Starting phenix.real_space_refine on Tue Aug 26 10:48:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m2r_63590/08_2025/9m2r_63590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m2r_63590/08_2025/9m2r_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9m2r_63590/08_2025/9m2r_63590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m2r_63590/08_2025/9m2r_63590.map" model { file = "/net/cci-nas-00/data/ceres_data/9m2r_63590/08_2025/9m2r_63590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m2r_63590/08_2025/9m2r_63590.cif" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 2.70, per 1000 atoms: 0.07 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: 2.63 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.32 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: 7.48 Time building geometry restraints manager: 3.51 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 2.320 nonbonded pdb="MN MN S 302 " pdb=" O HOH S 428 " model vdw 2.199 2.320 nonbonded pdb="MN MN U 302 " pdb=" O HOH U 428 " model vdw 2.199 2.320 nonbonded pdb="MN MN E 302 " pdb=" O HOH E 428 " model vdw 2.199 2.320 nonbonded pdb="MN MN I 302 " pdb=" O HOH I 428 " model vdw 2.200 2.320 ... (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: 0.09 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: 2.290 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: 0.040 Extract box with map and model: 0.410 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 25.900 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 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 aren 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 covalent geometry : bond 0.00721 (35976) covalent geometry : angle 1.17326 (48912) hydrogen bonds : bond 0.15460 ( 2136) hydrogen bonds : angle 5.68949 ( 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 : 1.248 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: 0.6389 (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: 0.6390 (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: 0.6387 (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: 0.6390 (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: 0.6390 (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: 0.6389 (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: 0.6388 (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: 0.6374 (mmp) REVERT: H 63 ARG cc_start: 0.6058 (ttt180) cc_final: 0.5651 (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: 0.6701 (mmp) cc_final: 0.6375 (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: 0.6375 (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: 0.6389 (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: 0.6390 (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: 0.6388 (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: 0.6376 (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: 0.6711 (mmp) cc_final: 0.6387 (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: 0.6390 (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: 0.5096 (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: 0.6248 (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: 0.6389 (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: 0.5934 (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: 0.6391 (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: 0.6390 (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: 0.6390 (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: 0.6390 (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: 0.6389 (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: 0.6390 (mmp) REVERT: W 63 ARG cc_start: 0.6056 (ttt180) cc_final: 0.5651 (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: 0.6391 (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: 0.8888 time to fit residues: 754.5121 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 : 0.992 ------------------------------------------------------------------------------- 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: 9.9990 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.141756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.115955 restraints weight = 28628.573| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.02 r_work: 0.3085 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 35976 Z= 0.173 Angle : 0.644 4.902 48912 Z= 0.353 Chirality : 0.049 0.151 5592 Planarity : 0.006 0.041 6504 Dihedral : 5.538 19.859 5088 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.95 % Allowed : 8.25 % Favored : 87.80 % 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 aren not related in a simple way. whole: 0.91 (0.13), residues: 4512 helix: 1.95 (0.12), residues: 1848 sheet: -0.00 (0.13), residues: 1344 loop : -0.58 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG W 18 TYR 0.010 0.002 TYR S 145 PHE 0.007 0.002 PHE T 44 HIS 0.007 0.002 HIS O 176 Details of bonding type rmsd covalent geometry : bond 0.00367 (35976) covalent geometry : angle 0.64418 (48912) hydrogen bonds : bond 0.04967 ( 2136) hydrogen bonds : angle 4.11879 ( 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 624 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 480 time to evaluate : 1.388 Fit side-chains REVERT: A 23 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7201 (t70) REVERT: A 27 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7320 (mp0) REVERT: A 102 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7907 (p0) REVERT: B 23 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7199 (t70) REVERT: B 27 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7325 (mp0) REVERT: B 102 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7915 (p0) REVERT: C 23 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7188 (t70) REVERT: C 27 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7316 (mp0) REVERT: C 102 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7916 (p0) REVERT: D 23 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7195 (t70) REVERT: D 27 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7319 (mp0) REVERT: D 102 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7902 (p0) REVERT: E 23 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7196 (t70) REVERT: E 27 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7325 (mp0) REVERT: E 102 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7905 (p0) REVERT: F 23 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7197 (t70) REVERT: F 27 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7322 (mp0) REVERT: F 102 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7910 (p0) REVERT: G 23 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7195 (t70) REVERT: G 27 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7321 (mp0) REVERT: G 102 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7914 (p0) REVERT: H 23 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7188 (t70) REVERT: H 27 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7318 (mp0) REVERT: H 102 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7913 (p0) REVERT: I 23 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7198 (t70) REVERT: I 27 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7324 (mp0) REVERT: I 102 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7909 (p0) REVERT: J 23 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7205 (t70) REVERT: J 27 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7315 (mp0) REVERT: J 102 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7905 (p0) REVERT: K 23 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7208 (t70) REVERT: K 27 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7323 (mp0) REVERT: K 102 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7908 (p0) REVERT: L 23 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7184 (t70) REVERT: L 27 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7321 (mp0) REVERT: L 102 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7912 (p0) REVERT: M 23 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7194 (t70) REVERT: M 27 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7312 (mp0) REVERT: M 102 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7914 (p0) REVERT: N 23 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7205 (t70) REVERT: N 27 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7323 (mp0) REVERT: N 102 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7910 (p0) REVERT: O 23 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7184 (t70) REVERT: O 27 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7319 (mp0) REVERT: O 102 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7909 (p0) REVERT: P 23 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7195 (t70) REVERT: P 27 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7323 (mp0) REVERT: P 102 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7908 (p0) REVERT: Q 23 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7194 (t70) REVERT: Q 27 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7316 (mp0) REVERT: Q 102 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7910 (p0) REVERT: R 23 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7192 (t70) REVERT: R 27 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7315 (mp0) REVERT: R 102 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7907 (p0) REVERT: S 23 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7198 (t70) REVERT: S 27 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7320 (mp0) REVERT: S 102 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7911 (p0) REVERT: T 23 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7203 (t70) REVERT: T 27 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7329 (mp0) REVERT: T 102 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7914 (p0) REVERT: U 23 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7190 (t70) REVERT: U 27 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7316 (mp0) REVERT: U 102 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7902 (p0) REVERT: V 23 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7183 (t70) REVERT: V 27 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7321 (mp0) REVERT: V 102 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7911 (p0) REVERT: W 23 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7192 (t70) REVERT: W 27 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7323 (mp0) REVERT: W 102 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7917 (p0) REVERT: X 23 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7182 (t70) REVERT: X 27 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7324 (mp0) REVERT: X 102 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7910 (p0) outliers start: 144 outliers final: 96 residues processed: 624 average time/residue: 0.8931 time to fit residues: 633.6928 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 : 0.952 ------------------------------------------------------------------------------- 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: 5.9990 chunk 48 optimal weight: 5.9990 chunk 324 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 436 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 342 optimal weight: 10.0000 chunk 390 optimal weight: 20.0000 chunk 81 optimal weight: 30.0000 chunk 285 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 J 160 ASN K 134 GLN K 160 ASN L 134 GLN L 160 ASN M 134 GLN M 160 ASN 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: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.114579 restraints weight = 28804.008| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.06 r_work: 0.3069 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 35976 Z= 0.227 Angle : 0.713 5.300 48912 Z= 0.397 Chirality : 0.052 0.157 5592 Planarity : 0.007 0.052 6504 Dihedral : 5.761 20.265 5088 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.92 % Allowed : 8.55 % Favored : 85.53 % 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 aren not related in a simple way. whole: 0.77 (0.12), residues: 4512 helix: 1.73 (0.12), residues: 1848 sheet: 0.03 (0.13), residues: 1344 loop : -0.59 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 18 TYR 0.013 0.003 TYR A 145 PHE 0.010 0.002 PHE H 44 HIS 0.008 0.003 HIS H 176 Details of bonding type rmsd covalent geometry : bond 0.00493 (35976) covalent geometry : angle 0.71259 (48912) hydrogen bonds : bond 0.05543 ( 2136) hydrogen bonds : angle 4.24554 ( 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 698 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 482 time to evaluate : 1.235 Fit side-chains REVERT: A 23 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7304 (t70) REVERT: A 27 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7436 (mp0) REVERT: B 23 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7303 (t70) REVERT: B 27 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7380 (mp0) REVERT: C 23 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7306 (t70) REVERT: C 27 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7430 (mp0) REVERT: D 23 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7303 (t70) REVERT: D 27 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7388 (mp0) REVERT: E 23 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7305 (t70) REVERT: E 27 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7387 (mp0) REVERT: F 23 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7297 (t70) REVERT: F 27 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7373 (mp0) REVERT: G 23 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7301 (t70) REVERT: G 27 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7430 (mp0) REVERT: H 23 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7306 (t70) REVERT: H 27 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7386 (mp0) REVERT: I 23 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7299 (t70) REVERT: I 27 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7370 (mp0) REVERT: J 23 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7302 (t70) REVERT: J 27 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7434 (mp0) REVERT: K 23 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7304 (t70) REVERT: K 27 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7431 (mp0) REVERT: L 23 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7299 (t70) REVERT: L 27 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7382 (mp0) REVERT: M 23 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7301 (t70) REVERT: M 27 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7389 (mp0) REVERT: N 23 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7301 (t70) REVERT: N 27 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7379 (mp0) REVERT: O 23 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7307 (t70) REVERT: O 27 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7386 (mp0) REVERT: O 94 LYS cc_start: 0.7718 (mttm) cc_final: 0.7473 (mttm) REVERT: P 23 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7305 (t70) REVERT: P 27 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7424 (mp0) REVERT: P 94 LYS cc_start: 0.7710 (mttm) cc_final: 0.7463 (mttm) REVERT: Q 23 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7299 (t70) REVERT: Q 27 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7368 (mp0) REVERT: R 23 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7300 (t70) REVERT: R 27 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7384 (mp0) REVERT: S 23 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7303 (t70) REVERT: S 27 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7380 (mp0) REVERT: T 23 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7305 (t70) REVERT: T 27 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7383 (mp0) REVERT: U 23 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7306 (t70) REVERT: U 27 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7428 (mp0) REVERT: V 23 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7303 (t70) REVERT: V 27 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7433 (mp0) REVERT: W 23 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7303 (t70) REVERT: W 27 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7419 (mp0) REVERT: X 23 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7301 (t70) REVERT: X 27 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7380 (mp0) outliers start: 216 outliers final: 144 residues processed: 661 average time/residue: 0.8202 time to fit residues: 623.8101 Evaluate side-chains 626 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 458 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 71 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 195 GLU 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 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 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 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 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 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 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 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 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 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 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 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 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 71 GLU Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 195 GLU 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 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 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 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 71 GLU Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 195 GLU 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 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 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 381 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 0.0870 chunk 110 optimal weight: 20.0000 chunk 317 optimal weight: 0.0070 chunk 305 optimal weight: 6.9990 chunk 444 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 342 optimal weight: 10.0000 chunk 411 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 overall best weight: 2.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3628 r_free = 0.3628 target = 0.144544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117874 restraints weight = 28492.754| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.03 r_work: 0.3125 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 35976 Z= 0.123 Angle : 0.530 3.827 48912 Z= 0.296 Chirality : 0.045 0.147 5592 Planarity : 0.005 0.027 6504 Dihedral : 5.202 17.895 5088 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.26 % Allowed : 8.58 % Favored : 86.16 % 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 aren not related in a simple way. whole: 1.16 (0.13), residues: 4512 helix: 2.25 (0.12), residues: 1848 sheet: 0.09 (0.13), residues: 1344 loop : -0.57 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 162 TYR 0.009 0.002 TYR D 145 PHE 0.006 0.001 PHE N 44 HIS 0.005 0.001 HIS L 176 Details of bonding type rmsd covalent geometry : bond 0.00250 (35976) covalent geometry : angle 0.53014 (48912) hydrogen bonds : bond 0.04122 ( 2136) hydrogen bonds : angle 3.82044 ( 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 657 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 465 time to evaluate : 1.095 Fit side-chains REVERT: A 27 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7349 (mp0) REVERT: A 102 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7969 (p0) REVERT: B 27 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7359 (mp0) REVERT: B 102 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7988 (p0) REVERT: C 27 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7356 (mp0) REVERT: C 102 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7978 (p0) REVERT: D 27 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7351 (mp0) REVERT: D 102 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7980 (p0) REVERT: E 27 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7351 (mp0) REVERT: E 102 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7979 (p0) REVERT: F 27 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7340 (mp0) REVERT: F 102 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7966 (p0) REVERT: G 27 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7342 (mp0) REVERT: G 102 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7984 (p0) REVERT: H 27 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7356 (mp0) REVERT: H 102 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7965 (p0) REVERT: I 27 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7340 (mp0) REVERT: I 102 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7972 (p0) REVERT: J 27 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7349 (mp0) REVERT: J 102 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7970 (p0) REVERT: K 27 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7348 (mp0) REVERT: K 102 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7967 (p0) REVERT: L 27 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7338 (mp0) REVERT: L 102 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7986 (p0) REVERT: M 27 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7338 (mp0) REVERT: M 102 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7987 (p0) REVERT: N 27 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7337 (mp0) REVERT: N 102 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7977 (p0) REVERT: O 27 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7353 (mp0) REVERT: O 102 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7986 (p0) REVERT: P 27 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7338 (mp0) REVERT: P 102 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7968 (p0) REVERT: Q 27 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7342 (mp0) REVERT: Q 102 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7962 (p0) REVERT: R 27 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7341 (mp0) REVERT: R 102 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7981 (p0) REVERT: S 27 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7352 (mp0) REVERT: S 102 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7995 (p0) REVERT: T 27 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7337 (mp0) REVERT: T 102 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7965 (p0) REVERT: U 27 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7354 (mp0) REVERT: U 102 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7979 (p0) REVERT: V 27 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7345 (mp0) REVERT: V 102 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7985 (p0) REVERT: W 27 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7357 (mp0) REVERT: W 102 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7991 (p0) REVERT: X 27 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7338 (mp0) REVERT: X 102 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7975 (p0) outliers start: 192 outliers final: 120 residues processed: 609 average time/residue: 0.8970 time to fit residues: 622.1636 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 : 1.075 ------------------------------------------------------------------------------- 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 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP 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 102 ASP Chi-restraints excluded: chain X residue 142 SER Chi-restraints excluded: chain X residue 195 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 164 optimal weight: 8.9990 chunk 308 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 441 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 365 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 373 optimal weight: 6.9990 chunk 398 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 134 GLN C 134 GLN D 134 GLN E 134 GLN F 134 GLN G 134 GLN H 134 GLN H 160 ASN I 134 GLN J 134 GLN 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.116200 restraints weight = 28284.653| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.03 r_work: 0.3092 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2853 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= 0.206 Angle : 0.665 4.944 48912 Z= 0.372 Chirality : 0.050 0.153 5592 Planarity : 0.007 0.040 6504 Dihedral : 5.598 18.593 5088 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 7.48 % Allowed : 8.31 % 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 aren not related in a simple way. whole: 0.89 (0.13), residues: 4512 helix: 1.89 (0.12), residues: 1848 sheet: 0.01 (0.13), residues: 1344 loop : -0.53 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 162 TYR 0.013 0.003 TYR Q 145 PHE 0.010 0.002 PHE V 44 HIS 0.008 0.002 HIS Q 176 Details of bonding type rmsd covalent geometry : bond 0.00444 (35976) covalent geometry : angle 0.66451 (48912) hydrogen bonds : bond 0.05307 ( 2136) hydrogen bonds : angle 4.15051 ( 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 657 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 273 poor density : 384 time to evaluate : 1.365 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 23 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7281 (t70) REVERT: A 27 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7384 (mp0) REVERT: B 23 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7282 (t70) REVERT: B 27 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7371 (mp0) REVERT: C 23 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7280 (t70) REVERT: C 27 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7370 (mp0) REVERT: D 23 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7289 (t70) REVERT: D 27 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7390 (mp0) REVERT: E 23 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7288 (t70) REVERT: E 27 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7390 (mp0) REVERT: F 23 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7271 (t70) REVERT: F 27 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7378 (mp0) REVERT: G 23 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7266 (t70) REVERT: G 27 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7380 (mp0) REVERT: H 23 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7278 (t70) REVERT: H 27 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7384 (mp0) REVERT: I 23 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7275 (t70) REVERT: I 27 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7356 (mp0) REVERT: J 23 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7280 (t70) REVERT: J 27 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7376 (mp0) REVERT: K 23 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7278 (t70) REVERT: K 27 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7385 (mp0) REVERT: L 23 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7281 (t70) REVERT: L 27 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7357 (mp0) REVERT: M 23 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7270 (t70) REVERT: M 27 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7381 (mp0) REVERT: N 23 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7274 (t70) REVERT: N 27 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7369 (mp0) REVERT: O 23 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7283 (t70) REVERT: O 27 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7390 (mp0) REVERT: P 23 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7272 (t70) REVERT: P 27 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7374 (mp0) REVERT: Q 23 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7272 (t70) REVERT: Q 27 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7352 (mp0) REVERT: R 23 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7280 (t70) REVERT: R 27 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7358 (mp0) REVERT: S 23 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7281 (t70) REVERT: S 27 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7382 (mp0) REVERT: T 23 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7273 (t70) REVERT: T 27 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7376 (mp0) REVERT: U 23 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7287 (t70) REVERT: U 27 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7377 (mp0) REVERT: V 23 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7270 (t70) REVERT: V 27 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7382 (mp0) REVERT: W 23 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7283 (t70) REVERT: W 27 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7372 (mp0) REVERT: X 23 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7279 (t70) REVERT: X 27 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7359 (mp0) outliers start: 273 outliers final: 129 residues processed: 633 average time/residue: 0.7670 time to fit residues: 563.4822 Evaluate side-chains 561 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 408 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 142 SER Chi-restraints excluded: chain A residue 195 GLU 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 142 SER Chi-restraints excluded: chain B residue 195 GLU 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 142 SER Chi-restraints excluded: chain C residue 195 GLU 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 142 SER Chi-restraints excluded: chain D residue 195 GLU 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 142 SER Chi-restraints excluded: chain E residue 195 GLU 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 142 SER Chi-restraints excluded: chain F residue 195 GLU 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 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 142 SER Chi-restraints excluded: chain H residue 195 GLU 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 142 SER Chi-restraints excluded: chain I residue 195 GLU 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 142 SER Chi-restraints excluded: chain J residue 195 GLU 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 142 SER Chi-restraints excluded: chain K residue 195 GLU 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 142 SER Chi-restraints excluded: chain L residue 195 GLU 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 142 SER Chi-restraints excluded: chain M residue 195 GLU 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 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 142 SER Chi-restraints excluded: chain O residue 195 GLU 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 142 SER Chi-restraints excluded: chain P residue 195 GLU 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 142 SER Chi-restraints excluded: chain Q residue 195 GLU 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 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 142 SER Chi-restraints excluded: chain S residue 195 GLU 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 142 SER Chi-restraints excluded: chain T residue 195 GLU 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 142 SER Chi-restraints excluded: chain U residue 195 GLU 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 142 SER Chi-restraints excluded: chain V residue 195 GLU 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 142 SER Chi-restraints excluded: chain W residue 195 GLU 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 142 SER Chi-restraints excluded: chain X residue 195 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 324 optimal weight: 20.0000 chunk 379 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 453 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 308 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 211 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3615 r_free = 0.3615 target = 0.143823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.117441 restraints weight = 28632.948| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.03 r_work: 0.3109 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 35976 Z= 0.163 Angle : 0.592 4.467 48912 Z= 0.331 Chirality : 0.047 0.154 5592 Planarity : 0.005 0.030 6504 Dihedral : 5.392 17.663 5088 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 7.24 % Allowed : 9.02 % Favored : 83.74 % 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 aren not related in a simple way. whole: 0.97 (0.13), residues: 4512 helix: 2.00 (0.12), residues: 1848 sheet: -0.00 (0.13), residues: 1344 loop : -0.51 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 162 TYR 0.011 0.002 TYR M 145 PHE 0.008 0.002 PHE N 44 HIS 0.006 0.002 HIS P 176 Details of bonding type rmsd covalent geometry : bond 0.00345 (35976) covalent geometry : angle 0.59200 (48912) hydrogen bonds : bond 0.04656 ( 2136) hydrogen bonds : angle 4.00892 ( 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 673 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 409 time to evaluate : 1.320 Fit side-chains REVERT: A 27 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7266 (mp0) REVERT: B 27 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7273 (mp0) REVERT: C 27 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7275 (mp0) REVERT: D 27 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7271 (mp0) REVERT: E 27 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7270 (mp0) REVERT: F 27 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7258 (mp0) REVERT: G 27 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7270 (mp0) REVERT: H 27 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7273 (mp0) REVERT: I 27 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7265 (mp0) REVERT: J 27 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7271 (mp0) REVERT: K 27 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7267 (mp0) REVERT: L 27 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7274 (mp0) REVERT: M 27 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7268 (mp0) REVERT: N 27 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7290 (mp0) REVERT: O 27 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7276 (mp0) REVERT: P 27 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7287 (mp0) REVERT: Q 27 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7260 (mp0) REVERT: R 27 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7279 (mp0) REVERT: S 27 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7273 (mp0) REVERT: T 27 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7289 (mp0) REVERT: U 27 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7271 (mp0) REVERT: V 27 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7273 (mp0) REVERT: W 27 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7269 (mp0) REVERT: X 27 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7277 (mp0) outliers start: 264 outliers final: 168 residues processed: 625 average time/residue: 0.7162 time to fit residues: 530.0677 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 : 1.144 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 5.9990 chunk 329 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 444 optimal weight: 10.0000 chunk 423 optimal weight: 10.0000 chunk 284 optimal weight: 5.9990 chunk 449 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 375 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.144043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117854 restraints weight = 28305.813| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.02 r_work: 0.3111 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 35976 Z= 0.168 Angle : 0.602 4.514 48912 Z= 0.337 Chirality : 0.048 0.163 5592 Planarity : 0.005 0.039 6504 Dihedral : 5.411 17.543 5088 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 6.17 % Allowed : 9.65 % Favored : 84.18 % 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 aren not related in a simple way. whole: 1.01 (0.13), residues: 4512 helix: 2.04 (0.12), residues: 1848 sheet: 0.01 (0.13), residues: 1344 loop : -0.48 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 162 TYR 0.011 0.002 TYR F 145 PHE 0.008 0.002 PHE N 44 HIS 0.007 0.002 HIS X 176 Details of bonding type rmsd covalent geometry : bond 0.00357 (35976) covalent geometry : angle 0.60205 (48912) hydrogen bonds : bond 0.04780 ( 2136) hydrogen bonds : angle 4.02719 ( 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 656 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 431 time to evaluate : 1.380 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: 0.7665 (mt-10) cc_final: 0.7299 (mp0) REVERT: B 27 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7287 (mp0) REVERT: C 27 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7296 (mp0) REVERT: D 27 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7295 (mp0) REVERT: E 27 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7294 (mp0) REVERT: F 27 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7283 (mp0) REVERT: G 27 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7291 (mp0) REVERT: H 27 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7297 (mp0) REVERT: I 27 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7284 (mp0) REVERT: J 27 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7299 (mp0) REVERT: K 27 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7299 (mp0) REVERT: L 27 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7280 (mp0) REVERT: M 27 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7290 (mp0) REVERT: N 27 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7299 (mp0) REVERT: O 27 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7296 (mp0) REVERT: P 27 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7298 (mp0) REVERT: P 94 LYS cc_start: 0.7648 (mttm) cc_final: 0.7419 (mttm) REVERT: Q 27 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7280 (mp0) REVERT: R 27 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7286 (mp0) REVERT: S 27 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7288 (mp0) REVERT: T 27 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7299 (mp0) REVERT: U 27 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7293 (mp0) REVERT: V 27 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7291 (mp0) REVERT: W 27 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7286 (mp0) REVERT: X 27 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7279 (mp0) outliers start: 225 outliers final: 177 residues processed: 608 average time/residue: 0.8675 time to fit residues: 608.5706 Evaluate side-chains 585 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 408 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 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 133 LEU 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 419 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 394 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 319 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 443 optimal weight: 20.0000 chunk 208 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 342 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3610 r_free = 0.3610 target = 0.143457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117214 restraints weight = 28214.115| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.02 r_work: 0.3098 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2955 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= 0.201 Angle : 0.657 5.009 48912 Z= 0.367 Chirality : 0.050 0.168 5592 Planarity : 0.006 0.038 6504 Dihedral : 5.573 17.859 5088 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 6.17 % Allowed : 10.36 % 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 aren not related in a simple way. whole: 0.90 (0.13), residues: 4512 helix: 1.85 (0.12), residues: 1848 sheet: 0.00 (0.13), residues: 1344 loop : -0.42 (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 F 145 PHE 0.009 0.002 PHE B 44 HIS 0.007 0.002 HIS S 132 Details of bonding type rmsd covalent geometry : bond 0.00435 (35976) covalent geometry : angle 0.65727 (48912) hydrogen bonds : bond 0.05154 ( 2136) hydrogen bonds : angle 4.16808 ( 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 631 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 406 time to evaluate : 1.239 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: 0.7662 (mt-10) cc_final: 0.7293 (mp0) REVERT: B 27 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7290 (mp0) REVERT: C 27 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7294 (mp0) REVERT: D 27 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7292 (mp0) REVERT: E 27 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7291 (mp0) REVERT: F 27 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7285 (mp0) REVERT: G 27 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7289 (mp0) REVERT: H 27 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7291 (mp0) REVERT: I 27 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7288 (mp0) REVERT: J 27 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7294 (mp0) REVERT: K 27 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7294 (mp0) REVERT: L 27 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7290 (mp0) REVERT: M 27 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7288 (mp0) REVERT: N 27 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7301 (mp0) REVERT: O 27 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7293 (mp0) REVERT: P 27 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7299 (mp0) REVERT: Q 27 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7285 (mp0) REVERT: R 27 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7291 (mp0) REVERT: S 27 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7289 (mp0) REVERT: T 27 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7300 (mp0) REVERT: U 27 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7287 (mp0) REVERT: V 27 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7286 (mp0) REVERT: W 27 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7290 (mp0) REVERT: X 27 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7296 (mp0) outliers start: 225 outliers final: 201 residues processed: 583 average time/residue: 0.7354 time to fit residues: 500.2798 Evaluate side-chains 607 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 406 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 133 LEU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 152 HIS 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 133 LEU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 152 HIS 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 133 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 152 HIS 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 133 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 152 HIS 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 133 LEU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 152 HIS 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 133 LEU Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 152 HIS 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 133 LEU Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 152 HIS 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 152 HIS 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 133 LEU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 152 HIS 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 133 LEU Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain J residue 152 HIS 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 133 LEU Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 152 HIS 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 133 LEU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 152 HIS 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 133 LEU Chi-restraints excluded: chain M residue 142 SER Chi-restraints excluded: chain M residue 152 HIS 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 133 LEU Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 152 HIS 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 152 HIS 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 133 LEU Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 152 HIS 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 152 HIS 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 133 LEU Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 152 HIS 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 133 LEU Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 152 HIS 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 133 LEU Chi-restraints excluded: chain T residue 142 SER Chi-restraints excluded: chain T residue 152 HIS 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 133 LEU Chi-restraints excluded: chain U residue 142 SER Chi-restraints excluded: chain U residue 152 HIS 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 133 LEU Chi-restraints excluded: chain V residue 142 SER Chi-restraints excluded: chain V residue 152 HIS 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 133 LEU Chi-restraints excluded: chain W residue 142 SER Chi-restraints excluded: chain W residue 152 HIS 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 133 LEU Chi-restraints excluded: chain X residue 142 SER Chi-restraints excluded: chain X residue 152 HIS 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: 10.0000 chunk 365 optimal weight: 10.0000 chunk 346 optimal weight: 9.9990 chunk 314 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 434 optimal weight: 2.9990 chunk 444 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 355 optimal weight: 10.0000 chunk 262 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3604 r_free = 0.3604 target = 0.142927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116577 restraints weight = 28186.639| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.02 r_work: 0.3091 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 35976 Z= 0.221 Angle : 0.684 5.207 48912 Z= 0.383 Chirality : 0.051 0.177 5592 Planarity : 0.006 0.036 6504 Dihedral : 5.639 18.054 5088 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 6.20 % Allowed : 10.33 % 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 aren not related in a simple way. whole: 0.83 (0.13), residues: 4512 helix: 1.73 (0.12), residues: 1848 sheet: -0.02 (0.13), residues: 1344 loop : -0.36 (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 M 145 PHE 0.010 0.002 PHE S 44 HIS 0.007 0.003 HIS Q 132 Details of bonding type rmsd covalent geometry : bond 0.00482 (35976) covalent geometry : angle 0.68403 (48912) hydrogen bonds : bond 0.05349 ( 2136) hydrogen bonds : angle 4.22402 ( 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 632 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 406 time to evaluate : 1.128 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 23 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7220 (t70) REVERT: A 27 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7309 (mp0) REVERT: B 27 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7310 (mp0) REVERT: C 27 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7314 (mp0) REVERT: D 27 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7319 (mp0) REVERT: E 27 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7319 (mp0) REVERT: F 27 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7303 (mp0) REVERT: G 23 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7222 (t70) REVERT: G 27 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7309 (mp0) REVERT: H 27 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7316 (mp0) REVERT: I 27 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7305 (mp0) REVERT: J 23 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7219 (t70) REVERT: J 27 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7313 (mp0) REVERT: K 27 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7312 (mp0) REVERT: L 27 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7307 (mp0) REVERT: M 27 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7314 (mp0) REVERT: N 27 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7319 (mp0) REVERT: O 27 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7316 (mp0) REVERT: P 27 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7316 (mp0) REVERT: Q 27 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7303 (mp0) REVERT: R 27 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7307 (mp0) REVERT: S 27 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7309 (mp0) REVERT: T 27 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7319 (mp0) REVERT: U 27 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7317 (mp0) REVERT: V 23 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7219 (t70) REVERT: V 27 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7312 (mp0) REVERT: W 27 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7310 (mp0) REVERT: X 27 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7307 (mp0) outliers start: 226 outliers final: 177 residues processed: 584 average time/residue: 0.7483 time to fit residues: 509.4566 Evaluate side-chains 587 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 406 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 71 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 152 HIS 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 142 SER Chi-restraints excluded: chain B residue 152 HIS 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 152 HIS 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 142 SER Chi-restraints excluded: chain D residue 152 HIS 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 142 SER Chi-restraints excluded: chain E residue 152 HIS 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 142 SER Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 195 GLU 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 152 HIS 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 152 HIS 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 152 HIS Chi-restraints excluded: chain I residue 195 GLU 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 152 HIS 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 142 SER Chi-restraints excluded: chain K residue 152 HIS 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 152 HIS 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 142 SER Chi-restraints excluded: chain M residue 152 HIS 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 152 HIS 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 152 HIS 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 142 SER Chi-restraints excluded: chain P residue 152 HIS 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 152 HIS 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 152 HIS 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 142 SER Chi-restraints excluded: chain S residue 152 HIS 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 142 SER Chi-restraints excluded: chain T residue 152 HIS 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 142 SER Chi-restraints excluded: chain U residue 152 HIS Chi-restraints excluded: chain U residue 195 GLU 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 152 HIS 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 142 SER Chi-restraints excluded: chain W residue 152 HIS 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 152 HIS 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: 5.9990 chunk 273 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 223 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 413 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3605 r_free = 0.3605 target = 0.143038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.116719 restraints weight = 28372.588| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.03 r_work: 0.3088 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 35976 Z= 0.214 Angle : 0.674 5.069 48912 Z= 0.377 Chirality : 0.051 0.178 5592 Planarity : 0.006 0.036 6504 Dihedral : 5.643 18.327 5088 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.48 % Allowed : 10.33 % Favored : 84.18 % 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 aren not related in a simple way. whole: 0.81 (0.13), residues: 4512 helix: 1.73 (0.12), residues: 1848 sheet: -0.02 (0.14), residues: 1344 loop : -0.41 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 162 TYR 0.014 0.003 TYR I 123 PHE 0.010 0.002 PHE U 44 HIS 0.007 0.002 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00465 (35976) covalent geometry : angle 0.67399 (48912) hydrogen bonds : bond 0.05286 ( 2136) hydrogen bonds : angle 4.22674 ( 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 606 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 406 time to evaluate : 1.317 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: 0.7655 (mt-10) cc_final: 0.7287 (mp0) REVERT: B 23 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7226 (t70) REVERT: B 27 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7286 (mp0) REVERT: C 23 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7224 (t70) REVERT: C 27 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7288 (mp0) REVERT: D 23 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7228 (t70) REVERT: D 27 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7287 (mp0) REVERT: E 23 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7229 (t70) REVERT: E 27 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7286 (mp0) REVERT: F 23 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7224 (t70) REVERT: F 27 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7276 (mp0) REVERT: G 23 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7221 (t70) REVERT: G 27 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7287 (mp0) REVERT: H 23 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7223 (t70) REVERT: H 27 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7288 (mp0) REVERT: I 27 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7277 (mp0) REVERT: J 27 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7291 (mp0) REVERT: K 23 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7220 (t70) REVERT: K 27 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7286 (mp0) REVERT: L 23 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7231 (t70) REVERT: L 27 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7278 (mp0) REVERT: M 23 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7222 (t70) REVERT: M 27 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7386 (mp0) REVERT: N 23 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7218 (t70) REVERT: N 27 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7285 (mp0) REVERT: O 23 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7225 (t70) REVERT: O 27 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7284 (mp0) REVERT: P 23 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7218 (t70) REVERT: P 27 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7383 (mp0) REVERT: Q 23 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7222 (t70) REVERT: Q 27 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7271 (mp0) REVERT: R 23 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7229 (t70) REVERT: R 27 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7278 (mp0) REVERT: S 23 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7227 (t70) REVERT: S 27 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7286 (mp0) REVERT: T 23 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7220 (t70) REVERT: T 27 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7292 (mp0) REVERT: U 23 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7228 (t70) REVERT: U 27 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7285 (mp0) REVERT: V 27 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7293 (mp0) REVERT: W 23 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7227 (t70) REVERT: W 27 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7286 (mp0) REVERT: X 23 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7230 (t70) REVERT: X 27 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7279 (mp0) outliers start: 200 outliers final: 177 residues processed: 558 average time/residue: 0.7684 time to fit residues: 499.2984 Evaluate side-chains 603 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 406 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 142 SER Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 195 GLU 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 152 HIS Chi-restraints excluded: chain B residue 195 GLU 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 152 HIS Chi-restraints excluded: chain C residue 195 GLU 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 152 HIS Chi-restraints excluded: chain D residue 195 GLU 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 152 HIS Chi-restraints excluded: chain E residue 195 GLU 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 152 HIS Chi-restraints excluded: chain F residue 195 GLU 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 152 HIS 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 152 HIS 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 152 HIS 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 142 SER Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 195 GLU 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 152 HIS Chi-restraints excluded: chain K residue 195 GLU 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 152 HIS Chi-restraints excluded: chain L residue 195 GLU 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 152 HIS Chi-restraints excluded: chain M residue 195 GLU 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 71 GLU Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain N residue 152 HIS Chi-restraints excluded: chain N residue 195 GLU 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 152 HIS Chi-restraints excluded: chain O residue 195 GLU 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 152 HIS Chi-restraints excluded: chain P residue 195 GLU 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 152 HIS Chi-restraints excluded: chain Q residue 195 GLU 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 71 GLU Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain R residue 195 GLU 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 152 HIS Chi-restraints excluded: chain S residue 195 GLU 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 152 HIS Chi-restraints excluded: chain T residue 195 GLU 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 152 HIS 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 142 SER Chi-restraints excluded: chain V residue 152 HIS Chi-restraints excluded: chain V residue 195 GLU 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 152 HIS Chi-restraints excluded: chain W residue 195 GLU 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 152 HIS 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: 5.9990 chunk 363 optimal weight: 10.0000 chunk 333 optimal weight: 0.8980 chunk 362 optimal weight: 10.0000 chunk 381 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3602 r_free = 0.3602 target = 0.142837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116646 restraints weight = 28016.380| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.02 r_work: 0.3089 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2929 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= 0.227 Angle : 0.696 5.318 48912 Z= 0.389 Chirality : 0.051 0.179 5592 Planarity : 0.007 0.036 6504 Dihedral : 5.679 18.242 5088 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 6.74 % Allowed : 9.07 % Favored : 84.18 % 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 aren not related in a simple way. whole: 0.76 (0.13), residues: 4512 helix: 1.65 (0.12), residues: 1848 sheet: -0.01 (0.14), residues: 1344 loop : -0.42 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 162 TYR 0.016 0.004 TYR G 123 PHE 0.010 0.002 PHE U 44 HIS 0.008 0.003 HIS M 176 Details of bonding type rmsd covalent geometry : bond 0.00496 (35976) covalent geometry : angle 0.69634 (48912) hydrogen bonds : bond 0.05423 ( 2136) hydrogen bonds : angle 4.26036 ( 5904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14944.17 seconds wall clock time: 254 minutes 5.21 seconds (15245.21 seconds total)