Starting phenix.real_space_refine on Mon Jul 6 13:59:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m2r_63590/07_2026/9m2r_63590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m2r_63590/07_2026/9m2r_63590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m2r_63590/07_2026/9m2r_63590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m2r_63590/07_2026/9m2r_63590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m2r_63590/07_2026/9m2r_63590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m2r_63590/07_2026/9m2r_63590.map" } resolution = 2.2 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= 0.000 sd= 0.013 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: 5 Type Number sf(0) Gaussians Mn 48 7.51 5 S 72 5.16 5 C 21840 2.51 5 N 6696 2.21 5 O 7680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36336 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "N" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "P" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "S" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "T" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "U" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "V" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "W" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "X" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 3.92, per 1000 atoms: 0.11 Number of scatterers: 36336 At special positions: 0 Unit cell: (131.88, 131.88, 131.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 48 24.99 S 72 16.00 O 7680 8.00 N 6696 7.00 C 21840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.5 seconds 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8448 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 72 sheets defined 41.6% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 72 through 92 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 56 Processing helix chain 'B' and resid 72 through 92 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 72 through 92 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 56 Processing helix chain 'D' and resid 72 through 92 Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 56 Processing helix chain 'E' and resid 72 through 92 Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU E 195 " --> pdb=" O ARG E 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 56 Processing helix chain 'F' and resid 72 through 92 Processing helix chain 'F' and resid 130 through 135 Processing helix chain 'F' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU F 195 " --> pdb=" O ARG F 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 56 Processing helix chain 'G' and resid 72 through 92 Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'G' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU G 195 " --> pdb=" O ARG G 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 56 Processing helix chain 'H' and resid 72 through 92 Processing helix chain 'H' and resid 130 through 135 Processing helix chain 'H' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS H 152 " --> pdb=" O VAL H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU H 195 " --> pdb=" O ARG H 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 56 Processing helix chain 'I' and resid 72 through 92 Processing helix chain 'I' and resid 130 through 135 Processing helix chain 'I' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS I 152 " --> pdb=" O VAL I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU I 195 " --> pdb=" O ARG I 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 56 Processing helix chain 'J' and resid 72 through 92 Processing helix chain 'J' and resid 130 through 135 Processing helix chain 'J' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS J 152 " --> pdb=" O VAL J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU J 195 " --> pdb=" O ARG J 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 56 Processing helix chain 'K' and resid 72 through 92 Processing helix chain 'K' and resid 130 through 135 Processing helix chain 'K' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS K 152 " --> pdb=" O VAL K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU K 195 " --> pdb=" O ARG K 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 56 Processing helix chain 'L' and resid 72 through 92 Processing helix chain 'L' and resid 130 through 135 Processing helix chain 'L' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS L 152 " --> pdb=" O VAL L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU L 195 " --> pdb=" O ARG L 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 56 Processing helix chain 'M' and resid 72 through 92 Processing helix chain 'M' and resid 130 through 135 Processing helix chain 'M' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS M 152 " --> pdb=" O VAL M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU M 195 " --> pdb=" O ARG M 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 56 Processing helix chain 'N' and resid 72 through 92 Processing helix chain 'N' and resid 130 through 135 Processing helix chain 'N' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS N 152 " --> pdb=" O VAL N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU N 195 " --> pdb=" O ARG N 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 56 Processing helix chain 'O' and resid 72 through 92 Processing helix chain 'O' and resid 130 through 135 Processing helix chain 'O' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS O 152 " --> pdb=" O VAL O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU O 195 " --> pdb=" O ARG O 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 56 Processing helix chain 'P' and resid 72 through 92 Processing helix chain 'P' and resid 130 through 135 Processing helix chain 'P' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS P 152 " --> pdb=" O VAL P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU P 195 " --> pdb=" O ARG P 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 56 Processing helix chain 'Q' and resid 72 through 92 Processing helix chain 'Q' and resid 130 through 135 Processing helix chain 'Q' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS Q 152 " --> pdb=" O VAL Q 148 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU Q 195 " --> pdb=" O ARG Q 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 56 Processing helix chain 'R' and resid 72 through 92 Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS R 152 " --> pdb=" O VAL R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU R 195 " --> pdb=" O ARG R 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 56 Processing helix chain 'S' and resid 72 through 92 Processing helix chain 'S' and resid 130 through 135 Processing helix chain 'S' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS S 152 " --> pdb=" O VAL S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU S 195 " --> pdb=" O ARG S 191 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 56 Processing helix chain 'T' and resid 72 through 92 Processing helix chain 'T' and resid 130 through 135 Processing helix chain 'T' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS T 152 " --> pdb=" O VAL T 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU T 195 " --> pdb=" O ARG T 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 56 Processing helix chain 'U' and resid 72 through 92 Processing helix chain 'U' and resid 130 through 135 Processing helix chain 'U' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS U 152 " --> pdb=" O VAL U 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU U 195 " --> pdb=" O ARG U 191 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 56 Processing helix chain 'V' and resid 72 through 92 Processing helix chain 'V' and resid 130 through 135 Processing helix chain 'V' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS V 152 " --> pdb=" O VAL V 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU V 195 " --> pdb=" O ARG V 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 56 Processing helix chain 'W' and resid 72 through 92 Processing helix chain 'W' and resid 130 through 135 Processing helix chain 'W' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS W 152 " --> pdb=" O VAL W 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU W 195 " --> pdb=" O ARG W 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 56 Processing helix chain 'X' and resid 72 through 92 Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'X' and resid 148 through 162 removed outlier: 4.603A pdb=" N HIS X 152 " --> pdb=" O VAL X 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 174 through 195 removed outlier: 3.562A pdb=" N GLU X 195 " --> pdb=" O ARG X 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA A 37 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA A 64 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP A 39 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY A 66 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU A 111 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR A 123 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL A 167 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 125 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL A 169 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR A 127 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR A 171 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 137 through 138 Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA B 37 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA B 64 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP B 39 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY B 66 " --> pdb=" O ASP B 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU B 111 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR B 123 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL B 167 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL B 125 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL B 169 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B 127 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR B 171 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 137 through 138 Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA C 37 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA C 64 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP C 39 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY C 66 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU C 111 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR C 123 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL C 167 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL C 125 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL C 169 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C 127 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR C 171 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 137 through 138 Processing sheet with id=AB1, first strand: chain 'D' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA D 37 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA D 64 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP D 39 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY D 66 " --> pdb=" O ASP D 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU D 111 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR D 123 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL D 167 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL D 125 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL D 169 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR D 127 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR D 171 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 137 through 138 Processing sheet with id=AB4, first strand: chain 'E' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA E 37 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA E 64 " --> pdb=" O ALA E 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP E 39 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY E 66 " --> pdb=" O ASP E 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU E 111 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR E 123 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL E 167 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL E 125 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL E 169 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR E 127 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR E 171 " --> pdb=" O THR E 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 137 through 138 Processing sheet with id=AB7, first strand: chain 'F' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA F 37 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA F 64 " --> pdb=" O ALA F 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP F 39 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY F 66 " --> pdb=" O ASP F 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU F 111 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR F 123 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL F 167 " --> pdb=" O TYR F 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL F 125 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL F 169 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR F 127 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR F 171 " --> pdb=" O THR F 127 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 137 through 138 Processing sheet with id=AC1, first strand: chain 'G' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA G 37 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA G 64 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP G 39 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY G 66 " --> pdb=" O ASP G 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU G 111 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR G 123 " --> pdb=" O LEU G 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL G 167 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL G 125 " --> pdb=" O VAL G 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL G 169 " --> pdb=" O VAL G 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR G 127 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR G 171 " --> pdb=" O THR G 127 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 137 through 138 Processing sheet with id=AC4, first strand: chain 'H' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA H 37 " --> pdb=" O VAL H 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA H 64 " --> pdb=" O ALA H 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP H 39 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY H 66 " --> pdb=" O ASP H 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU H 111 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR H 123 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL H 167 " --> pdb=" O TYR H 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL H 125 " --> pdb=" O VAL H 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL H 169 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR H 127 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR H 171 " --> pdb=" O THR H 127 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 137 through 138 Processing sheet with id=AC7, first strand: chain 'I' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA I 37 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA I 64 " --> pdb=" O ALA I 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP I 39 " --> pdb=" O ALA I 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY I 66 " --> pdb=" O ASP I 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU I 111 " --> pdb=" O LEU I 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR I 123 " --> pdb=" O LEU I 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL I 167 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL I 125 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL I 169 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR I 127 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR I 171 " --> pdb=" O THR I 127 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 137 through 138 Processing sheet with id=AD1, first strand: chain 'J' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA J 37 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA J 64 " --> pdb=" O ALA J 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP J 39 " --> pdb=" O ALA J 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY J 66 " --> pdb=" O ASP J 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU J 111 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR J 123 " --> pdb=" O LEU J 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL J 167 " --> pdb=" O TYR J 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL J 125 " --> pdb=" O VAL J 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL J 169 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR J 127 " --> pdb=" O VAL J 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR J 171 " --> pdb=" O THR J 127 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 137 through 138 Processing sheet with id=AD4, first strand: chain 'K' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA K 37 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA K 64 " --> pdb=" O ALA K 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP K 39 " --> pdb=" O ALA K 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY K 66 " --> pdb=" O ASP K 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU K 111 " --> pdb=" O LEU K 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR K 123 " --> pdb=" O LEU K 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL K 167 " --> pdb=" O TYR K 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL K 125 " --> pdb=" O VAL K 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL K 169 " --> pdb=" O VAL K 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR K 127 " --> pdb=" O VAL K 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR K 171 " --> pdb=" O THR K 127 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 137 through 138 Processing sheet with id=AD7, first strand: chain 'L' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA L 37 " --> pdb=" O VAL L 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA L 64 " --> pdb=" O ALA L 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP L 39 " --> pdb=" O ALA L 64 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY L 66 " --> pdb=" O ASP L 39 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU L 111 " --> pdb=" O LEU L 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR L 123 " --> pdb=" O LEU L 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL L 167 " --> pdb=" O TYR L 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL L 125 " --> pdb=" O VAL L 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL L 169 " --> pdb=" O VAL L 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR L 127 " --> pdb=" O VAL L 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR L 171 " --> pdb=" O THR L 127 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 137 through 138 Processing sheet with id=AE1, first strand: chain 'M' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA M 37 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA M 64 " --> pdb=" O ALA M 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP M 39 " --> pdb=" O ALA M 64 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY M 66 " --> pdb=" O ASP M 39 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU M 111 " --> pdb=" O LEU M 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR M 123 " --> pdb=" O LEU M 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL M 167 " --> pdb=" O TYR M 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL M 125 " --> pdb=" O VAL M 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL M 169 " --> pdb=" O VAL M 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR M 127 " --> pdb=" O VAL M 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR M 171 " --> pdb=" O THR M 127 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 137 through 138 Processing sheet with id=AE4, first strand: chain 'N' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA N 37 " --> pdb=" O VAL N 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA N 64 " --> pdb=" O ALA N 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP N 39 " --> pdb=" O ALA N 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY N 66 " --> pdb=" O ASP N 39 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU N 111 " --> pdb=" O LEU N 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR N 123 " --> pdb=" O LEU N 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL N 167 " --> pdb=" O TYR N 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL N 125 " --> pdb=" O VAL N 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL N 169 " --> pdb=" O VAL N 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR N 127 " --> pdb=" O VAL N 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR N 171 " --> pdb=" O THR N 127 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 137 through 138 Processing sheet with id=AE7, first strand: chain 'O' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA O 37 " --> pdb=" O VAL O 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA O 64 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP O 39 " --> pdb=" O ALA O 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY O 66 " --> pdb=" O ASP O 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU O 111 " --> pdb=" O LEU O 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR O 123 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL O 167 " --> pdb=" O TYR O 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL O 125 " --> pdb=" O VAL O 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL O 169 " --> pdb=" O VAL O 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR O 127 " --> pdb=" O VAL O 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR O 171 " --> pdb=" O THR O 127 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 137 through 138 Processing sheet with id=AF1, first strand: chain 'P' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA P 37 " --> pdb=" O VAL P 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA P 64 " --> pdb=" O ALA P 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP P 39 " --> pdb=" O ALA P 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY P 66 " --> pdb=" O ASP P 39 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU P 111 " --> pdb=" O LEU P 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR P 123 " --> pdb=" O LEU P 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL P 167 " --> pdb=" O TYR P 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL P 125 " --> pdb=" O VAL P 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL P 169 " --> pdb=" O VAL P 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR P 127 " --> pdb=" O VAL P 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR P 171 " --> pdb=" O THR P 127 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 137 through 138 Processing sheet with id=AF4, first strand: chain 'Q' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA Q 37 " --> pdb=" O VAL Q 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA Q 64 " --> pdb=" O ALA Q 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP Q 39 " --> pdb=" O ALA Q 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY Q 66 " --> pdb=" O ASP Q 39 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU Q 111 " --> pdb=" O LEU Q 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR Q 123 " --> pdb=" O LEU Q 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL Q 167 " --> pdb=" O TYR Q 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL Q 125 " --> pdb=" O VAL Q 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL Q 169 " --> pdb=" O VAL Q 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR Q 127 " --> pdb=" O VAL Q 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR Q 171 " --> pdb=" O THR Q 127 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 137 through 138 Processing sheet with id=AF7, first strand: chain 'R' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA R 37 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA R 64 " --> pdb=" O ALA R 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP R 39 " --> pdb=" O ALA R 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY R 66 " --> pdb=" O ASP R 39 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU R 111 " --> pdb=" O LEU R 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR R 123 " --> pdb=" O LEU R 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL R 167 " --> pdb=" O TYR R 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL R 125 " --> pdb=" O VAL R 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL R 169 " --> pdb=" O VAL R 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR R 127 " --> pdb=" O VAL R 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR R 171 " --> pdb=" O THR R 127 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 137 through 138 Processing sheet with id=AG1, first strand: chain 'S' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA S 37 " --> pdb=" O VAL S 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA S 64 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP S 39 " --> pdb=" O ALA S 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY S 66 " --> pdb=" O ASP S 39 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU S 111 " --> pdb=" O LEU S 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR S 123 " --> pdb=" O LEU S 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL S 167 " --> pdb=" O TYR S 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL S 125 " --> pdb=" O VAL S 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL S 169 " --> pdb=" O VAL S 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR S 127 " --> pdb=" O VAL S 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR S 171 " --> pdb=" O THR S 127 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 137 through 138 Processing sheet with id=AG4, first strand: chain 'T' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA T 37 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA T 64 " --> pdb=" O ALA T 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP T 39 " --> pdb=" O ALA T 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY T 66 " --> pdb=" O ASP T 39 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU T 111 " --> pdb=" O LEU T 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR T 123 " --> pdb=" O LEU T 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL T 167 " --> pdb=" O TYR T 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL T 125 " --> pdb=" O VAL T 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL T 169 " --> pdb=" O VAL T 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR T 127 " --> pdb=" O VAL T 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR T 171 " --> pdb=" O THR T 127 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'T' and resid 137 through 138 Processing sheet with id=AG7, first strand: chain 'U' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA U 37 " --> pdb=" O VAL U 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA U 64 " --> pdb=" O ALA U 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP U 39 " --> pdb=" O ALA U 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY U 66 " --> pdb=" O ASP U 39 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU U 111 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR U 123 " --> pdb=" O LEU U 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL U 167 " --> pdb=" O TYR U 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL U 125 " --> pdb=" O VAL U 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL U 169 " --> pdb=" O VAL U 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR U 127 " --> pdb=" O VAL U 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR U 171 " --> pdb=" O THR U 127 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 137 through 138 Processing sheet with id=AH1, first strand: chain 'V' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA V 37 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA V 64 " --> pdb=" O ALA V 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP V 39 " --> pdb=" O ALA V 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY V 66 " --> pdb=" O ASP V 39 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU V 111 " --> pdb=" O LEU V 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR V 123 " --> pdb=" O LEU V 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL V 167 " --> pdb=" O TYR V 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL V 125 " --> pdb=" O VAL V 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL V 169 " --> pdb=" O VAL V 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR V 127 " --> pdb=" O VAL V 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR V 171 " --> pdb=" O THR V 127 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'V' and resid 137 through 138 Processing sheet with id=AH4, first strand: chain 'W' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA W 37 " --> pdb=" O VAL W 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA W 64 " --> pdb=" O ALA W 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP W 39 " --> pdb=" O ALA W 64 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY W 66 " --> pdb=" O ASP W 39 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'W' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU W 111 " --> pdb=" O LEU W 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR W 123 " --> pdb=" O LEU W 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL W 167 " --> pdb=" O TYR W 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL W 125 " --> pdb=" O VAL W 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL W 169 " --> pdb=" O VAL W 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR W 127 " --> pdb=" O VAL W 169 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N TYR W 171 " --> pdb=" O THR W 127 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 137 through 138 Processing sheet with id=AH7, first strand: chain 'X' and resid 12 through 18 removed outlier: 6.458A pdb=" N ALA X 37 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA X 64 " --> pdb=" O ALA X 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP X 39 " --> pdb=" O ALA X 64 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY X 66 " --> pdb=" O ASP X 39 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 100 through 107 removed outlier: 6.736A pdb=" N LEU X 111 " --> pdb=" O LEU X 170 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR X 123 " --> pdb=" O LEU X 165 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL X 167 " --> pdb=" O TYR X 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL X 125 " --> pdb=" O VAL X 167 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL X 169 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR X 127 " --> pdb=" O VAL X 169 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N TYR X 171 " --> pdb=" O THR X 127 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 137 through 138 2136 hydrogen bonds defined for protein. 5904 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: 8.14 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12576 1.34 - 1.46: 7512 1.46 - 1.58: 15768 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 35976 Sorted by residual: bond pdb=" C VAL G 143 " pdb=" N PRO G 144 " ideal model delta sigma weight residual 1.328 1.355 -0.027 1.26e-02 6.30e+03 4.50e+00 bond pdb=" C VAL A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 1.328 1.355 -0.027 1.26e-02 6.30e+03 4.50e+00 bond pdb=" C VAL M 143 " pdb=" N PRO M 144 " ideal model delta sigma weight residual 1.328 1.355 -0.027 1.26e-02 6.30e+03 4.50e+00 bond pdb=" C VAL S 143 " pdb=" N PRO S 144 " ideal model delta sigma weight residual 1.328 1.355 -0.027 1.26e-02 6.30e+03 4.50e+00 bond pdb=" C VAL W 143 " pdb=" N PRO W 144 " ideal model delta sigma weight residual 1.328 1.355 -0.027 1.26e-02 6.30e+03 4.50e+00 ... (remaining 35971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 35370 1.12 - 2.24: 10253 2.24 - 3.36: 2545 3.36 - 4.48: 696 4.48 - 5.60: 48 Bond angle restraints: 48912 Sorted by residual: angle pdb=" CA ASP V 93 " pdb=" CB ASP V 93 " pdb=" CG ASP V 93 " ideal model delta sigma weight residual 112.60 116.46 -3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CA ASP U 93 " pdb=" CB ASP U 93 " pdb=" CG ASP U 93 " ideal model delta sigma weight residual 112.60 116.46 -3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CA ASP M 93 " pdb=" CB ASP M 93 " pdb=" CG ASP M 93 " ideal model delta sigma weight residual 112.60 116.42 -3.82 1.00e+00 1.00e+00 1.46e+01 angle pdb=" CA ASP X 93 " pdb=" CB ASP X 93 " pdb=" CG ASP X 93 " ideal model delta sigma weight residual 112.60 116.42 -3.82 1.00e+00 1.00e+00 1.46e+01 angle pdb=" CA ASP Q 93 " pdb=" CB ASP Q 93 " pdb=" CG ASP Q 93 " ideal model delta sigma weight residual 112.60 116.42 -3.82 1.00e+00 1.00e+00 1.46e+01 ... (remaining 48907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 19968 16.78 - 33.56: 1032 33.56 - 50.33: 288 50.33 - 67.11: 120 67.11 - 83.88: 72 Dihedral angle restraints: 21480 sinusoidal: 8376 harmonic: 13104 Sorted by residual: dihedral pdb=" CA PHE L 58 " pdb=" C PHE L 58 " pdb=" N ASP L 59 " pdb=" CA ASP L 59 " ideal model delta harmonic sigma weight residual 180.00 158.69 21.31 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA PHE G 58 " pdb=" C PHE G 58 " pdb=" N ASP G 59 " pdb=" CA ASP G 59 " ideal model delta harmonic sigma weight residual 180.00 158.71 21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PHE M 58 " pdb=" C PHE M 58 " pdb=" N ASP M 59 " pdb=" CA ASP M 59 " ideal model delta harmonic sigma weight residual 180.00 158.71 21.29 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 21477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2678 0.041 - 0.083: 1314 0.083 - 0.124: 1193 0.124 - 0.166: 311 0.166 - 0.207: 96 Chirality restraints: 5592 Sorted by residual: chirality pdb=" CA HIS J 132 " pdb=" N HIS J 132 " pdb=" C HIS J 132 " pdb=" CB HIS J 132 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA HIS I 132 " pdb=" N HIS I 132 " pdb=" C HIS I 132 " pdb=" CB HIS I 132 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA HIS O 132 " pdb=" N HIS O 132 " pdb=" C HIS O 132 " pdb=" CB HIS O 132 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 5589 not shown) Planarity restraints: 6504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG U 199 " 0.149 9.50e-02 1.11e+02 6.68e-02 3.02e+00 pdb=" NE ARG U 199 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG U 199 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG U 199 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG U 199 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG V 199 " -0.149 9.50e-02 1.11e+02 6.68e-02 3.02e+00 pdb=" NE ARG V 199 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG V 199 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG V 199 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG V 199 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 199 " 0.148 9.50e-02 1.11e+02 6.66e-02 3.01e+00 pdb=" NE ARG C 199 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 199 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 199 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 199 " 0.002 2.00e-02 2.50e+03 ... (remaining 6501 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2587 2.74 - 3.28: 35849 3.28 - 3.82: 63742 3.82 - 4.36: 81267 4.36 - 4.90: 137300 Nonbonded interactions: 320745 Sorted by model distance: nonbonded pdb="MN MN P 302 " pdb=" O HOH P 429 " model vdw 2.199 3.060 nonbonded pdb="MN MN S 302 " pdb=" O HOH S 428 " model vdw 2.199 3.060 nonbonded pdb="MN MN U 302 " pdb=" O HOH U 428 " model vdw 2.199 3.060 nonbonded pdb="MN MN E 302 " pdb=" O HOH E 428 " model vdw 2.199 3.060 nonbonded pdb="MN MN I 302 " pdb=" O HOH I 428 " model vdw 2.200 3.060 ... (remaining 320740 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 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: 0.580 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 29.510 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.110 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:8.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 35976 Z= 0.479 Angle : 1.173 5.601 48912 Z= 0.813 Chirality : 0.070 0.207 5592 Planarity : 0.008 0.067 6504 Dihedral : 13.753 83.884 13032 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.66 % Allowed : 3.34 % Favored : 96.00 % 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: -0.29 (0.12), residues: 4512 helix: 0.57 (0.11), residues: 1848 sheet: 0.02 (0.14), residues: 1344 loop : -1.33 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG G 199 TYR 0.013 0.004 TYR J 171 PHE 0.013 0.003 PHE R 44 HIS 0.008 0.002 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.48 (35976) covalent geometry : angle 1.17326 / 0.81 (48912) hydrogen bonds : bond 0.15460 / 10.87 ( 2136) hydrogen bonds : angle 5.68949 / 3.97 ( 5904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 720 time to evaluate : 1.378 Fit side-chains REVERT: A 27 GLU cc_start: 0.6464 (mt-10) cc_final: 0.5561 (mp0) REVERT: A 48 MET cc_start: 0.6713 (mmp) cc_final: 0.6393 (mmp) REVERT: A 63 ARG cc_start: 0.6057 (ttt180) cc_final: 0.5651 (ttp80) REVERT: A 71 GLU cc_start: 0.6060 (pt0) cc_final: 0.5855 (pt0) REVERT: A 121 ARG cc_start: 0.5099 (mmt180) cc_final: 0.4897 (mmm160) REVERT: A 162 ARG cc_start: 0.5965 (mtt180) cc_final: 0.5415 (mtp85) REVERT: A 195 GLU cc_start: 0.6251 (mt-10) cc_final: 0.5933 (mt-10) REVERT: B 27 GLU cc_start: 0.6462 (mt-10) cc_final: 0.5561 (mp0) REVERT: B 48 MET cc_start: 0.6712 (mmp) cc_final: 0.6395 (mmp) REVERT: B 63 ARG cc_start: 0.6057 (ttt180) cc_final: 0.5651 (ttp80) REVERT: B 71 GLU cc_start: 0.6061 (pt0) cc_final: 0.5853 (pt0) REVERT: B 121 ARG cc_start: 0.5096 (mmt180) cc_final: 0.4895 (mmm160) REVERT: B 162 ARG cc_start: 0.5964 (mtt180) cc_final: 0.5414 (mtp85) REVERT: B 195 GLU cc_start: 0.6248 (mt-10) cc_final: 0.5930 (mt-10) REVERT: C 27 GLU cc_start: 0.6465 (mt-10) cc_final: 0.5561 (mp0) REVERT: C 48 MET cc_start: 0.6711 (mmp) cc_final: 0.6393 (mmp) REVERT: C 63 ARG cc_start: 0.6057 (ttt180) cc_final: 0.5651 (ttp80) REVERT: C 71 GLU cc_start: 0.6058 (pt0) cc_final: 0.5853 (pt0) REVERT: C 162 ARG cc_start: 0.5965 (mtt180) cc_final: 0.5414 (mtp85) REVERT: C 195 GLU cc_start: 0.6247 (mt-10) cc_final: 0.5929 (mt-10) REVERT: D 27 GLU cc_start: 0.6465 (mt-10) cc_final: 0.5564 (mp0) REVERT: D 48 MET cc_start: 0.6713 (mmp) cc_final: 0.6395 (mmp) REVERT: D 63 ARG cc_start: 0.6059 (ttt180) cc_final: 0.5652 (ttp80) REVERT: D 71 GLU cc_start: 0.6061 (pt0) cc_final: 0.5853 (pt0) REVERT: D 121 ARG cc_start: 0.5096 (mmt180) cc_final: 0.4895 (mmm160) REVERT: D 162 ARG cc_start: 0.5964 (mtt180) cc_final: 0.5414 (mtp85) REVERT: D 195 GLU cc_start: 0.6250 (mt-10) cc_final: 0.5932 (mt-10) REVERT: E 27 GLU cc_start: 0.6465 (mt-10) cc_final: 0.5565 (mp0) REVERT: E 48 MET cc_start: 0.6714 (mmp) cc_final: 0.6395 (mmp) REVERT: E 63 ARG cc_start: 0.6059 (ttt180) cc_final: 0.5653 (ttp80) REVERT: E 71 GLU cc_start: 0.6060 (pt0) cc_final: 0.5852 (pt0) REVERT: E 121 ARG cc_start: 0.5096 (mmt180) cc_final: 0.4896 (mmm160) REVERT: E 162 ARG cc_start: 0.5964 (mtt180) cc_final: 0.5414 (mtp85) REVERT: E 195 GLU cc_start: 0.6251 (mt-10) cc_final: 0.5932 (mt-10) REVERT: F 27 GLU cc_start: 0.6463 (mt-10) cc_final: 0.5562 (mp0) REVERT: F 48 MET cc_start: 0.6714 (mmp) cc_final: 0.6394 (mmp) REVERT: F 63 ARG cc_start: 0.6058 (ttt180) cc_final: 0.5652 (ttp80) REVERT: F 71 GLU cc_start: 0.6060 (pt0) cc_final: 0.5853 (pt0) REVERT: F 121 ARG cc_start: 0.5096 (mmt180) cc_final: 0.4896 (mmm160) REVERT: F 162 ARG cc_start: 0.5967 (mtt180) cc_final: 0.5416 (mtp85) REVERT: F 195 GLU cc_start: 0.6250 (mt-10) cc_final: 0.5933 (mt-10) REVERT: G 27 GLU cc_start: 0.6466 (mt-10) cc_final: 0.5563 (mp0) REVERT: G 48 MET cc_start: 0.6712 (mmp) cc_final: 0.6393 (mmp) REVERT: G 63 ARG cc_start: 0.6058 (ttt180) cc_final: 0.5652 (ttp80) REVERT: G 71 GLU cc_start: 0.6059 (pt0) cc_final: 0.5855 (pt0) REVERT: G 121 ARG cc_start: 0.5099 (mmt180) cc_final: 0.4897 (mmm160) REVERT: G 162 ARG cc_start: 0.5966 (mtt180) cc_final: 0.5416 (mtp85) REVERT: G 195 GLU cc_start: 0.6250 (mt-10) cc_final: 0.5932 (mt-10) REVERT: H 27 GLU cc_start: 0.6465 (mt-10) cc_final: 0.5563 (mp0) REVERT: H 48 MET cc_start: 0.6698 (mmp) cc_final: 0.6379 (mmp) REVERT: H 63 ARG cc_start: 0.6054 (ttt180) cc_final: 0.5649 (ttp80) REVERT: H 71 GLU cc_start: 0.6058 (pt0) cc_final: 0.5852 (pt0) REVERT: H 162 ARG cc_start: 0.5965 (mtt180) cc_final: 0.5414 (mtp85) REVERT: H 195 GLU cc_start: 0.6248 (mt-10) cc_final: 0.5930 (mt-10) REVERT: I 27 GLU cc_start: 0.6463 (mt-10) cc_final: 0.5562 (mp0) REVERT: I 48 MET cc_start: 0.6700 (mmp) cc_final: 0.6380 (mmp) REVERT: I 63 ARG cc_start: 0.6058 (ttt180) cc_final: 0.5652 (ttp80) REVERT: I 71 GLU cc_start: 0.6060 (pt0) cc_final: 0.5853 (pt0) REVERT: I 162 ARG cc_start: 0.5966 (mtt180) cc_final: 0.5416 (mtp85) REVERT: I 195 GLU cc_start: 0.6250 (mt-10) cc_final: 0.5933 (mt-10) REVERT: J 27 GLU cc_start: 0.6464 (mt-10) cc_final: 0.5561 (mp0) REVERT: J 48 MET cc_start: 0.6700 (mmp) cc_final: 0.6380 (mmp) REVERT: J 63 ARG cc_start: 0.6057 (ttt180) cc_final: 0.5651 (ttp80) REVERT: J 71 GLU cc_start: 0.6060 (pt0) cc_final: 0.5853 (pt0) REVERT: J 121 ARG cc_start: 0.5098 (mmt180) cc_final: 0.4897 (mmm160) REVERT: J 162 ARG cc_start: 0.5966 (mtt180) cc_final: 0.5415 (mtp85) REVERT: J 195 GLU cc_start: 0.6251 (mt-10) cc_final: 0.5933 (mt-10) REVERT: K 27 GLU cc_start: 0.6464 (mt-10) cc_final: 0.5562 (mp0) REVERT: K 48 MET cc_start: 0.6714 (mmp) cc_final: 0.6394 (mmp) REVERT: K 63 ARG cc_start: 0.6057 (ttt180) cc_final: 0.5651 (ttp80) REVERT: K 71 GLU cc_start: 0.6060 (pt0) cc_final: 0.5853 (pt0) REVERT: K 121 ARG cc_start: 0.5099 (mmt180) cc_final: 0.4897 (mmm160) REVERT: K 162 ARG cc_start: 0.5966 (mtt180) cc_final: 0.5415 (mtp85) REVERT: K 195 GLU cc_start: 0.6251 (mt-10) cc_final: 0.5933 (mt-10) REVERT: L 27 GLU cc_start: 0.6466 (mt-10) cc_final: 0.5630 (mp0) REVERT: L 48 MET cc_start: 0.6715 (mmp) cc_final: 0.6396 (mmp) REVERT: L 63 ARG cc_start: 0.6057 (ttt180) cc_final: 0.5652 (ttp80) REVERT: L 71 GLU cc_start: 0.6061 (pt0) cc_final: 0.5855 (pt0) REVERT: L 162 ARG cc_start: 0.5967 (mtt180) cc_final: 0.5415 (mtp85) REVERT: L 195 GLU cc_start: 0.6247 (mt-10) cc_final: 0.5930 (mt-10) REVERT: M 27 GLU cc_start: 0.6465 (mt-10) cc_final: 0.5628 (mp0) REVERT: M 48 MET cc_start: 0.6712 (mmp) cc_final: 0.6393 (mmp) REVERT: M 63 ARG cc_start: 0.6058 (ttt180) cc_final: 0.5653 (ttp80) REVERT: M 71 GLU cc_start: 0.6060 (pt0) cc_final: 0.5854 (pt0) REVERT: M 121 ARG cc_start: 0.5099 (mmt180) cc_final: 0.4897 (mmm160) REVERT: M 162 ARG cc_start: 0.5966 (mtt180) cc_final: 0.5416 (mtp85) REVERT: M 195 GLU cc_start: 0.6250 (mt-10) cc_final: 0.5932 (mt-10) REVERT: N 27 GLU cc_start: 0.6463 (mt-10) cc_final: 0.5561 (mp0) REVERT: N 48 MET cc_start: 0.6700 (mmp) cc_final: 0.6381 (mmp) REVERT: N 63 ARG cc_start: 0.6057 (ttt180) cc_final: 0.5652 (ttp80) REVERT: N 71 GLU cc_start: 0.6061 (pt0) cc_final: 0.5854 (pt0) REVERT: N 162 ARG cc_start: 0.5966 (mtt180) cc_final: 0.5415 (mtp85) REVERT: N 195 GLU cc_start: 0.6248 (mt-10) cc_final: 0.5930 (mt-10) REVERT: O 27 GLU cc_start: 0.6465 (mt-10) cc_final: 0.5563 (mp0) REVERT: O 48 MET cc_start: 0.6710 (mmp) cc_final: 0.6392 (mmp) REVERT: O 63 ARG cc_start: 0.6054 (ttt180) cc_final: 0.5648 (ttp80) REVERT: O 71 GLU cc_start: 0.6058 (pt0) cc_final: 0.5852 (pt0) REVERT: O 162 ARG cc_start: 0.5966 (mtt180) cc_final: 0.5414 (mtp85) REVERT: O 195 GLU cc_start: 0.6247 (mt-10) cc_final: 0.5929 (mt-10) REVERT: P 27 GLU cc_start: 0.6463 (mt-10) cc_final: 0.5561 (mp0) REVERT: P 48 MET cc_start: 0.6713 (mmp) cc_final: 0.6395 (mmp) REVERT: P 63 ARG cc_start: 0.6057 (ttt180) cc_final: 0.5652 (ttp80) REVERT: P 71 GLU cc_start: 0.6061 (pt0) cc_final: 0.5853 (pt0) REVERT: P 121 ARG cc_start: 0.5095 (mmt180) cc_final: 0.4893 (mmm160) REVERT: P 162 ARG cc_start: 0.5967 (mtt180) cc_final: 0.5416 (mtp85) REVERT: P 195 GLU cc_start: 0.6247 (mt-10) cc_final: 0.5930 (mt-10) REVERT: Q 27 GLU cc_start: 0.6463 (mt-10) cc_final: 0.5562 (mp0) REVERT: Q 48 MET cc_start: 0.6714 (mmp) cc_final: 0.6394 (mmp) REVERT: Q 63 ARG cc_start: 0.6058 (ttt180) cc_final: 0.5652 (ttp80) REVERT: Q 71 GLU cc_start: 0.6060 (pt0) cc_final: 0.5853 (pt0) REVERT: Q 162 ARG cc_start: 0.5966 (mtt180) cc_final: 0.5416 (mtp85) REVERT: Q 195 GLU cc_start: 0.6251 (mt-10) cc_final: 0.5933 (mt-10) REVERT: R 27 GLU cc_start: 0.6466 (mt-10) cc_final: 0.5564 (mp0) REVERT: R 48 MET cc_start: 0.6715 (mmp) cc_final: 0.6396 (mmp) REVERT: R 63 ARG cc_start: 0.6058 (ttt180) cc_final: 0.5652 (ttp80) REVERT: R 71 GLU cc_start: 0.6061 (pt0) cc_final: 0.5854 (pt0) REVERT: R 162 ARG cc_start: 0.5967 (mtt180) cc_final: 0.5415 (mtp85) REVERT: R 195 GLU cc_start: 0.6247 (mt-10) cc_final: 0.5930 (mt-10) REVERT: S 27 GLU cc_start: 0.6462 (mt-10) cc_final: 0.5561 (mp0) REVERT: S 48 MET cc_start: 0.6712 (mmp) cc_final: 0.6395 (mmp) REVERT: S 63 ARG cc_start: 0.6056 (ttt180) cc_final: 0.5650 (ttp80) REVERT: S 71 GLU cc_start: 0.6060 (pt0) cc_final: 0.5854 (pt0) REVERT: S 121 ARG cc_start: 0.5096 (mmt180) cc_final: 0.4895 (mmm160) REVERT: S 162 ARG cc_start: 0.5964 (mtt180) cc_final: 0.5414 (mtp85) REVERT: S 195 GLU cc_start: 0.6248 (mt-10) cc_final: 0.5930 (mt-10) REVERT: T 27 GLU cc_start: 0.6463 (mt-10) cc_final: 0.5561 (mp0) REVERT: T 48 MET cc_start: 0.6713 (mmp) cc_final: 0.6395 (mmp) REVERT: T 63 ARG cc_start: 0.6057 (ttt180) cc_final: 0.5652 (ttp80) REVERT: T 71 GLU cc_start: 0.6060 (pt0) cc_final: 0.5853 (pt0) REVERT: T 121 ARG cc_start: 0.5095 (mmt180) cc_final: 0.4893 (mmm160) REVERT: T 162 ARG cc_start: 0.5967 (mtt180) cc_final: 0.5416 (mtp85) REVERT: T 195 GLU cc_start: 0.6247 (mt-10) cc_final: 0.5930 (mt-10) REVERT: U 27 GLU cc_start: 0.6465 (mt-10) cc_final: 0.5564 (mp0) REVERT: U 48 MET cc_start: 0.6713 (mmp) cc_final: 0.6395 (mmp) REVERT: U 63 ARG cc_start: 0.6055 (ttt180) cc_final: 0.5649 (ttp80) REVERT: U 71 GLU cc_start: 0.6061 (pt0) cc_final: 0.5854 (pt0) REVERT: U 121 ARG cc_start: 0.5095 (mmt180) cc_final: 0.4895 (mmm160) REVERT: U 162 ARG cc_start: 0.5964 (mtt180) cc_final: 0.5414 (mtp85) REVERT: U 195 GLU cc_start: 0.6251 (mt-10) cc_final: 0.5933 (mt-10) REVERT: V 27 GLU cc_start: 0.6465 (mt-10) cc_final: 0.5563 (mp0) REVERT: V 48 MET cc_start: 0.6712 (mmp) cc_final: 0.6394 (mmp) REVERT: V 63 ARG cc_start: 0.6058 (ttt180) cc_final: 0.5653 (ttp80) REVERT: V 71 GLU cc_start: 0.6060 (pt0) cc_final: 0.5854 (pt0) REVERT: V 121 ARG cc_start: 0.5100 (mmt180) cc_final: 0.4897 (mmm160) REVERT: V 162 ARG cc_start: 0.5966 (mtt180) cc_final: 0.5416 (mtp85) REVERT: V 195 GLU cc_start: 0.6250 (mt-10) cc_final: 0.5933 (mt-10) REVERT: W 27 GLU cc_start: 0.6462 (mt-10) cc_final: 0.5561 (mp0) REVERT: W 48 MET cc_start: 0.6712 (mmp) cc_final: 0.6395 (mmp) REVERT: W 63 ARG cc_start: 0.6056 (ttt180) cc_final: 0.5650 (ttp80) REVERT: W 71 GLU cc_start: 0.6060 (pt0) cc_final: 0.5853 (pt0) REVERT: W 121 ARG cc_start: 0.5096 (mmt180) cc_final: 0.4895 (mmm160) REVERT: W 162 ARG cc_start: 0.5964 (mtt180) cc_final: 0.5414 (mtp85) REVERT: W 195 GLU cc_start: 0.6248 (mt-10) cc_final: 0.5930 (mt-10) REVERT: X 27 GLU cc_start: 0.6466 (mt-10) cc_final: 0.5566 (mp0) REVERT: X 48 MET cc_start: 0.6715 (mmp) cc_final: 0.6396 (mmp) REVERT: X 63 ARG cc_start: 0.6058 (ttt180) cc_final: 0.5652 (ttp80) REVERT: X 71 GLU cc_start: 0.6061 (pt0) cc_final: 0.5854 (pt0) REVERT: X 162 ARG cc_start: 0.5967 (mtt180) cc_final: 0.5415 (mtp85) REVERT: X 195 GLU cc_start: 0.6247 (mt-10) cc_final: 0.5930 (mt-10) outliers start: 24 outliers final: 0 residues processed: 744 average time/residue: 0.9333 time to fit residues: 795.6380 Evaluate side-chains 495 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN I 134 GLN J 134 GLN K 134 GLN L 134 GLN M 134 GLN N 134 GLN O 134 GLN P 134 GLN Q 134 GLN R 134 GLN S 134 GLN T 134 GLN U 134 GLN V 134 GLN W 134 GLN X 134 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.118409 restraints weight = 25737.357| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 0.95 r_work: 0.3124 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 35976 Z= 0.168 Angle : 0.628 4.684 48912 Z= 0.345 Chirality : 0.048 0.149 5592 Planarity : 0.006 0.040 6504 Dihedral : 5.485 19.783 5088 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.95 % Allowed : 8.50 % Favored : 87.55 % 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: 0.98 (0.13), residues: 4512 helix: 2.07 (0.12), residues: 1848 sheet: 0.02 (0.13), residues: 1344 loop : -0.62 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 18 TYR 0.010 0.002 TYR V 145 PHE 0.007 0.002 PHE B 58 HIS 0.006 0.002 HIS P 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (35976) covalent geometry : angle 0.62802 / 0.35 (48912) hydrogen bonds : bond 0.04911 / 3.42 ( 2136) hydrogen bonds : angle 4.08387 / 2.84 ( 5904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 485 time to evaluate : 1.426 Fit side-chains REVERT: A 23 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7165 (t70) REVERT: A 27 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7309 (mp0) REVERT: A 102 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7869 (p0) REVERT: B 23 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7163 (t70) REVERT: B 27 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7302 (mp0) REVERT: B 102 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7880 (p0) REVERT: C 23 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7155 (t70) REVERT: C 27 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7304 (mp0) REVERT: C 102 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7880 (p0) REVERT: D 23 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7157 (t70) REVERT: D 27 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7316 (mp0) REVERT: D 102 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7867 (p0) REVERT: E 23 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7163 (t70) REVERT: E 27 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7308 (mp0) REVERT: E 102 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7866 (p0) REVERT: F 23 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.7161 (t70) REVERT: F 27 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7311 (mp0) REVERT: F 102 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7873 (p0) REVERT: G 23 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7156 (t70) REVERT: G 27 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7309 (mp0) REVERT: G 102 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7879 (p0) REVERT: H 23 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.7158 (t70) REVERT: H 27 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7294 (mp0) REVERT: H 102 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7876 (p0) REVERT: I 23 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7163 (t70) REVERT: I 27 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7307 (mp0) REVERT: I 102 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7878 (p0) REVERT: J 23 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7174 (t70) REVERT: J 27 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7303 (mp0) REVERT: J 102 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7867 (p0) REVERT: K 23 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.7176 (t70) REVERT: K 27 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7309 (mp0) REVERT: K 102 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7866 (p0) REVERT: L 23 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.7143 (t70) REVERT: L 27 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7308 (mp0) REVERT: L 102 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7873 (p0) REVERT: M 23 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.7157 (t70) REVERT: M 27 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7312 (mp0) REVERT: M 102 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7879 (p0) REVERT: N 23 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7159 (t70) REVERT: N 27 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7300 (mp0) REVERT: N 102 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7877 (p0) REVERT: O 23 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7153 (t70) REVERT: O 27 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7302 (mp0) REVERT: O 102 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7875 (p0) REVERT: P 23 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.7156 (t70) REVERT: P 27 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7303 (mp0) REVERT: P 102 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7876 (p0) REVERT: Q 23 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7158 (t70) REVERT: Q 27 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7299 (mp0) REVERT: Q 102 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7879 (p0) REVERT: R 23 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.7144 (t70) REVERT: R 27 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7294 (mp0) REVERT: R 102 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7866 (p0) REVERT: S 23 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7164 (t70) REVERT: S 27 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7304 (mp0) REVERT: S 102 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7877 (p0) REVERT: T 23 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7160 (t70) REVERT: T 27 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7306 (mp0) REVERT: T 102 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7879 (p0) REVERT: U 23 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.7153 (t70) REVERT: U 27 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7307 (mp0) REVERT: U 102 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7863 (p0) REVERT: V 23 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7160 (t70) REVERT: V 27 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7309 (mp0) REVERT: V 102 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7878 (p0) REVERT: W 23 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7159 (t70) REVERT: W 27 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7305 (mp0) REVERT: W 102 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7882 (p0) REVERT: X 23 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7144 (t70) REVERT: X 27 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7304 (mp0) REVERT: X 102 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7872 (p0) outliers start: 144 outliers final: 96 residues processed: 624 average time/residue: 0.9552 time to fit residues: 680.8567 Evaluate side-chains 552 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 408 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain L residue 23 ASP Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 102 ASP Chi-restraints excluded: chain M residue 142 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 102 ASP Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 102 ASP Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain Q residue 54 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 142 SER Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 54 SER Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain S residue 23 ASP Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 54 SER Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 102 ASP Chi-restraints excluded: chain T residue 142 SER Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 102 ASP Chi-restraints excluded: chain U residue 142 SER Chi-restraints excluded: chain V residue 23 ASP Chi-restraints excluded: chain V residue 54 SER Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 102 ASP Chi-restraints excluded: chain V residue 142 SER Chi-restraints excluded: chain W residue 23 ASP Chi-restraints excluded: chain W residue 54 SER Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain W residue 142 SER Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 102 ASP Chi-restraints excluded: chain X residue 142 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 10 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 324 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 436 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 342 optimal weight: 3.9990 chunk 390 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 285 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN B 134 GLN C 134 GLN D 134 GLN D 160 ASN E 134 GLN F 134 GLN G 134 GLN H 134 GLN I 134 GLN J 134 GLN K 134 GLN L 134 GLN M 134 GLN M 160 ASN N 134 GLN O 134 GLN P 134 GLN Q 134 GLN R 134 GLN S 134 GLN T 134 GLN U 134 GLN V 134 GLN W 134 GLN X 134 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118763 restraints weight = 26131.026| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 0.95 r_work: 0.3141 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 35976 Z= 0.162 Angle : 0.601 4.458 48912 Z= 0.335 Chirality : 0.047 0.150 5592 Planarity : 0.006 0.037 6504 Dihedral : 5.400 18.894 5088 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.26 % Allowed : 8.55 % Favored : 86.18 % 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: 1.08 (0.12), residues: 4512 helix: 2.21 (0.12), residues: 1848 sheet: 0.09 (0.13), residues: 1344 loop : -0.71 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 162 TYR 0.010 0.002 TYR F 145 PHE 0.007 0.002 PHE W 44 HIS 0.007 0.002 HIS H 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (35976) covalent geometry : angle 0.60115 / 0.34 (48912) hydrogen bonds : bond 0.04774 / 3.32 ( 2136) hydrogen bonds : angle 4.02712 / 2.80 ( 5904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 489 time to evaluate : 1.392 Fit side-chains REVERT: A 27 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7269 (mp0) REVERT: A 102 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7874 (p0) REVERT: B 27 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7261 (mp0) REVERT: B 102 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7877 (p0) REVERT: C 27 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7271 (mp0) REVERT: C 102 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7876 (p0) REVERT: D 27 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7265 (mp0) REVERT: D 102 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7896 (p0) REVERT: E 27 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7266 (mp0) REVERT: E 102 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7865 (p0) REVERT: F 27 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7266 (mp0) REVERT: F 102 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7865 (p0) REVERT: G 27 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7279 (mp0) REVERT: G 102 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7878 (p0) REVERT: H 27 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7272 (mp0) REVERT: H 102 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7878 (p0) REVERT: I 27 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7267 (mp0) REVERT: I 102 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7864 (p0) REVERT: J 27 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7273 (mp0) REVERT: J 102 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7873 (p0) REVERT: K 27 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7270 (mp0) REVERT: K 102 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7878 (p0) REVERT: L 27 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7259 (mp0) REVERT: L 102 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7872 (p0) REVERT: M 27 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7278 (mp0) REVERT: M 102 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7879 (p0) REVERT: N 27 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7262 (mp0) REVERT: N 102 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7885 (p0) REVERT: O 27 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7274 (mp0) REVERT: O 102 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7876 (p0) REVERT: P 27 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7264 (mp0) REVERT: P 102 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7883 (p0) REVERT: Q 27 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7264 (mp0) REVERT: Q 102 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7863 (p0) REVERT: R 27 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7264 (mp0) REVERT: S 27 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7265 (mp0) REVERT: S 102 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7874 (p0) REVERT: T 27 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7265 (mp0) REVERT: T 102 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7908 (p0) REVERT: U 27 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7264 (mp0) REVERT: U 102 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7870 (p0) REVERT: V 27 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7275 (mp0) REVERT: V 102 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7877 (p0) REVERT: W 27 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7268 (mp0) REVERT: W 102 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7871 (p0) REVERT: X 27 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7262 (mp0) REVERT: X 102 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7868 (p0) outliers start: 192 outliers final: 96 residues processed: 633 average time/residue: 0.8745 time to fit residues: 636.9949 Evaluate side-chains 505 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 386 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 102 ASP Chi-restraints excluded: chain M residue 142 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 102 ASP Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 102 ASP Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain Q residue 54 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 142 SER Chi-restraints excluded: chain R residue 54 SER Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain T residue 54 SER Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 102 ASP Chi-restraints excluded: chain T residue 142 SER Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 102 ASP Chi-restraints excluded: chain U residue 142 SER Chi-restraints excluded: chain V residue 54 SER Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 102 ASP Chi-restraints excluded: chain V residue 142 SER Chi-restraints excluded: chain W residue 54 SER Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain W residue 142 SER Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 102 ASP Chi-restraints excluded: chain X residue 142 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 381 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 317 optimal weight: 0.7980 chunk 305 optimal weight: 2.9990 chunk 444 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 342 optimal weight: 5.9990 chunk 411 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN I 134 GLN J 134 GLN K 134 GLN L 134 GLN M 134 GLN N 134 GLN O 134 GLN P 134 GLN Q 134 GLN R 134 GLN S 134 GLN T 134 GLN U 134 GLN V 134 GLN W 134 GLN X 134 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.146607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.119542 restraints weight = 25580.343| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 0.97 r_work: 0.3149 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 35976 Z= 0.146 Angle : 0.564 4.174 48912 Z= 0.314 Chirality : 0.046 0.148 5592 Planarity : 0.005 0.031 6504 Dihedral : 5.258 17.802 5088 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.82 % Allowed : 10.96 % Favored : 84.21 % 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: 1.19 (0.13), residues: 4512 helix: 2.31 (0.12), residues: 1848 sheet: 0.13 (0.13), residues: 1344 loop : -0.64 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 162 TYR 0.010 0.002 TYR R 145 PHE 0.007 0.002 PHE B 44 HIS 0.006 0.002 HIS D 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (35976) covalent geometry : angle 0.56411 / 0.31 (48912) hydrogen bonds : bond 0.04463 / 3.10 ( 2136) hydrogen bonds : angle 3.89590 / 2.70 ( 5904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 423 time to evaluate : 1.513 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: A 27 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7286 (mp0) REVERT: A 102 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7880 (p0) REVERT: B 27 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7285 (mp0) REVERT: B 102 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7902 (p0) REVERT: C 27 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7265 (mp0) REVERT: C 102 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7874 (p0) REVERT: D 27 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7282 (mp0) REVERT: D 102 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7875 (p0) REVERT: E 27 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7284 (mp0) REVERT: E 102 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7871 (p0) REVERT: F 27 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7293 (mp0) REVERT: F 102 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7871 (p0) REVERT: G 27 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7289 (mp0) REVERT: G 102 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7876 (p0) REVERT: H 27 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7292 (mp0) REVERT: H 102 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7878 (p0) REVERT: I 27 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7294 (mp0) REVERT: I 102 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7873 (p0) REVERT: J 27 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7288 (mp0) REVERT: J 102 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7877 (p0) REVERT: K 27 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7289 (mp0) REVERT: K 102 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7891 (p0) REVERT: L 27 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7284 (mp0) REVERT: L 102 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7876 (p0) REVERT: M 27 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7295 (mp0) REVERT: M 102 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7904 (p0) REVERT: N 27 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7281 (mp0) REVERT: N 102 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7879 (p0) REVERT: O 27 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7291 (mp0) REVERT: O 102 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7878 (p0) REVERT: P 27 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7282 (mp0) REVERT: P 102 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7882 (p0) REVERT: Q 27 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7292 (mp0) REVERT: Q 102 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7870 (p0) REVERT: R 27 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7284 (mp0) REVERT: S 27 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7289 (mp0) REVERT: S 102 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7880 (p0) REVERT: T 27 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7283 (mp0) REVERT: T 102 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7879 (p0) REVERT: U 27 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7282 (mp0) REVERT: U 102 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7873 (p0) REVERT: V 27 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7292 (mp0) REVERT: V 102 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7876 (p0) REVERT: W 27 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7287 (mp0) REVERT: W 102 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7877 (p0) REVERT: X 27 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7262 (mp0) REVERT: X 102 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7875 (p0) outliers start: 176 outliers final: 105 residues processed: 575 average time/residue: 0.9815 time to fit residues: 648.7738 Evaluate side-chains 521 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 393 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 102 ASP Chi-restraints excluded: chain M residue 142 SER Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 102 ASP Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 102 ASP Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain Q residue 12 ARG Chi-restraints excluded: chain Q residue 54 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 142 SER Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain R residue 54 SER Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain T residue 54 SER Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 102 ASP Chi-restraints excluded: chain T residue 142 SER Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 102 ASP Chi-restraints excluded: chain U residue 142 SER Chi-restraints excluded: chain V residue 54 SER Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 102 ASP Chi-restraints excluded: chain V residue 142 SER Chi-restraints excluded: chain W residue 54 SER Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain W residue 142 SER Chi-restraints excluded: chain X residue 12 ARG Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 102 ASP Chi-restraints excluded: chain X residue 142 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 164 optimal weight: 9.9990 chunk 308 optimal weight: 20.0000 chunk 56 optimal weight: 0.0570 chunk 441 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 365 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 373 optimal weight: 7.9990 chunk 398 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 overall best weight: 5.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A 160 ASN B 134 GLN B 160 ASN C 134 GLN D 134 GLN E 134 GLN E 160 ASN F 134 GLN F 160 ASN G 134 GLN G 160 ASN H 134 GLN I 134 GLN I 160 ASN J 134 GLN K 134 GLN K 160 ASN L 134 GLN L 160 ASN M 134 GLN N 134 GLN O 134 GLN O 160 ASN P 134 GLN P 160 ASN Q 134 GLN Q 160 ASN R 134 GLN R 160 ASN S 134 GLN S 160 ASN T 134 GLN T 160 ASN U 134 GLN U 160 ASN V 134 GLN W 134 GLN X 134 GLN X 160 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.145034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118031 restraints weight = 25164.208| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 0.97 r_work: 0.3126 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 35976 Z= 0.207 Angle : 0.660 4.889 48912 Z= 0.369 Chirality : 0.050 0.153 5592 Planarity : 0.007 0.042 6504 Dihedral : 5.569 18.537 5088 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 7.21 % Allowed : 8.28 % Favored : 84.51 % 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: 0.97 (0.13), residues: 4512 helix: 2.00 (0.12), residues: 1848 sheet: 0.05 (0.13), residues: 1344 loop : -0.57 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 162 TYR 0.013 0.003 TYR Q 145 PHE 0.010 0.002 PHE S 44 HIS 0.008 0.002 HIS P 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (35976) covalent geometry : angle 0.66044 / 0.37 (48912) hydrogen bonds : bond 0.05272 / 3.67 ( 2136) hydrogen bonds : angle 4.15616 / 2.89 ( 5904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 263 poor density : 406 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7342 (t70) REVERT: A 27 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7296 (mp0) REVERT: A 199 ARG cc_start: 0.5512 (OUTLIER) cc_final: 0.5300 (tpt-90) REVERT: B 23 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7330 (t70) REVERT: B 27 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7203 (mp0) REVERT: B 199 ARG cc_start: 0.5509 (OUTLIER) cc_final: 0.5300 (tpt-90) REVERT: C 23 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7339 (t70) REVERT: C 27 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7196 (mp0) REVERT: C 199 ARG cc_start: 0.5504 (OUTLIER) cc_final: 0.5298 (tpt-90) REVERT: D 23 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7337 (t70) REVERT: D 27 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7289 (mp0) REVERT: D 199 ARG cc_start: 0.5505 (OUTLIER) cc_final: 0.5297 (tpt-90) REVERT: E 23 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7334 (t70) REVERT: E 27 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7290 (mp0) REVERT: E 199 ARG cc_start: 0.5506 (OUTLIER) cc_final: 0.5158 (tpt-90) REVERT: F 23 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7330 (t70) REVERT: F 27 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7207 (mp0) REVERT: F 199 ARG cc_start: 0.5506 (OUTLIER) cc_final: 0.5160 (tpt-90) REVERT: G 23 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7335 (t70) REVERT: G 27 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7304 (mp0) REVERT: H 23 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7340 (t70) REVERT: H 27 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7191 (mp0) REVERT: H 199 ARG cc_start: 0.5504 (OUTLIER) cc_final: 0.5296 (tpt-90) REVERT: I 23 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7331 (t70) REVERT: I 27 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7204 (mp0) REVERT: I 199 ARG cc_start: 0.5502 (OUTLIER) cc_final: 0.5288 (tpt-90) REVERT: J 23 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7340 (t70) REVERT: J 27 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7304 (mp0) REVERT: J 199 ARG cc_start: 0.5509 (OUTLIER) cc_final: 0.5296 (tpt-90) REVERT: K 23 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7341 (t70) REVERT: K 27 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7300 (mp0) REVERT: K 199 ARG cc_start: 0.5505 (OUTLIER) cc_final: 0.5297 (tpt-90) REVERT: L 23 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7329 (t70) REVERT: L 27 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7205 (mp0) REVERT: L 199 ARG cc_start: 0.5501 (OUTLIER) cc_final: 0.5159 (tpt-90) REVERT: M 23 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7333 (t70) REVERT: M 27 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7302 (mp0) REVERT: M 199 ARG cc_start: 0.5498 (OUTLIER) cc_final: 0.5298 (tpt-90) REVERT: N 23 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7327 (t70) REVERT: N 27 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7200 (mp0) REVERT: N 199 ARG cc_start: 0.5505 (OUTLIER) cc_final: 0.5159 (tpt-90) REVERT: O 23 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7337 (t70) REVERT: O 27 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7192 (mp0) REVERT: O 199 ARG cc_start: 0.5503 (OUTLIER) cc_final: 0.5298 (tpt-90) REVERT: P 23 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7327 (t70) REVERT: P 27 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7199 (mp0) REVERT: P 199 ARG cc_start: 0.5503 (OUTLIER) cc_final: 0.5298 (tpt-90) REVERT: Q 23 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7331 (t70) REVERT: Q 27 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7201 (mp0) REVERT: Q 199 ARG cc_start: 0.5500 (OUTLIER) cc_final: 0.5157 (tpt-90) REVERT: R 23 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7334 (t70) REVERT: R 27 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7201 (mp0) REVERT: R 199 ARG cc_start: 0.5504 (OUTLIER) cc_final: 0.5157 (tpt-90) REVERT: S 23 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7331 (t70) REVERT: S 27 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7195 (mp0) REVERT: S 199 ARG cc_start: 0.5508 (OUTLIER) cc_final: 0.5297 (tpt-90) REVERT: T 23 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7326 (t70) REVERT: T 27 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7200 (mp0) REVERT: T 199 ARG cc_start: 0.5502 (OUTLIER) cc_final: 0.5300 (tpt-90) REVERT: U 23 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7339 (t70) REVERT: U 27 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7291 (mp0) REVERT: U 199 ARG cc_start: 0.5507 (OUTLIER) cc_final: 0.5160 (tpt-90) REVERT: V 23 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7336 (t70) REVERT: V 27 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7303 (mp0) REVERT: V 199 ARG cc_start: 0.5499 (OUTLIER) cc_final: 0.5157 (tpt-90) REVERT: W 23 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7329 (t70) REVERT: W 27 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7200 (mp0) REVERT: W 199 ARG cc_start: 0.5505 (OUTLIER) cc_final: 0.5295 (tpt-90) REVERT: X 23 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7332 (t70) REVERT: X 27 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7205 (mp0) REVERT: X 199 ARG cc_start: 0.5503 (OUTLIER) cc_final: 0.5155 (tpt-90) outliers start: 263 outliers final: 166 residues processed: 623 average time/residue: 0.9270 time to fit residues: 663.1347 Evaluate side-chains 621 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 408 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 199 ARG Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 199 ARG Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 199 ARG Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 199 ARG Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain I residue 199 ARG Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 199 ARG Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 199 ARG Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 23 ASP Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 199 ARG Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 142 SER Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 199 ARG Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain N residue 199 ARG Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 71 GLU Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 199 ARG Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 199 ARG Chi-restraints excluded: chain Q residue 12 ARG Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain Q residue 54 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 142 SER Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 199 ARG Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 54 SER Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 195 GLU Chi-restraints excluded: chain R residue 199 ARG Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 23 ASP Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain S residue 199 ARG Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 54 SER Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 142 SER Chi-restraints excluded: chain T residue 195 GLU Chi-restraints excluded: chain T residue 199 ARG Chi-restraints excluded: chain U residue 12 ARG Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 142 SER Chi-restraints excluded: chain U residue 195 GLU Chi-restraints excluded: chain U residue 199 ARG Chi-restraints excluded: chain V residue 12 ARG Chi-restraints excluded: chain V residue 23 ASP Chi-restraints excluded: chain V residue 54 SER Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 71 GLU Chi-restraints excluded: chain V residue 142 SER Chi-restraints excluded: chain V residue 195 GLU Chi-restraints excluded: chain V residue 199 ARG Chi-restraints excluded: chain W residue 12 ARG Chi-restraints excluded: chain W residue 23 ASP Chi-restraints excluded: chain W residue 54 SER Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain W residue 142 SER Chi-restraints excluded: chain W residue 195 GLU Chi-restraints excluded: chain W residue 199 ARG Chi-restraints excluded: chain X residue 12 ARG Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 71 GLU Chi-restraints excluded: chain X residue 142 SER Chi-restraints excluded: chain X residue 195 GLU Chi-restraints excluded: chain X residue 199 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 324 optimal weight: 3.9990 chunk 379 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 453 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 308 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 211 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN I 134 GLN J 134 GLN K 134 GLN L 134 GLN M 134 GLN N 134 GLN O 134 GLN P 134 GLN Q 134 GLN R 134 GLN S 134 GLN T 134 GLN U 134 GLN V 134 GLN W 134 GLN X 134 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.146593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120493 restraints weight = 24911.732| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 0.92 r_work: 0.3163 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 35976 Z= 0.152 Angle : 0.570 4.281 48912 Z= 0.319 Chirality : 0.047 0.152 5592 Planarity : 0.005 0.029 6504 Dihedral : 5.306 17.482 5088 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 6.55 % Allowed : 9.24 % Favored : 84.21 % 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: 1.07 (0.13), residues: 4512 helix: 2.20 (0.12), residues: 1848 sheet: 0.01 (0.13), residues: 1344 loop : -0.59 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 162 TYR 0.010 0.002 TYR V 145 PHE 0.007 0.002 PHE P 44 HIS 0.005 0.002 HIS V 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (35976) covalent geometry : angle 0.57002 / 0.32 (48912) hydrogen bonds : bond 0.04524 / 3.14 ( 2136) hydrogen bonds : angle 3.94838 / 2.74 ( 5904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 408 time to evaluate : 1.444 Fit side-chains REVERT: A 27 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7182 (mp0) REVERT: A 102 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7831 (p0) REVERT: B 27 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7180 (mp0) REVERT: B 102 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7830 (p0) REVERT: C 27 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7170 (mp0) REVERT: C 102 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7828 (p0) REVERT: D 27 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7173 (mp0) REVERT: D 102 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7834 (p0) REVERT: E 27 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7174 (mp0) REVERT: E 102 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7825 (p0) REVERT: F 27 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7182 (mp0) REVERT: F 102 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7828 (p0) REVERT: G 27 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7196 (mp0) REVERT: G 102 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7834 (p0) REVERT: H 27 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7177 (mp0) REVERT: H 102 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7832 (p0) REVERT: I 27 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7182 (mp0) REVERT: I 102 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7834 (p0) REVERT: J 27 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7187 (mp0) REVERT: J 102 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7833 (p0) REVERT: K 27 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7182 (mp0) REVERT: K 102 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7841 (p0) REVERT: L 27 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7173 (mp0) REVERT: L 102 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7828 (p0) REVERT: M 27 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7190 (mp0) REVERT: M 102 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7842 (p0) REVERT: N 27 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7184 (mp0) REVERT: N 102 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7838 (p0) REVERT: O 27 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7177 (mp0) REVERT: O 102 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7832 (p0) REVERT: P 27 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7180 (mp0) REVERT: P 102 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7837 (p0) REVERT: Q 27 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7186 (mp0) REVERT: Q 102 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7824 (p0) REVERT: R 27 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7175 (mp0) REVERT: S 27 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7178 (mp0) REVERT: S 102 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7833 (p0) REVERT: T 27 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7176 (mp0) REVERT: T 102 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7837 (p0) REVERT: U 27 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7175 (mp0) REVERT: U 102 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7823 (p0) REVERT: V 27 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7197 (mp0) REVERT: V 102 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7836 (p0) REVERT: W 27 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7184 (mp0) REVERT: W 102 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7831 (p0) REVERT: X 27 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7176 (mp0) REVERT: X 102 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7831 (p0) outliers start: 239 outliers final: 168 residues processed: 599 average time/residue: 0.8753 time to fit residues: 612.6310 Evaluate side-chains 575 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 384 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 102 ASP Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 142 SER Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain N residue 102 ASP Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 71 GLU Chi-restraints excluded: chain O residue 102 ASP Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain Q residue 54 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 142 SER Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain R residue 54 SER Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 195 GLU Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain T residue 54 SER Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 102 ASP Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 142 SER Chi-restraints excluded: chain T residue 195 GLU Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 102 ASP Chi-restraints excluded: chain U residue 133 LEU Chi-restraints excluded: chain U residue 142 SER Chi-restraints excluded: chain U residue 195 GLU Chi-restraints excluded: chain V residue 54 SER Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 71 GLU Chi-restraints excluded: chain V residue 102 ASP Chi-restraints excluded: chain V residue 133 LEU Chi-restraints excluded: chain V residue 142 SER Chi-restraints excluded: chain V residue 195 GLU Chi-restraints excluded: chain W residue 54 SER Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain W residue 142 SER Chi-restraints excluded: chain W residue 195 GLU Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 71 GLU Chi-restraints excluded: chain X residue 102 ASP Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 142 SER Chi-restraints excluded: chain X residue 195 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 6.9990 chunk 329 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 444 optimal weight: 9.9990 chunk 423 optimal weight: 8.9990 chunk 284 optimal weight: 20.0000 chunk 449 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 375 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN B 134 GLN C 134 GLN C 160 ASN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN H 160 ASN I 134 GLN J 134 GLN J 160 ASN K 134 GLN L 134 GLN M 134 GLN N 134 GLN N 160 ASN O 134 GLN P 134 GLN Q 134 GLN R 134 GLN S 134 GLN T 134 GLN U 134 GLN V 134 GLN V 160 ASN W 134 GLN W 160 ASN X 134 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.145260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118350 restraints weight = 24976.845| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 0.96 r_work: 0.3129 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 35976 Z= 0.207 Angle : 0.661 4.982 48912 Z= 0.369 Chirality : 0.050 0.165 5592 Planarity : 0.007 0.041 6504 Dihedral : 5.563 17.975 5088 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 6.52 % Allowed : 9.92 % Favored : 83.55 % 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: 0.92 (0.13), residues: 4512 helix: 1.98 (0.12), residues: 1848 sheet: -0.06 (0.13), residues: 1344 loop : -0.53 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 162 TYR 0.013 0.003 TYR K 145 PHE 0.010 0.002 PHE R 44 HIS 0.007 0.002 HIS T 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (35976) covalent geometry : angle 0.66106 / 0.37 (48912) hydrogen bonds : bond 0.05226 / 3.63 ( 2136) hydrogen bonds : angle 4.14179 / 2.88 ( 5904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 384 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7232 (mp0) REVERT: A 199 ARG cc_start: 0.5477 (OUTLIER) cc_final: 0.5252 (tpt-90) REVERT: B 27 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7217 (mp0) REVERT: B 199 ARG cc_start: 0.5472 (OUTLIER) cc_final: 0.5244 (tpt-90) REVERT: C 27 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7213 (mp0) REVERT: C 199 ARG cc_start: 0.5469 (OUTLIER) cc_final: 0.5239 (tpt-90) REVERT: D 27 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7219 (mp0) REVERT: D 199 ARG cc_start: 0.5484 (OUTLIER) cc_final: 0.5257 (tpt-90) REVERT: E 27 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7221 (mp0) REVERT: E 199 ARG cc_start: 0.5452 (OUTLIER) cc_final: 0.5229 (tpt-90) REVERT: F 27 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7230 (mp0) REVERT: F 199 ARG cc_start: 0.5467 (OUTLIER) cc_final: 0.5241 (tpt-90) REVERT: G 27 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7232 (mp0) REVERT: H 27 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7215 (mp0) REVERT: H 199 ARG cc_start: 0.5475 (OUTLIER) cc_final: 0.5247 (tpt-90) REVERT: I 27 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7229 (mp0) REVERT: I 199 ARG cc_start: 0.5446 (OUTLIER) cc_final: 0.5224 (tpt-90) REVERT: J 27 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7230 (mp0) REVERT: J 199 ARG cc_start: 0.5479 (OUTLIER) cc_final: 0.5252 (tpt-90) REVERT: K 27 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7232 (mp0) REVERT: K 199 ARG cc_start: 0.5481 (OUTLIER) cc_final: 0.5254 (tpt-90) REVERT: L 27 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7231 (mp0) REVERT: L 199 ARG cc_start: 0.5443 (OUTLIER) cc_final: 0.5217 (tpt-90) REVERT: M 27 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7228 (mp0) REVERT: M 199 ARG cc_start: 0.5441 (OUTLIER) cc_final: 0.5222 (tpt-90) REVERT: N 27 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7235 (mp0) REVERT: N 199 ARG cc_start: 0.5472 (OUTLIER) cc_final: 0.5251 (tpt-90) REVERT: O 27 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7217 (mp0) REVERT: O 199 ARG cc_start: 0.5477 (OUTLIER) cc_final: 0.5249 (tpt-90) REVERT: P 27 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7228 (mp0) REVERT: P 199 ARG cc_start: 0.5481 (OUTLIER) cc_final: 0.5257 (tpt-90) REVERT: Q 27 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7230 (mp0) REVERT: Q 199 ARG cc_start: 0.5450 (OUTLIER) cc_final: 0.5228 (tpt-90) REVERT: R 27 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7229 (mp0) REVERT: R 199 ARG cc_start: 0.5442 (OUTLIER) cc_final: 0.5225 (tpt-90) REVERT: S 27 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7220 (mp0) REVERT: S 199 ARG cc_start: 0.5468 (OUTLIER) cc_final: 0.5240 (tpt-90) REVERT: T 27 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7232 (mp0) REVERT: T 199 ARG cc_start: 0.5475 (OUTLIER) cc_final: 0.5255 (tpt-90) REVERT: U 27 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7224 (mp0) REVERT: U 199 ARG cc_start: 0.5480 (OUTLIER) cc_final: 0.5253 (tpt-90) REVERT: V 27 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7233 (mp0) REVERT: V 199 ARG cc_start: 0.5444 (OUTLIER) cc_final: 0.5228 (tpt-90) REVERT: W 27 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7220 (mp0) REVERT: W 199 ARG cc_start: 0.5468 (OUTLIER) cc_final: 0.5242 (tpt-90) REVERT: X 27 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7230 (mp0) REVERT: X 199 ARG cc_start: 0.5444 (OUTLIER) cc_final: 0.5220 (tpt-90) outliers start: 238 outliers final: 168 residues processed: 574 average time/residue: 0.9877 time to fit residues: 652.9845 Evaluate side-chains 575 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 384 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 199 ARG Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 199 ARG Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 199 ARG Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 199 ARG Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain I residue 199 ARG Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 199 ARG Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 199 ARG Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 199 ARG Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 142 SER Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 199 ARG Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain N residue 199 ARG Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 71 GLU Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 199 ARG Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 199 ARG Chi-restraints excluded: chain Q residue 12 ARG Chi-restraints excluded: chain Q residue 54 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 142 SER Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 199 ARG Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain R residue 54 SER Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 195 GLU Chi-restraints excluded: chain R residue 199 ARG Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain S residue 199 ARG Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 54 SER Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 142 SER Chi-restraints excluded: chain T residue 195 GLU Chi-restraints excluded: chain T residue 199 ARG Chi-restraints excluded: chain U residue 12 ARG Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 142 SER Chi-restraints excluded: chain U residue 195 GLU Chi-restraints excluded: chain U residue 199 ARG Chi-restraints excluded: chain V residue 12 ARG Chi-restraints excluded: chain V residue 54 SER Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 71 GLU Chi-restraints excluded: chain V residue 142 SER Chi-restraints excluded: chain V residue 195 GLU Chi-restraints excluded: chain V residue 199 ARG Chi-restraints excluded: chain W residue 12 ARG Chi-restraints excluded: chain W residue 54 SER Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain W residue 142 SER Chi-restraints excluded: chain W residue 195 GLU Chi-restraints excluded: chain W residue 199 ARG Chi-restraints excluded: chain X residue 12 ARG Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 71 GLU Chi-restraints excluded: chain X residue 142 SER Chi-restraints excluded: chain X residue 195 GLU Chi-restraints excluded: chain X residue 199 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 419 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 394 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 319 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 443 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 342 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN I 134 GLN J 134 GLN K 134 GLN L 134 GLN M 134 GLN N 134 GLN O 134 GLN P 134 GLN Q 134 GLN R 134 GLN S 134 GLN T 134 GLN U 134 GLN V 134 GLN W 134 GLN X 134 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.145537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118687 restraints weight = 24945.022| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 0.96 r_work: 0.3137 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 35976 Z= 0.196 Angle : 0.643 4.757 48912 Z= 0.359 Chirality : 0.049 0.172 5592 Planarity : 0.006 0.037 6504 Dihedral : 5.531 17.775 5088 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.92 % Allowed : 10.61 % Favored : 83.47 % 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: 0.90 (0.13), residues: 4512 helix: 1.96 (0.12), residues: 1848 sheet: -0.09 (0.13), residues: 1344 loop : -0.50 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 162 TYR 0.012 0.003 TYR F 145 PHE 0.009 0.002 PHE B 44 HIS 0.006 0.002 HIS J 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (35976) covalent geometry : angle 0.64258 / 0.36 (48912) hydrogen bonds : bond 0.05044 / 3.51 ( 2136) hydrogen bonds : angle 4.11049 / 2.86 ( 5904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 408 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7207 (mp0) REVERT: B 27 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7202 (mp0) REVERT: C 27 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7198 (mp0) REVERT: D 27 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7197 (mp0) REVERT: E 27 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7197 (mp0) REVERT: F 27 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7204 (mp0) REVERT: G 27 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7208 (mp0) REVERT: H 27 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7200 (mp0) REVERT: I 27 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7205 (mp0) REVERT: J 27 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7207 (mp0) REVERT: K 27 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7212 (mp0) REVERT: L 27 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7202 (mp0) REVERT: M 27 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7208 (mp0) REVERT: N 27 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7208 (mp0) REVERT: O 27 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7200 (mp0) REVERT: P 27 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7204 (mp0) REVERT: Q 27 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7207 (mp0) REVERT: R 27 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7202 (mp0) REVERT: S 27 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7203 (mp0) REVERT: T 27 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7207 (mp0) REVERT: U 27 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7190 (mp0) REVERT: V 27 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7207 (mp0) REVERT: W 27 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7205 (mp0) REVERT: X 27 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7207 (mp0) outliers start: 216 outliers final: 168 residues processed: 576 average time/residue: 0.9994 time to fit residues: 661.8341 Evaluate side-chains 576 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 408 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 142 SER Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 71 GLU Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain Q residue 12 ARG Chi-restraints excluded: chain Q residue 54 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 142 SER Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain R residue 54 SER Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 195 GLU Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 54 SER Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 142 SER Chi-restraints excluded: chain T residue 195 GLU Chi-restraints excluded: chain U residue 12 ARG Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 142 SER Chi-restraints excluded: chain U residue 195 GLU Chi-restraints excluded: chain V residue 12 ARG Chi-restraints excluded: chain V residue 54 SER Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 71 GLU Chi-restraints excluded: chain V residue 142 SER Chi-restraints excluded: chain V residue 195 GLU Chi-restraints excluded: chain W residue 12 ARG Chi-restraints excluded: chain W residue 54 SER Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain W residue 142 SER Chi-restraints excluded: chain W residue 195 GLU Chi-restraints excluded: chain X residue 12 ARG Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 71 GLU Chi-restraints excluded: chain X residue 142 SER Chi-restraints excluded: chain X residue 195 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 255 optimal weight: 9.9990 chunk 365 optimal weight: 9.9990 chunk 346 optimal weight: 10.0000 chunk 314 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 434 optimal weight: 0.9980 chunk 444 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 355 optimal weight: 10.0000 chunk 262 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN I 134 GLN J 134 GLN K 134 GLN L 134 GLN M 134 GLN N 134 GLN O 134 GLN P 134 GLN Q 134 GLN R 134 GLN S 134 GLN T 134 GLN U 134 GLN V 134 GLN W 134 GLN X 134 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.146241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119349 restraints weight = 24999.925| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 0.96 r_work: 0.3146 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 35976 Z= 0.169 Angle : 0.597 4.390 48912 Z= 0.334 Chirality : 0.048 0.167 5592 Planarity : 0.006 0.035 6504 Dihedral : 5.415 17.481 5088 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 6.58 % Allowed : 9.95 % Favored : 83.47 % 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: 1.00 (0.13), residues: 4512 helix: 2.12 (0.12), residues: 1848 sheet: -0.09 (0.13), residues: 1344 loop : -0.52 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 162 TYR 0.011 0.002 TYR I 145 PHE 0.008 0.002 PHE T 44 HIS 0.005 0.002 HIS G 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (35976) covalent geometry : angle 0.59732 / 0.33 (48912) hydrogen bonds : bond 0.04719 / 3.28 ( 2136) hydrogen bonds : angle 4.01915 / 2.79 ( 5904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 408 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7220 (mp0) REVERT: A 199 ARG cc_start: 0.5386 (OUTLIER) cc_final: 0.5186 (tpt-90) REVERT: B 27 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7221 (mp0) REVERT: B 199 ARG cc_start: 0.5385 (OUTLIER) cc_final: 0.5182 (tpt-90) REVERT: C 27 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7220 (mp0) REVERT: C 199 ARG cc_start: 0.5384 (OUTLIER) cc_final: 0.5183 (tpt-90) REVERT: D 27 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7214 (mp0) REVERT: D 199 ARG cc_start: 0.5397 (OUTLIER) cc_final: 0.5195 (tpt-90) REVERT: E 27 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7216 (mp0) REVERT: E 199 ARG cc_start: 0.5394 (OUTLIER) cc_final: 0.5192 (tpt-90) REVERT: F 27 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7219 (mp0) REVERT: G 27 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7338 (mp0) REVERT: H 27 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7216 (mp0) REVERT: H 199 ARG cc_start: 0.5388 (OUTLIER) cc_final: 0.5186 (tpt-90) REVERT: I 27 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7220 (mp0) REVERT: J 27 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7220 (mp0) REVERT: K 27 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7325 (mp0) REVERT: K 199 ARG cc_start: 0.5392 (OUTLIER) cc_final: 0.5188 (tpt-90) REVERT: L 27 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7221 (mp0) REVERT: M 27 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7332 (mp0) REVERT: M 199 ARG cc_start: 0.5392 (OUTLIER) cc_final: 0.5191 (tpt-90) REVERT: N 27 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7226 (mp0) REVERT: O 27 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7222 (mp0) REVERT: P 27 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7332 (mp0) REVERT: Q 27 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7327 (mp0) REVERT: Q 199 ARG cc_start: 0.5390 (OUTLIER) cc_final: 0.5189 (tpt-90) REVERT: R 27 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7220 (mp0) REVERT: S 27 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7325 (mp0) REVERT: S 199 ARG cc_start: 0.5384 (OUTLIER) cc_final: 0.5183 (tpt-90) REVERT: T 27 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7332 (mp0) REVERT: U 27 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7217 (mp0) REVERT: V 27 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7340 (mp0) REVERT: W 27 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7326 (mp0) REVERT: W 199 ARG cc_start: 0.5386 (OUTLIER) cc_final: 0.5184 (tpt-90) REVERT: X 27 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7223 (mp0) outliers start: 240 outliers final: 192 residues processed: 599 average time/residue: 0.9333 time to fit residues: 638.5404 Evaluate side-chains 587 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 384 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 199 ARG Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 199 ARG Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 199 ARG Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 199 ARG Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 199 ARG Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 142 SER Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 199 ARG Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 71 GLU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain Q residue 12 ARG Chi-restraints excluded: chain Q residue 54 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 142 SER Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 199 ARG Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain R residue 54 SER Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 195 GLU Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain S residue 199 ARG Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 54 SER Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 142 SER Chi-restraints excluded: chain T residue 195 GLU Chi-restraints excluded: chain U residue 12 ARG Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 133 LEU Chi-restraints excluded: chain U residue 142 SER Chi-restraints excluded: chain U residue 195 GLU Chi-restraints excluded: chain V residue 12 ARG Chi-restraints excluded: chain V residue 54 SER Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 71 GLU Chi-restraints excluded: chain V residue 133 LEU Chi-restraints excluded: chain V residue 142 SER Chi-restraints excluded: chain V residue 195 GLU Chi-restraints excluded: chain W residue 12 ARG Chi-restraints excluded: chain W residue 54 SER Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain W residue 142 SER Chi-restraints excluded: chain W residue 195 GLU Chi-restraints excluded: chain W residue 199 ARG Chi-restraints excluded: chain X residue 12 ARG Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 71 GLU Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 142 SER Chi-restraints excluded: chain X residue 195 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 35 optimal weight: 6.9990 chunk 273 optimal weight: 8.9990 chunk 40 optimal weight: 30.0000 chunk 26 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 413 optimal weight: 4.9990 chunk 198 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 209 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 134 GLN B 74 HIS B 134 GLN C 74 HIS C 134 GLN D 74 HIS D 134 GLN E 74 HIS E 134 GLN F 74 HIS F 134 GLN G 74 HIS G 134 GLN H 74 HIS H 134 GLN I 74 HIS I 134 GLN J 74 HIS J 134 GLN K 74 HIS K 134 GLN L 74 HIS L 134 GLN M 74 HIS M 134 GLN N 74 HIS N 134 GLN O 74 HIS O 134 GLN P 74 HIS P 134 GLN Q 74 HIS Q 134 GLN R 74 HIS R 134 GLN S 74 HIS S 134 GLN T 74 HIS T 134 GLN U 74 HIS U 134 GLN V 74 HIS V 134 GLN W 74 HIS W 134 GLN X 74 HIS X 134 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.117666 restraints weight = 25194.984| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 0.98 r_work: 0.3120 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 35976 Z= 0.235 Angle : 0.704 5.289 48912 Z= 0.392 Chirality : 0.052 0.179 5592 Planarity : 0.007 0.048 6504 Dihedral : 5.681 18.034 5088 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.65 % Allowed : 10.88 % Favored : 83.47 % 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: 0.84 (0.13), residues: 4512 helix: 1.85 (0.12), residues: 1848 sheet: -0.08 (0.13), residues: 1344 loop : -0.47 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 162 TYR 0.014 0.003 TYR F 145 PHE 0.010 0.003 PHE W 44 HIS 0.008 0.002 HIS J 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.24 (35976) covalent geometry : angle 0.70448 / 0.39 (48912) hydrogen bonds : bond 0.05474 / 3.81 ( 2136) hydrogen bonds : angle 4.24387 / 2.95 ( 5904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 406 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7354 (t70) REVERT: A 27 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7341 (mp0) REVERT: A 199 ARG cc_start: 0.5420 (OUTLIER) cc_final: 0.5097 (mmm160) REVERT: B 27 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7340 (mp0) REVERT: B 199 ARG cc_start: 0.5418 (OUTLIER) cc_final: 0.5091 (mmm160) REVERT: C 27 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7224 (mp0) REVERT: C 199 ARG cc_start: 0.5434 (OUTLIER) cc_final: 0.5105 (mmm160) REVERT: D 27 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7327 (mp0) REVERT: D 199 ARG cc_start: 0.5431 (OUTLIER) cc_final: 0.5101 (mmm160) REVERT: E 27 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7338 (mp0) REVERT: E 199 ARG cc_start: 0.5433 (OUTLIER) cc_final: 0.5106 (mmm160) REVERT: F 27 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7337 (mp0) REVERT: G 27 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7347 (mp0) REVERT: H 27 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7224 (mp0) REVERT: H 199 ARG cc_start: 0.5437 (OUTLIER) cc_final: 0.5108 (mmm160) REVERT: I 27 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7222 (mp0) REVERT: J 23 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7357 (t70) REVERT: J 27 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7232 (mp0) REVERT: K 27 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7335 (mp0) REVERT: K 199 ARG cc_start: 0.5423 (OUTLIER) cc_final: 0.5092 (mmm160) REVERT: L 27 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7347 (mp0) REVERT: M 27 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7347 (mp0) REVERT: M 199 ARG cc_start: 0.5429 (OUTLIER) cc_final: 0.5110 (mmm160) REVERT: N 27 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7334 (mp0) REVERT: O 27 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7225 (mp0) REVERT: P 27 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7240 (mp0) REVERT: Q 27 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7333 (mp0) REVERT: Q 199 ARG cc_start: 0.5419 (OUTLIER) cc_final: 0.5097 (mmm160) REVERT: R 27 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7336 (mp0) REVERT: S 27 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7334 (mp0) REVERT: S 199 ARG cc_start: 0.5414 (OUTLIER) cc_final: 0.5089 (mmm160) REVERT: T 27 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7247 (mp0) REVERT: U 27 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7231 (mp0) REVERT: V 27 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7359 (mp0) REVERT: W 23 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7348 (t70) REVERT: W 27 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7339 (mp0) REVERT: W 199 ARG cc_start: 0.5418 (OUTLIER) cc_final: 0.5094 (mmm160) REVERT: X 27 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7336 (mp0) outliers start: 206 outliers final: 192 residues processed: 564 average time/residue: 1.0017 time to fit residues: 645.7963 Evaluate side-chains 612 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 406 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 199 ARG Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 199 ARG Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 199 ARG Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 199 ARG Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 199 ARG Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 142 SER Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 199 ARG Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 71 GLU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain Q residue 12 ARG Chi-restraints excluded: chain Q residue 54 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 142 SER Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 199 ARG Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain R residue 54 SER Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 195 GLU Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain S residue 199 ARG Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 54 SER Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 142 SER Chi-restraints excluded: chain T residue 195 GLU Chi-restraints excluded: chain U residue 12 ARG Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 133 LEU Chi-restraints excluded: chain U residue 142 SER Chi-restraints excluded: chain U residue 195 GLU Chi-restraints excluded: chain V residue 12 ARG Chi-restraints excluded: chain V residue 54 SER Chi-restraints excluded: chain V residue 57 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 71 GLU Chi-restraints excluded: chain V residue 133 LEU Chi-restraints excluded: chain V residue 142 SER Chi-restraints excluded: chain V residue 195 GLU Chi-restraints excluded: chain W residue 12 ARG Chi-restraints excluded: chain W residue 23 ASP Chi-restraints excluded: chain W residue 54 SER Chi-restraints excluded: chain W residue 57 SER Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain W residue 142 SER Chi-restraints excluded: chain W residue 195 GLU Chi-restraints excluded: chain W residue 199 ARG Chi-restraints excluded: chain X residue 12 ARG Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 71 GLU Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 142 SER Chi-restraints excluded: chain X residue 195 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 56 optimal weight: 4.9990 chunk 363 optimal weight: 10.0000 chunk 333 optimal weight: 5.9990 chunk 362 optimal weight: 3.9990 chunk 381 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN I 134 GLN J 134 GLN K 134 GLN L 134 GLN M 134 GLN N 134 GLN O 134 GLN P 134 GLN Q 134 GLN R 134 GLN S 134 GLN T 134 GLN U 134 GLN V 134 GLN W 134 GLN X 134 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.145149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118335 restraints weight = 25738.865| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 0.97 r_work: 0.3133 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 35976 Z= 0.241 Angle : 0.712 5.389 48912 Z= 0.397 Chirality : 0.052 0.180 5592 Planarity : 0.007 0.046 6504 Dihedral : 5.704 18.351 5088 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 6.88 % Allowed : 9.62 % Favored : 83.50 % 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: 0.79 (0.13), residues: 4512 helix: 1.75 (0.12), residues: 1848 sheet: -0.06 (0.14), residues: 1344 loop : -0.46 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 162 TYR 0.013 0.004 TYR N 123 PHE 0.011 0.003 PHE A 44 HIS 0.008 0.002 HIS N 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.24 (35976) covalent geometry : angle 0.71184 / 0.40 (48912) hydrogen bonds : bond 0.05458 / 3.79 ( 2136) hydrogen bonds : angle 4.25875 / 2.97 ( 5904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16105.34 seconds wall clock time: 274 minutes 8.74 seconds (16448.74 seconds total)