR X 2 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET X 28 " --> pdb=" O TYR X 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA X 31 " --> pdb=" O TYR X 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR X 35 " --> pdb=" O ALA X 31 " (cutoff:3.500A) Proline residue: X 36 - end of helix removed outlier: 4.529A pdb=" N THR X 45 " --> pdb=" O ALA X 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA X 46 " --> pdb=" O ALA X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 108 through 112 Processing helix chain 'X' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA X 142 " --> pdb=" O VAL X 138 " (cutoff:3.500A) Processing helix chain 'X' and resid 161 through 165 Processing helix chain 'Y' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA Y 6 " --> pdb=" O THR Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET Y 28 " --> pdb=" O TYR Y 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA Y 31 " --> pdb=" O TYR Y 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR Y 35 " --> pdb=" O ALA Y 31 " (cutoff:3.500A) Proline residue: Y 36 - end of helix removed outlier: 4.528A pdb=" N THR Y 45 " --> pdb=" O ALA Y 41 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA Y 46 " --> pdb=" O ALA Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 108 through 112 Processing helix chain 'Y' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA Y 142 " --> pdb=" O VAL Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 161 through 165 Processing helix chain 'Z' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA Z 6 " --> pdb=" O THR Z 2 " (cutoff:3.500A) Processing helix chain 'Z' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET Z 28 " --> pdb=" O TYR Z 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA Z 31 " --> pdb=" O TYR Z 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR Z 35 " --> pdb=" O ALA Z 31 " (cutoff:3.500A) Proline residue: Z 36 - end of helix removed outlier: 4.528A pdb=" N THR Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 108 through 112 Processing helix chain 'Z' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA Z 142 " --> pdb=" O VAL Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 165 Processing helix chain 'a' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA a 6 " --> pdb=" O THR a 2 " (cutoff:3.500A) Processing helix chain 'a' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET a 28 " --> pdb=" O TYR a 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA a 31 " --> pdb=" O TYR a 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR a 35 " --> pdb=" O ALA a 31 " (cutoff:3.500A) Proline residue: a 36 - end of helix removed outlier: 4.528A pdb=" N THR a 45 " --> pdb=" O ALA a 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA a 46 " --> pdb=" O ALA a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 112 Processing helix chain 'a' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA a 142 " --> pdb=" O VAL a 138 " (cutoff:3.500A) Processing helix chain 'a' and resid 161 through 165 Processing helix chain 'b' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA b 6 " --> pdb=" O THR b 2 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET b 28 " --> pdb=" O TYR b 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA b 31 " --> pdb=" O TYR b 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR b 35 " --> pdb=" O ALA b 31 " (cutoff:3.500A) Proline residue: b 36 - end of helix removed outlier: 4.528A pdb=" N THR b 45 " --> pdb=" O ALA b 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA b 46 " --> pdb=" O ALA b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 108 through 112 Processing helix chain 'b' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA b 142 " --> pdb=" O VAL b 138 " (cutoff:3.500A) Processing helix chain 'b' and resid 161 through 165 Processing helix chain 'c' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA c 6 " --> pdb=" O THR c 2 " (cutoff:3.500A) Processing helix chain 'c' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET c 28 " --> pdb=" O TYR c 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA c 31 " --> pdb=" O TYR c 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR c 35 " --> pdb=" O ALA c 31 " (cutoff:3.500A) Proline residue: c 36 - end of helix removed outlier: 4.528A pdb=" N THR c 45 " --> pdb=" O ALA c 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA c 46 " --> pdb=" O ALA c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 112 Processing helix chain 'c' and resid 136 through 143 removed outlier: 3.519A pdb=" N ALA c 142 " --> pdb=" O VAL c 138 " (cutoff:3.500A) Processing helix chain 'c' and resid 161 through 165 Processing helix chain 'd' and resid 2 through 18 removed outlier: 3.587A pdb=" N ALA d 6 " --> pdb=" O THR d 2 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 54 removed outlier: 3.586A pdb=" N MET d 28 " --> pdb=" O TYR d 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA d 31 " --> pdb=" O TYR d 27 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR d 35 " --> pdb=" O ALA d 31 " (cutoff:3.500A) Proline residue: d 36 - end of helix removed outlier: 4.528A pdb=" N THR d 45 " --> pdb=" O ALA d 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA d 46 " --> pdb=" O ALA d 42 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 112 Processing helix chain 'd' and resid 136 through 143 removed outlier: 3.518A pdb=" N ALA d 142 " --> pdb=" O VAL d 138 " (cutoff:3.500A) Processing helix chain 'd' and resid 161 through 165 Processing sheet with id=AA1, first strand: chain 'I' and resid 89 through 92 removed outlier: 7.138A pdb=" N THR I 103 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 154 through 156 Processing sheet with id=AA3, first strand: chain 'J' and resid 89 through 92 removed outlier: 7.137A pdb=" N THR J 103 " --> pdb=" O THR J 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 154 through 156 Processing sheet with id=AA5, first strand: chain 'K' and resid 89 through 92 removed outlier: 7.138A pdb=" N THR K 103 " --> pdb=" O THR K 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 154 through 156 Processing sheet with id=AA7, first strand: chain 'L' and resid 89 through 92 removed outlier: 7.137A pdb=" N THR L 103 " --> pdb=" O THR L 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 154 through 156 Processing sheet with id=AA9, first strand: chain 'M' and resid 89 through 92 removed outlier: 7.137A pdb=" N THR M 103 " --> pdb=" O THR M 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 154 through 156 Processing sheet with id=AB2, first strand: chain 'N' and resid 89 through 92 removed outlier: 7.137A pdb=" N THR N 103 " --> pdb=" O THR N 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 154 through 156 Processing sheet with id=AB4, first strand: chain 'O' and resid 89 through 92 removed outlier: 7.138A pdb=" N THR O 103 " --> pdb=" O THR O 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 154 through 156 Processing sheet with id=AB6, first strand: chain 'P' and resid 89 through 92 removed outlier: 7.137A pdb=" N THR P 103 " --> pdb=" O THR P 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 154 through 156 Processing sheet with id=AB8, first strand: chain 'Q' and resid 89 through 92 removed outlier: 7.137A pdb=" N THR Q 103 " --> pdb=" O THR Q 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 154 through 156 Processing sheet with id=AC1, first strand: chain 'R' and resid 89 through 92 removed outlier: 7.138A pdb=" N THR R 103 " --> pdb=" O THR R 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 154 through 156 Processing sheet with id=AC3, first strand: chain 'S' and resid 89 through 92 removed outlier: 7.138A pdb=" N THR S 103 " --> pdb=" O THR S 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 154 through 156 Processing sheet with id=AC5, first strand: chain 'T' and resid 89 through 92 removed outlier: 7.138A pdb=" N THR T 103 " --> pdb=" O THR T 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'T' and resid 154 through 156 Processing sheet with id=AC7, first strand: chain 'U' and resid 89 through 92 removed outlier: 7.138A pdb=" N THR U 103 " --> pdb=" O THR U 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 154 through 156 Processing sheet with id=AC9, first strand: chain 'V' and resid 89 through 92 removed outlier: 7.138A pdb=" N THR V 103 " --> pdb=" O THR V 90 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 154 through 156 Processing sheet with id=AD2, first strand: chain 'W' and resid 89 through 92 removed outlier: 7.138A pdb=" N THR W 103 " --> pdb=" O THR W 90 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'W' and resid 154 through 156 Processing sheet with id=AD4, first strand: chain 'X' and resid 89 through 92 removed outlier: 7.137A pdb=" N THR X 103 " --> pdb=" O THR X 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 154 through 156 Processing sheet with id=AD6, first strand: chain 'Y' and resid 89 through 92 removed outlier: 7.137A pdb=" N THR Y 103 " --> pdb=" O THR Y 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Y' and resid 154 through 156 Processing sheet with id=AD8, first strand: chain 'Z' and resid 89 through 92 removed outlier: 7.138A pdb=" N THR Z 103 " --> pdb=" O THR Z 90 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 154 through 156 Processing sheet with id=AE1, first strand: chain 'a' and resid 89 through 92 removed outlier: 7.138A pdb=" N THR a 103 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'a' and resid 154 through 156 Processing sheet with id=AE3, first strand: chain 'b' and resid 89 through 92 removed outlier: 7.137A pdb=" N THR b 103 " --> pdb=" O THR b 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'b' and resid 154 through 156 Processing sheet with id=AE5, first strand: chain 'c' and resid 89 through 92 removed outlier: 7.137A pdb=" N THR c 103 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'c' and resid 154 through 156 Processing sheet with id=AE7, first strand: chain 'd' and resid 89 through 92 removed outlier: 7.138A pdb=" N THR d 103 " --> pdb=" O THR d 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'd' and resid 154 through 156 902 hydrogen bonds defined for protein. 2442 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.21 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8690 1.35 - 1.46: 5374 1.46 - 1.58: 12930 1.58 - 1.70: 0 1.70 - 1.82: 220 Bond restraints: 27214 Sorted by residual: bond pdb=" N GLY O 76 " pdb=" CA GLY O 76 " ideal model delta sigma weight residual 1.438 1.475 -0.037 1.41e-02 5.03e+03 6.88e+00 bond pdb=" N GLY T 76 " pdb=" CA GLY T 76 " ideal model delta sigma weight residual 1.438 1.475 -0.037 1.41e-02 5.03e+03 6.86e+00 bond pdb=" N GLY d 76 " pdb=" CA GLY d 76 " ideal model delta sigma weight residual 1.438 1.475 -0.037 1.41e-02 5.03e+03 6.85e+00 bond pdb=" N GLY Y 76 " pdb=" CA GLY Y 76 " ideal model delta sigma weight residual 1.438 1.475 -0.037 1.41e-02 5.03e+03 6.84e+00 bond pdb=" N GLY J 76 " pdb=" CA GLY J 76 " ideal model delta sigma weight residual 1.438 1.475 -0.037 1.41e-02 5.03e+03 6.81e+00 ... (remaining 27209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 35506 1.47 - 2.95: 1534 2.95 - 4.42: 294 4.42 - 5.89: 66 5.89 - 7.36: 22 Bond angle restraints: 37422 Sorted by residual: angle pdb=" N VAL L 165 " pdb=" CA VAL L 165 " pdb=" C VAL L 165 " ideal model delta sigma weight residual 113.53 108.66 4.87 9.80e-01 1.04e+00 2.47e+01 angle pdb=" N VAL P 165 " pdb=" CA VAL P 165 " pdb=" C VAL P 165 " ideal model delta sigma weight residual 113.53 108.66 4.87 9.80e-01 1.04e+00 2.47e+01 angle pdb=" N VAL V 165 " pdb=" CA VAL V 165 " pdb=" C VAL V 165 " ideal model delta sigma weight residual 113.53 108.66 4.87 9.80e-01 1.04e+00 2.47e+01 angle pdb=" N VAL X 165 " pdb=" CA VAL X 165 " pdb=" C VAL X 165 " ideal model delta sigma weight residual 113.53 108.67 4.86 9.80e-01 1.04e+00 2.46e+01 angle pdb=" N VAL a 165 " pdb=" CA VAL a 165 " pdb=" C VAL a 165 " ideal model delta sigma weight residual 113.53 108.68 4.85 9.80e-01 1.04e+00 2.45e+01 ... (remaining 37417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 14298 17.02 - 34.03: 1454 34.03 - 51.05: 286 51.05 - 68.07: 110 68.07 - 85.09: 22 Dihedral angle restraints: 16170 sinusoidal: 4906 harmonic: 11264 Sorted by residual: dihedral pdb=" CB CYS X 43 " pdb=" SG CYS X 43 " pdb=" SG CYS X 69 " pdb=" CB CYS X 69 " ideal model delta sinusoidal sigma weight residual -86.00 -42.21 -43.79 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CB CYS d 43 " pdb=" SG CYS d 43 " pdb=" SG CYS d 69 " pdb=" CB CYS d 69 " ideal model delta sinusoidal sigma weight residual -86.00 -42.21 -43.79 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CB CYS P 43 " pdb=" SG CYS P 43 " pdb=" SG CYS P 69 " pdb=" CB CYS P 69 " ideal model delta sinusoidal sigma weight residual -86.00 -42.21 -43.79 1 1.00e+01 1.00e-02 2.67e+01 ... (remaining 16167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2773 0.028 - 0.057: 1278 0.057 - 0.085: 430 0.085 - 0.114: 359 0.114 - 0.142: 44 Chirality restraints: 4884 Sorted by residual: chirality pdb=" CB VAL T 125 " pdb=" CA VAL T 125 " pdb=" CG1 VAL T 125 " pdb=" CG2 VAL T 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CB VAL L 125 " pdb=" CA VAL L 125 " pdb=" CG1 VAL L 125 " pdb=" CG2 VAL L 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CB VAL M 125 " pdb=" CA VAL M 125 " pdb=" CG1 VAL M 125 " pdb=" CG2 VAL M 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 4881 not shown) Planarity restraints: 4752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL Z 100 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.59e+00 pdb=" N PRO Z 101 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO Z 101 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO Z 101 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL X 100 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO X 101 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO X 101 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO X 101 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 100 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO J 101 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO J 101 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO J 101 " 0.022 5.00e-02 4.00e+02 ... (remaining 4749 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.07: 19198 3.07 - 3.53: 28185 3.53 - 3.99: 38865 3.99 - 4.44: 49914 4.44 - 4.90: 73232 Nonbonded interactions: 209394 Sorted by model distance: nonbonded pdb=" N VAL O 165 " pdb=" N ALA O 166 " model vdw 2.617 2.560 nonbonded pdb=" N VAL d 165 " pdb=" N ALA d 166 " model vdw 2.617 2.560 nonbonded pdb=" N VAL L 165 " pdb=" N ALA L 166 " model vdw 2.617 2.560 nonbonded pdb=" N VAL b 165 " pdb=" N ALA b 166 " model vdw 2.617 2.560 nonbonded pdb=" N VAL M 165 " pdb=" N ALA M 166 " model vdw 2.617 2.560 ... (remaining 209389 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: 0.07 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 5.280 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: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.060 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.004 0.037 27258 Z= 0.255 Angle : 0.719 7.363 37510 Z= 0.461 Chirality : 0.043 0.142 4884 Planarity : 0.005 0.040 4752 Dihedral : 14.430 85.086 8910 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.61 % Allowed : 26.96 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.13), residues: 4004 helix: 0.38 (0.15), residues: 1122 sheet: -2.14 (0.22), residues: 770 loop : -1.66 (0.12), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG d 32 TYR 0.007 0.001 TYR T 27 PHE 0.004 0.001 PHE U 124 TRP 0.001 0.000 TRP d 67 Details of bonding type rmsd covalent geometry : bond 0.00390 (27214) covalent geometry : angle 0.71847 (37422) SS BOND : bond 0.00090 ( 44) SS BOND : angle 0.85637 ( 88) hydrogen bonds : bond 0.18718 ( 902) hydrogen bonds : angle 5.85513 ( 2442) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 268 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 MET cc_start: 0.8325 (tpp) cc_final: 0.8012 (tpp) REVERT: P 50 MET cc_start: 0.8233 (tpp) cc_final: 0.8025 (tpp) REVERT: Q 50 MET cc_start: 0.8197 (tpp) cc_final: 0.7872 (tpp) REVERT: R 50 MET cc_start: 0.8292 (tpp) cc_final: 0.7940 (tpp) REVERT: T 50 MET cc_start: 0.8346 (tpp) cc_final: 0.8093 (tpp) REVERT: Y 50 MET cc_start: 0.8247 (tpp) cc_final: 0.7880 (tpt) REVERT: b 50 MET cc_start: 0.8408 (tpp) cc_final: 0.8197 (tpp) REVERT: d 50 MET cc_start: 0.8265 (tpp) cc_final: 0.7897 (tpp) outliers start: 66 outliers final: 61 residues processed: 334 average time/residue: 0.1177 time to fit residues: 71.6844 Evaluate side-chains 301 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 240 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 43 CYS Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 13 THR Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain L residue 43 CYS Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 43 CYS Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 43 CYS Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 43 CYS Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 43 CYS Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 43 CYS Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain U residue 43 CYS Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 43 CYS Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Y residue 43 CYS Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 43 CYS Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 43 CYS Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 43 CYS Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 43 CYS Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 43 CYS Chi-restraints excluded: chain d residue 100 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.0570 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 overall best weight: 2.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 52 GLN J 39 GLN J 52 GLN K 39 GLN K 52 GLN L 39 GLN L 52 GLN M 39 GLN M 52 GLN N 39 GLN N 52 GLN O 39 GLN O 52 GLN P 39 GLN P 52 GLN Q 39 GLN Q 52 GLN R 52 GLN S 39 GLN S 52 GLN T 52 GLN U 39 GLN U 52 GLN V 39 GLN V 52 GLN W 39 GLN W 52 GLN X 52 GLN Y 39 GLN Y 52 GLN Z 39 GLN Z 52 GLN a 39 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.102023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.094458 restraints weight = 57106.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.096598 restraints weight = 29283.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.098012 restraints weight = 17161.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.098936 restraints weight = 11198.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.099581 restraints weight = 7888.675| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 27258 Z= 0.231 Angle : 0.637 5.094 37510 Z= 0.342 Chirality : 0.046 0.135 4884 Planarity : 0.006 0.049 4752 Dihedral : 5.802 53.633 4219 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 6.21 % Allowed : 23.52 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 4004 helix: 0.09 (0.15), residues: 1210 sheet: -2.62 (0.21), residues: 770 loop : -1.07 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Y 32 TYR 0.018 0.002 TYR S 27 PHE 0.013 0.002 PHE Q 181 TRP 0.016 0.003 TRP U 67 Details of bonding type rmsd covalent geometry : bond 0.00554 (27214) covalent geometry : angle 0.63631 (37422) SS BOND : bond 0.00143 ( 44) SS BOND : angle 0.79973 ( 88) hydrogen bonds : bond 0.06272 ( 902) hydrogen bonds : angle 5.69303 ( 2442) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 224 time to evaluate : 0.941 Fit side-chains REVERT: R 24 TYR cc_start: 0.8960 (m-80) cc_final: 0.8754 (m-10) REVERT: S 24 TYR cc_start: 0.8879 (m-80) cc_final: 0.8611 (m-10) REVERT: b 24 TYR cc_start: 0.8886 (m-80) cc_final: 0.8685 (m-10) outliers start: 157 outliers final: 66 residues processed: 376 average time/residue: 0.1226 time to fit residues: 82.9487 Evaluate side-chains 246 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 180 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 13 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 182 THR Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 108 LEU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 108 LEU Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 108 LEU Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain d residue 108 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 342 optimal weight: 0.8980 chunk 333 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 297 optimal weight: 6.9990 chunk 269 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 354 optimal weight: 0.1980 chunk 294 optimal weight: 0.0770 chunk 372 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 overall best weight: 1.2340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 39 GLN L 39 GLN N 39 GLN U 39 GLN Y 39 GLN Z 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.099731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.092346 restraints weight = 57939.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.094554 restraints weight = 28935.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.095959 restraints weight = 16618.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.096876 restraints weight = 10589.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.097536 restraints weight = 7304.818| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27258 Z= 0.146 Angle : 0.592 5.363 37510 Z= 0.310 Chirality : 0.045 0.150 4884 Planarity : 0.006 0.052 4752 Dihedral : 5.818 59.909 4197 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.51 % Allowed : 24.23 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.14), residues: 4004 helix: 0.14 (0.15), residues: 1210 sheet: -2.73 (0.21), residues: 770 loop : -0.99 (0.15), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG b 32 TYR 0.013 0.001 TYR O 27 PHE 0.005 0.001 PHE Q 181 TRP 0.004 0.001 TRP Z 67 Details of bonding type rmsd covalent geometry : bond 0.00333 (27214) covalent geometry : angle 0.59097 (37422) SS BOND : bond 0.00070 ( 44) SS BOND : angle 0.86153 ( 88) hydrogen bonds : bond 0.05110 ( 902) hydrogen bonds : angle 5.31579 ( 2442) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 211 time to evaluate : 0.901 Fit side-chains REVERT: R 24 TYR cc_start: 0.8997 (m-80) cc_final: 0.8764 (m-10) REVERT: S 24 TYR cc_start: 0.8882 (m-80) cc_final: 0.8649 (m-10) outliers start: 114 outliers final: 87 residues processed: 317 average time/residue: 0.1206 time to fit residues: 68.4170 Evaluate side-chains 255 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 168 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 13 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 182 THR Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 182 THR Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 108 LEU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 158 THR Chi-restraints excluded: chain Z residue 182 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 108 LEU Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 108 LEU Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 284 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 chunk 357 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 341 optimal weight: 0.7980 chunk 114 optimal weight: 0.0770 chunk 33 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 overall best weight: 1.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 39 GLN L 39 GLN U 39 GLN Y 39 GLN Z 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.090179 restraints weight = 58389.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.092502 restraints weight = 28482.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.093999 restraints weight = 16281.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.094979 restraints weight = 10348.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.095655 restraints weight = 7138.166| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27258 Z= 0.155 Angle : 0.587 6.908 37510 Z= 0.311 Chirality : 0.045 0.149 4884 Planarity : 0.006 0.051 4752 Dihedral : 5.093 39.536 4197 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.98 % Allowed : 23.87 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.14), residues: 4004 helix: 0.21 (0.15), residues: 1210 sheet: -2.88 (0.20), residues: 770 loop : -0.93 (0.15), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG c 32 TYR 0.013 0.001 TYR O 27 PHE 0.006 0.001 PHE Q 181 TRP 0.004 0.001 TRP S 67 Details of bonding type rmsd covalent geometry : bond 0.00358 (27214) covalent geometry : angle 0.58580 (37422) SS BOND : bond 0.00056 ( 44) SS BOND : angle 0.88631 ( 88) hydrogen bonds : bond 0.05073 ( 902) hydrogen bonds : angle 5.28341 ( 2442) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 186 time to evaluate : 0.980 Fit side-chains REVERT: R 28 MET cc_start: 0.8092 (mtm) cc_final: 0.7866 (mtm) outliers start: 126 outliers final: 109 residues processed: 307 average time/residue: 0.1253 time to fit residues: 68.1716 Evaluate side-chains 284 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 175 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 182 THR Chi-restraints excluded: chain K residue 13 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 182 THR Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 182 THR Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 182 THR Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 182 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 108 LEU Chi-restraints excluded: chain W residue 182 THR Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 182 THR Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 158 THR Chi-restraints excluded: chain Z residue 182 THR Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 108 LEU Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 108 LEU Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 92 optimal weight: 0.0060 chunk 307 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 277 optimal weight: 8.9990 chunk 234 optimal weight: 0.1980 chunk 391 optimal weight: 2.9990 chunk 319 optimal weight: 7.9990 chunk 389 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 39 GLN U 39 GLN U 147 GLN Z 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.099610 restraints weight = 56206.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.101724 restraints weight = 28350.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.103057 restraints weight = 16327.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.103957 restraints weight = 10417.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.104579 restraints weight = 7126.106| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27258 Z= 0.111 Angle : 0.549 7.364 37510 Z= 0.286 Chirality : 0.043 0.152 4884 Planarity : 0.005 0.052 4752 Dihedral : 4.440 23.838 4197 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.79 % Allowed : 25.61 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.14), residues: 4004 helix: 0.22 (0.15), residues: 1210 sheet: -2.68 (0.21), residues: 770 loop : -0.85 (0.15), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG L 32 TYR 0.010 0.001 TYR O 27 PHE 0.005 0.001 PHE Z 124 TRP 0.004 0.001 TRP V 67 Details of bonding type rmsd covalent geometry : bond 0.00229 (27214) covalent geometry : angle 0.54796 (37422) SS BOND : bond 0.00036 ( 44) SS BOND : angle 0.81261 ( 88) hydrogen bonds : bond 0.04088 ( 902) hydrogen bonds : angle 4.90628 ( 2442) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 215 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: K 7 ILE cc_start: 0.8509 (mt) cc_final: 0.8304 (mt) REVERT: Z 39 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8275 (mm-40) outliers start: 96 outliers final: 66 residues processed: 306 average time/residue: 0.1227 time to fit residues: 67.2364 Evaluate side-chains 257 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 190 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 108 LEU Chi-restraints excluded: chain X residue 9 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 39 GLN Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 108 LEU Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 331 optimal weight: 20.0000 chunk 118 optimal weight: 0.7980 chunk 383 optimal weight: 0.0570 chunk 301 optimal weight: 7.9990 chunk 164 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 165 optimal weight: 0.4980 chunk 211 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 340 optimal weight: 0.1980 chunk 294 optimal weight: 0.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN P 147 GLN T 39 GLN U 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103411 restraints weight = 56626.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.105659 restraints weight = 27891.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.107070 restraints weight = 16044.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.108019 restraints weight = 10300.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.108670 restraints weight = 7129.684| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27258 Z= 0.108 Angle : 0.542 7.549 37510 Z= 0.281 Chirality : 0.043 0.145 4884 Planarity : 0.005 0.048 4752 Dihedral : 4.231 19.566 4193 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.28 % Allowed : 25.73 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.14), residues: 4004 helix: 0.28 (0.15), residues: 1210 sheet: -2.38 (0.24), residues: 638 loop : -0.95 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG Z 32 TYR 0.010 0.001 TYR O 27 PHE 0.005 0.001 PHE T 124 TRP 0.007 0.000 TRP V 67 Details of bonding type rmsd covalent geometry : bond 0.00221 (27214) covalent geometry : angle 0.54152 (37422) SS BOND : bond 0.00045 ( 44) SS BOND : angle 0.74788 ( 88) hydrogen bonds : bond 0.03965 ( 902) hydrogen bonds : angle 4.84861 ( 2442) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 218 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 7 ILE cc_start: 0.8346 (mt) cc_final: 0.8135 (mt) outliers start: 83 outliers final: 64 residues processed: 294 average time/residue: 0.1233 time to fit residues: 64.5450 Evaluate side-chains 267 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 203 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain X residue 43 CYS Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 158 THR Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 43 CYS Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 108 LEU Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 192 optimal weight: 5.9990 chunk 371 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 320 optimal weight: 6.9990 chunk 213 optimal weight: 0.9980 chunk 304 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN ** Q 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 147 GLN ** W 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 GLN Y 39 GLN Z 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.093743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.086443 restraints weight = 57275.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.088534 restraints weight = 28926.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.089870 restraints weight = 16861.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.090765 restraints weight = 10986.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.091397 restraints weight = 7735.214| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 27258 Z= 0.276 Angle : 0.704 9.471 37510 Z= 0.379 Chirality : 0.050 0.166 4884 Planarity : 0.006 0.047 4752 Dihedral : 5.221 24.962 4180 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.11 % Allowed : 25.53 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.14), residues: 4004 helix: 0.06 (0.15), residues: 1210 sheet: -3.06 (0.20), residues: 770 loop : -1.17 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG V 32 TYR 0.021 0.002 TYR a 27 PHE 0.015 0.002 PHE Q 181 TRP 0.019 0.004 TRP N 67 Details of bonding type rmsd covalent geometry : bond 0.00669 (27214) covalent geometry : angle 0.70393 (37422) SS BOND : bond 0.00146 ( 44) SS BOND : angle 0.79890 ( 88) hydrogen bonds : bond 0.06801 ( 902) hydrogen bonds : angle 5.78090 ( 2442) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 236 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 71 residues processed: 332 average time/residue: 0.1245 time to fit residues: 73.2213 Evaluate side-chains 291 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 220 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 43 CYS Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain X residue 9 VAL Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 162 MET Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 158 THR Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 43 CYS Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 102 LEU Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 138 optimal weight: 0.1980 chunk 98 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 297 optimal weight: 0.6980 chunk 265 optimal weight: 3.9990 chunk 223 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN P 39 GLN R 39 GLN T 147 GLN U 147 GLN ** W 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 GLN X 147 GLN Y 39 GLN Y 147 GLN Z 39 GLN Z 147 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.096848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.089271 restraints weight = 58309.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.091465 restraints weight = 29130.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.092871 restraints weight = 16932.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.093799 restraints weight = 10938.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.094457 restraints weight = 7664.252| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27258 Z= 0.163 Angle : 0.626 9.865 37510 Z= 0.330 Chirality : 0.046 0.196 4884 Planarity : 0.006 0.052 4752 Dihedral : 4.732 22.429 4180 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.91 % Allowed : 26.92 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.14), residues: 4004 helix: 0.11 (0.15), residues: 1210 sheet: -2.96 (0.20), residues: 770 loop : -1.10 (0.15), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG I 32 TYR 0.014 0.001 TYR W 27 PHE 0.011 0.002 PHE K 124 TRP 0.005 0.001 TRP S 67 Details of bonding type rmsd covalent geometry : bond 0.00378 (27214) covalent geometry : angle 0.62520 (37422) SS BOND : bond 0.00066 ( 44) SS BOND : angle 0.86786 ( 88) hydrogen bonds : bond 0.05311 ( 902) hydrogen bonds : angle 5.30686 ( 2442) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 236 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 39 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8430 (mm-40) outliers start: 99 outliers final: 81 residues processed: 327 average time/residue: 0.1283 time to fit residues: 73.8257 Evaluate side-chains 303 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 221 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 162 MET Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 43 CYS Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 182 THR Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain R residue 39 GLN Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain U residue 43 CYS Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 182 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 162 MET Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 43 CYS Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 162 MET Chi-restraints excluded: chain Z residue 39 GLN Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 158 THR Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 43 CYS Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 108 LEU Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 108 LEU Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 240 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 390 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 295 optimal weight: 20.0000 chunk 238 optimal weight: 3.9990 chunk 219 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L 147 GLN N 39 GLN ** P 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN U 147 GLN W 147 GLN X 39 GLN Y 39 GLN Z 39 GLN Z 147 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.098754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.091279 restraints weight = 57126.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.093473 restraints weight = 28602.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.094864 restraints weight = 16575.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.095696 restraints weight = 10694.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.096422 restraints weight = 7635.543| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27258 Z= 0.141 Angle : 0.607 10.956 37510 Z= 0.317 Chirality : 0.045 0.188 4884 Planarity : 0.006 0.052 4752 Dihedral : 4.542 20.929 4180 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.95 % Allowed : 27.15 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.14), residues: 4004 helix: 0.16 (0.15), residues: 1210 sheet: -2.85 (0.24), residues: 638 loop : -1.13 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG R 32 TYR 0.012 0.001 TYR O 27 PHE 0.009 0.002 PHE R 124 TRP 0.003 0.000 TRP N 67 Details of bonding type rmsd covalent geometry : bond 0.00314 (27214) covalent geometry : angle 0.60618 (37422) SS BOND : bond 0.00052 ( 44) SS BOND : angle 0.83979 ( 88) hydrogen bonds : bond 0.04922 ( 902) hydrogen bonds : angle 5.16356 ( 2442) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 227 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 85 residues processed: 317 average time/residue: 0.1259 time to fit residues: 70.7110 Evaluate side-chains 306 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 221 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 43 CYS Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 43 CYS Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 158 THR Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 43 CYS Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 43 CYS Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 39 GLN Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain U residue 43 CYS Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 182 THR Chi-restraints excluded: chain X residue 9 VAL Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 162 MET Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 43 CYS Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 162 MET Chi-restraints excluded: chain Z residue 39 GLN Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 158 THR Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 43 CYS Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 108 LEU Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 108 LEU Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 133 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 222 optimal weight: 0.0980 chunk 313 optimal weight: 0.9980 chunk 242 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 375 optimal weight: 0.9990 chunk 369 optimal weight: 0.0270 chunk 309 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN J 147 GLN K 39 GLN L 147 GLN N 39 GLN P 39 GLN R 39 GLN U 147 GLN X 39 GLN Y 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.105884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.098260 restraints weight = 57411.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.100465 restraints weight = 28252.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101877 restraints weight = 16206.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.102797 restraints weight = 10276.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.103454 restraints weight = 7031.212| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27258 Z= 0.116 Angle : 0.588 10.225 37510 Z= 0.305 Chirality : 0.044 0.182 4884 Planarity : 0.006 0.052 4752 Dihedral : 4.303 19.910 4180 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.28 % Allowed : 27.71 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.14), residues: 4004 helix: 0.19 (0.15), residues: 1210 sheet: -2.68 (0.24), residues: 638 loop : -1.02 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG M 32 TYR 0.011 0.001 TYR U 27 PHE 0.006 0.001 PHE Y 124 TRP 0.007 0.001 TRP d 67 Details of bonding type rmsd covalent geometry : bond 0.00239 (27214) covalent geometry : angle 0.58720 (37422) SS BOND : bond 0.00081 ( 44) SS BOND : angle 0.79629 ( 88) hydrogen bonds : bond 0.04191 ( 902) hydrogen bonds : angle 4.90249 ( 2442) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 231 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 70 residues processed: 310 average time/residue: 0.1238 time to fit residues: 68.5358 Evaluate side-chains 288 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 218 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 43 CYS Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 43 CYS Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 43 CYS Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 43 CYS Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain U residue 43 CYS Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain X residue 9 VAL Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 43 CYS Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 158 THR Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 43 CYS Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 108 LEU Chi-restraints excluded: chain d residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 311 optimal weight: 2.9990 chunk 281 optimal weight: 6.9990 chunk 96 optimal weight: 0.0670 chunk 208 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 344 optimal weight: 0.8980 chunk 110 optimal weight: 0.0980 chunk 45 optimal weight: 8.9990 chunk 228 optimal weight: 0.5980 chunk 289 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN K 39 GLN L 147 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN U 147 GLN ** X 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.098314 restraints weight = 57205.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.100526 restraints weight = 28229.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.101919 restraints weight = 16190.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.102846 restraints weight = 10303.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.103486 restraints weight = 7053.546| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 27258 Z= 0.181 Angle : 0.826 59.200 37510 Z= 0.468 Chirality : 0.044 0.173 4884 Planarity : 0.006 0.052 4752 Dihedral : 4.300 19.914 4180 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.04 % Allowed : 28.10 % Favored : 68.85 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.14), residues: 4004 helix: 0.18 (0.15), residues: 1210 sheet: -2.67 (0.24), residues: 638 loop : -1.02 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG c 32 TYR 0.011 0.001 TYR U 27 PHE 0.006 0.001 PHE Y 124 TRP 0.007 0.001 TRP R 67 Details of bonding type rmsd covalent geometry : bond 0.00370 (27214) covalent geometry : angle 0.82594 (37422) SS BOND : bond 0.00079 ( 44) SS BOND : angle 0.78686 ( 88) hydrogen bonds : bond 0.04204 ( 902) hydrogen bonds : angle 4.89770 ( 2442) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3207.15 seconds wall clock time: 56 minutes 46.24 seconds (3406.24 seconds total)