Starting phenix.real_space_refine on Tue Jul 7 02:38:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v6l_64802/07_2026/9v6l_64802.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v6l_64802/07_2026/9v6l_64802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v6l_64802/07_2026/9v6l_64802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v6l_64802/07_2026/9v6l_64802.map" model { file = "/net/cci-nas-00/data/ceres_data/9v6l_64802/07_2026/9v6l_64802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v6l_64802/07_2026/9v6l_64802.cif" } resolution = 3.06 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= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 26248 2.51 5 N 7488 2.21 5 O 7976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41816 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3487 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 418} Chain: "B" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3487 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 418} Chain: "D" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1740 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 18, 'TRANS': 208} Chain breaks: 1 Chain: "E" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3487 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 418} Chain: "G" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1740 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 18, 'TRANS': 208} Chain breaks: 1 Chain: "I" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3487 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 418} Chain: "K" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1740 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 18, 'TRANS': 208} Chain breaks: 1 Chain: "L" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1740 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 18, 'TRANS': 208} Chain breaks: 1 Chain: "M" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3487 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 418} Chain: "O" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1740 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 18, 'TRANS': 208} Chain breaks: 1 Chain: "P" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3487 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 418} Chain: "R" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1740 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 18, 'TRANS': 208} Chain breaks: 1 Chain: "S" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3487 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 418} Chain: "V" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1740 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 18, 'TRANS': 208} Chain breaks: 1 Chain: "W" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3487 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 418} Chain: "Y" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1740 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 18, 'TRANS': 208} Chain breaks: 1 Time building chain proxies: 6.93, per 1000 atoms: 0.17 Number of scatterers: 41816 At special positions: 0 Unit cell: (133, 133, 319, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 7976 8.00 N 7488 7.00 C 26248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.4 seconds 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10080 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 34 sheets defined 55.0% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 30 through 39 removed outlier: 3.507A pdb=" N LEU A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 58 removed outlier: 3.608A pdb=" N THR A 58 " --> pdb=" O ARG A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 4.347A pdb=" N LEU A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 103 Processing helix chain 'A' and resid 111 through 135 Processing helix chain 'A' and resid 145 through 158 Processing helix chain 'A' and resid 177 through 197 removed outlier: 3.886A pdb=" N THR A 197 " --> pdb=" O MET A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 235 removed outlier: 4.078A pdb=" N ALA A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 280 Processing helix chain 'A' and resid 294 through 316 Processing helix chain 'A' and resid 324 through 340 Processing helix chain 'A' and resid 355 through 436 Proline residue: A 401 - end of helix Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'B' and resid 31 through 39 removed outlier: 3.508A pdb=" N LEU B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 removed outlier: 3.608A pdb=" N THR B 58 " --> pdb=" O ARG B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 removed outlier: 4.347A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 103 Processing helix chain 'B' and resid 111 through 135 Processing helix chain 'B' and resid 145 through 158 Processing helix chain 'B' and resid 177 through 197 removed outlier: 3.886A pdb=" N THR B 197 " --> pdb=" O MET B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 235 removed outlier: 4.078A pdb=" N ALA B 207 " --> pdb=" O LYS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 280 Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 324 through 340 Processing helix chain 'B' and resid 355 through 436 Proline residue: B 401 - end of helix Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'D' and resid 26 through 43 removed outlier: 4.007A pdb=" N ARG D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 43 " --> pdb=" O GLU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 116 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.168A pdb=" N MET D 198 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'E' and resid 31 through 39 removed outlier: 3.507A pdb=" N LEU E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 58 removed outlier: 3.608A pdb=" N THR E 58 " --> pdb=" O ARG E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 87 removed outlier: 4.347A pdb=" N LEU E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 103 Processing helix chain 'E' and resid 111 through 135 Processing helix chain 'E' and resid 145 through 158 Processing helix chain 'E' and resid 177 through 197 removed outlier: 3.886A pdb=" N THR E 197 " --> pdb=" O MET E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 235 removed outlier: 4.078A pdb=" N ALA E 207 " --> pdb=" O LYS E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 280 Processing helix chain 'E' and resid 294 through 316 Processing helix chain 'E' and resid 324 through 340 Processing helix chain 'E' and resid 355 through 436 Proline residue: E 401 - end of helix Processing helix chain 'E' and resid 457 through 465 Processing helix chain 'G' and resid 26 through 43 removed outlier: 4.007A pdb=" N ARG G 42 " --> pdb=" O GLU G 38 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU G 43 " --> pdb=" O GLU G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 116 Processing helix chain 'G' and resid 156 through 164 Processing helix chain 'G' and resid 193 through 198 removed outlier: 4.168A pdb=" N MET G 198 " --> pdb=" O SER G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 233 Processing helix chain 'I' and resid 31 through 39 removed outlier: 3.507A pdb=" N LEU I 39 " --> pdb=" O GLY I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 58 removed outlier: 3.608A pdb=" N THR I 58 " --> pdb=" O ARG I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 87 removed outlier: 4.347A pdb=" N LEU I 85 " --> pdb=" O ASP I 81 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR I 87 " --> pdb=" O GLU I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 103 Processing helix chain 'I' and resid 111 through 135 Processing helix chain 'I' and resid 145 through 158 Processing helix chain 'I' and resid 177 through 197 removed outlier: 3.886A pdb=" N THR I 197 " --> pdb=" O MET I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 235 removed outlier: 4.078A pdb=" N ALA I 207 " --> pdb=" O LYS I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 280 Processing helix chain 'I' and resid 294 through 316 Processing helix chain 'I' and resid 324 through 340 Processing helix chain 'I' and resid 355 through 436 Proline residue: I 401 - end of helix Processing helix chain 'I' and resid 457 through 465 Processing helix chain 'K' and resid 26 through 43 removed outlier: 4.007A pdb=" N ARG K 42 " --> pdb=" O GLU K 38 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 116 Processing helix chain 'K' and resid 156 through 164 Processing helix chain 'K' and resid 193 through 198 removed outlier: 4.168A pdb=" N MET K 198 " --> pdb=" O SER K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 233 Processing helix chain 'L' and resid 26 through 43 removed outlier: 4.007A pdb=" N ARG L 42 " --> pdb=" O GLU L 38 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU L 43 " --> pdb=" O GLU L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 116 Processing helix chain 'L' and resid 156 through 164 Processing helix chain 'L' and resid 193 through 198 removed outlier: 4.169A pdb=" N MET L 198 " --> pdb=" O SER L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 233 Processing helix chain 'M' and resid 31 through 39 removed outlier: 3.507A pdb=" N LEU M 39 " --> pdb=" O GLY M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 58 removed outlier: 3.608A pdb=" N THR M 58 " --> pdb=" O ARG M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 87 removed outlier: 4.347A pdb=" N LEU M 85 " --> pdb=" O ASP M 81 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR M 87 " --> pdb=" O GLU M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 103 Processing helix chain 'M' and resid 111 through 135 Processing helix chain 'M' and resid 145 through 158 Processing helix chain 'M' and resid 177 through 197 removed outlier: 3.886A pdb=" N THR M 197 " --> pdb=" O MET M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 235 removed outlier: 4.078A pdb=" N ALA M 207 " --> pdb=" O LYS M 203 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 280 Processing helix chain 'M' and resid 294 through 316 Processing helix chain 'M' and resid 324 through 340 Processing helix chain 'M' and resid 355 through 436 Proline residue: M 401 - end of helix Processing helix chain 'M' and resid 457 through 465 Processing helix chain 'O' and resid 26 through 43 removed outlier: 4.007A pdb=" N ARG O 42 " --> pdb=" O GLU O 38 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU O 43 " --> pdb=" O GLU O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 116 Processing helix chain 'O' and resid 156 through 164 Processing helix chain 'O' and resid 193 through 198 removed outlier: 4.168A pdb=" N MET O 198 " --> pdb=" O SER O 195 " (cutoff:3.500A) Processing helix chain 'O' and resid 221 through 233 Processing helix chain 'P' and resid 31 through 39 removed outlier: 3.508A pdb=" N LEU P 39 " --> pdb=" O GLY P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 58 removed outlier: 3.608A pdb=" N THR P 58 " --> pdb=" O ARG P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 87 removed outlier: 4.346A pdb=" N LEU P 85 " --> pdb=" O ASP P 81 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR P 87 " --> pdb=" O GLU P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 103 Processing helix chain 'P' and resid 111 through 135 Processing helix chain 'P' and resid 145 through 158 Processing helix chain 'P' and resid 177 through 197 removed outlier: 3.886A pdb=" N THR P 197 " --> pdb=" O MET P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 235 removed outlier: 4.078A pdb=" N ALA P 207 " --> pdb=" O LYS P 203 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 280 Processing helix chain 'P' and resid 294 through 316 Processing helix chain 'P' and resid 324 through 340 Processing helix chain 'P' and resid 355 through 436 Proline residue: P 401 - end of helix Processing helix chain 'P' and resid 457 through 465 Processing helix chain 'R' and resid 26 through 43 removed outlier: 4.007A pdb=" N ARG R 42 " --> pdb=" O GLU R 38 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU R 43 " --> pdb=" O GLU R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 116 Processing helix chain 'R' and resid 156 through 164 Processing helix chain 'R' and resid 193 through 198 removed outlier: 4.168A pdb=" N MET R 198 " --> pdb=" O SER R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 233 Processing helix chain 'S' and resid 31 through 39 removed outlier: 3.507A pdb=" N LEU S 39 " --> pdb=" O GLY S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 58 removed outlier: 3.608A pdb=" N THR S 58 " --> pdb=" O ARG S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 87 removed outlier: 4.347A pdb=" N LEU S 85 " --> pdb=" O ASP S 81 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR S 87 " --> pdb=" O GLU S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 103 Processing helix chain 'S' and resid 111 through 135 Processing helix chain 'S' and resid 145 through 158 Processing helix chain 'S' and resid 177 through 197 removed outlier: 3.886A pdb=" N THR S 197 " --> pdb=" O MET S 193 " (cutoff:3.500A) Processing helix chain 'S' and resid 203 through 235 removed outlier: 4.078A pdb=" N ALA S 207 " --> pdb=" O LYS S 203 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 280 Processing helix chain 'S' and resid 294 through 316 Processing helix chain 'S' and resid 324 through 340 Processing helix chain 'S' and resid 355 through 436 Proline residue: S 401 - end of helix Processing helix chain 'S' and resid 457 through 465 Processing helix chain 'V' and resid 26 through 43 removed outlier: 4.007A pdb=" N ARG V 42 " --> pdb=" O GLU V 38 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU V 43 " --> pdb=" O GLU V 39 " (cutoff:3.500A) Processing helix chain 'V' and resid 104 through 116 Processing helix chain 'V' and resid 156 through 164 Processing helix chain 'V' and resid 193 through 198 removed outlier: 4.168A pdb=" N MET V 198 " --> pdb=" O SER V 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 221 through 233 Processing helix chain 'W' and resid 31 through 39 removed outlier: 3.507A pdb=" N LEU W 39 " --> pdb=" O GLY W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 54 through 58 removed outlier: 3.607A pdb=" N THR W 58 " --> pdb=" O ARG W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 87 removed outlier: 4.347A pdb=" N LEU W 85 " --> pdb=" O ASP W 81 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR W 87 " --> pdb=" O GLU W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 88 through 103 Processing helix chain 'W' and resid 111 through 135 Processing helix chain 'W' and resid 145 through 158 Processing helix chain 'W' and resid 177 through 197 removed outlier: 3.886A pdb=" N THR W 197 " --> pdb=" O MET W 193 " (cutoff:3.500A) Processing helix chain 'W' and resid 203 through 235 removed outlier: 4.078A pdb=" N ALA W 207 " --> pdb=" O LYS W 203 " (cutoff:3.500A) Processing helix chain 'W' and resid 238 through 280 Processing helix chain 'W' and resid 294 through 316 Processing helix chain 'W' and resid 324 through 340 Processing helix chain 'W' and resid 355 through 436 Proline residue: W 401 - end of helix Processing helix chain 'W' and resid 457 through 465 Processing helix chain 'Y' and resid 26 through 43 removed outlier: 4.007A pdb=" N ARG Y 42 " --> pdb=" O GLU Y 38 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU Y 43 " --> pdb=" O GLU Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 116 Processing helix chain 'Y' and resid 156 through 164 Processing helix chain 'Y' and resid 193 through 198 removed outlier: 4.169A pdb=" N MET Y 198 " --> pdb=" O SER Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 221 through 233 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 161 removed outlier: 6.587A pdb=" N LEU A 50 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL A 443 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 284 through 293 removed outlier: 3.520A pdb=" N THR A 287 " --> pdb=" O ASP A 351 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASP A 351 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG A 289 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER A 349 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE A 291 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN A 347 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU A 293 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR A 345 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N SER A 348 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR W 287 " --> pdb=" O PRO A 354 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR W 287 " --> pdb=" O ASP W 351 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP W 351 " --> pdb=" O THR W 287 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARG W 289 " --> pdb=" O SER W 349 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER W 349 " --> pdb=" O ARG W 289 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE W 291 " --> pdb=" O GLN W 347 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLN W 347 " --> pdb=" O ILE W 291 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU W 293 " --> pdb=" O THR W 345 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR W 345 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N SER W 348 " --> pdb=" O LEU S 293 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR S 287 " --> pdb=" O PRO W 354 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR S 287 " --> pdb=" O ASP S 351 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASP S 351 " --> pdb=" O THR S 287 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG S 289 " --> pdb=" O SER S 349 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER S 349 " --> pdb=" O ARG S 289 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE S 291 " --> pdb=" O GLN S 347 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN S 347 " --> pdb=" O ILE S 291 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU S 293 " --> pdb=" O THR S 345 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR S 345 " --> pdb=" O LEU S 293 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N SER S 348 " --> pdb=" O LEU P 293 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N THR P 287 " --> pdb=" O PRO S 354 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR P 287 " --> pdb=" O ASP P 351 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP P 351 " --> pdb=" O THR P 287 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG P 289 " --> pdb=" O SER P 349 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER P 349 " --> pdb=" O ARG P 289 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE P 291 " --> pdb=" O GLN P 347 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN P 347 " --> pdb=" O ILE P 291 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU P 293 " --> pdb=" O THR P 345 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR P 345 " --> pdb=" O LEU P 293 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N SER P 348 " --> pdb=" O LEU M 293 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR M 287 " --> pdb=" O PRO P 354 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR M 287 " --> pdb=" O ASP M 351 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASP M 351 " --> pdb=" O THR M 287 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG M 289 " --> pdb=" O SER M 349 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER M 349 " --> pdb=" O ARG M 289 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE M 291 " --> pdb=" O GLN M 347 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN M 347 " --> pdb=" O ILE M 291 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU M 293 " --> pdb=" O THR M 345 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR M 345 " --> pdb=" O LEU M 293 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N SER M 348 " --> pdb=" O LEU I 293 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N THR I 287 " --> pdb=" O PRO M 354 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR I 287 " --> pdb=" O ASP I 351 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP I 351 " --> pdb=" O THR I 287 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARG I 289 " --> pdb=" O SER I 349 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER I 349 " --> pdb=" O ARG I 289 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE I 291 " --> pdb=" O GLN I 347 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN I 347 " --> pdb=" O ILE I 291 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU I 293 " --> pdb=" O THR I 345 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR I 345 " --> pdb=" O LEU I 293 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N SER I 348 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N THR E 287 " --> pdb=" O PRO I 354 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR E 287 " --> pdb=" O ASP E 351 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASP E 351 " --> pdb=" O THR E 287 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG E 289 " --> pdb=" O SER E 349 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER E 349 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE E 291 " --> pdb=" O GLN E 347 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN E 347 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU E 293 " --> pdb=" O THR E 345 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR E 345 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N SER E 348 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N THR B 287 " --> pdb=" O PRO E 354 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 287 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASP B 351 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARG B 289 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER B 349 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 291 " --> pdb=" O GLN B 347 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN B 347 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 293 " --> pdb=" O THR B 345 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR B 345 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N SER B 348 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR A 287 " --> pdb=" O PRO B 354 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 161 removed outlier: 6.586A pdb=" N LEU B 50 " --> pdb=" O VAL B 443 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL B 443 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.664A pdb=" N THR D 55 " --> pdb=" O ASN D 130 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL D 59 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 89 through 92 Processing sheet with id=AA6, first strand: chain 'D' and resid 148 through 150 removed outlier: 7.958A pdb=" N VAL D 216 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE D 138 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL D 218 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY D 140 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 243 through 253 removed outlier: 6.138A pdb=" N ILE D 244 " --> pdb=" O SER G 243 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLY G 245 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL D 246 " --> pdb=" O GLY G 245 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLY G 247 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL D 248 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N SER G 249 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N TYR D 250 " --> pdb=" O SER G 249 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR G 251 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL D 252 " --> pdb=" O THR G 251 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASN G 253 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE G 244 " --> pdb=" O SER L 243 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLY L 245 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL G 246 " --> pdb=" O GLY L 245 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLY L 247 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL G 248 " --> pdb=" O GLY L 247 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N SER L 249 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR G 250 " --> pdb=" O SER L 249 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR L 251 " --> pdb=" O TYR G 250 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL G 252 " --> pdb=" O THR L 251 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASN L 253 " --> pdb=" O VAL G 252 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE L 244 " --> pdb=" O SER O 243 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLY O 245 " --> pdb=" O ILE L 244 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL L 246 " --> pdb=" O GLY O 245 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLY O 247 " --> pdb=" O VAL L 246 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL L 248 " --> pdb=" O GLY O 247 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N SER O 249 " --> pdb=" O VAL L 248 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR L 250 " --> pdb=" O SER O 249 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N THR O 251 " --> pdb=" O TYR L 250 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL L 252 " --> pdb=" O THR O 251 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASN O 253 " --> pdb=" O VAL L 252 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE O 244 " --> pdb=" O SER R 243 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLY R 245 " --> pdb=" O ILE O 244 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL O 246 " --> pdb=" O GLY R 245 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY R 247 " --> pdb=" O VAL O 246 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL O 248 " --> pdb=" O GLY R 247 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N SER R 249 " --> pdb=" O VAL O 248 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR O 250 " --> pdb=" O SER R 249 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR R 251 " --> pdb=" O TYR O 250 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL O 252 " --> pdb=" O THR R 251 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASN R 253 " --> pdb=" O VAL O 252 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE R 244 " --> pdb=" O SER V 243 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLY V 245 " --> pdb=" O ILE R 244 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL R 246 " --> pdb=" O GLY V 245 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLY V 247 " --> pdb=" O VAL R 246 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL R 248 " --> pdb=" O GLY V 247 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N SER V 249 " --> pdb=" O VAL R 248 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR R 250 " --> pdb=" O SER V 249 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N THR V 251 " --> pdb=" O TYR R 250 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL R 252 " --> pdb=" O THR V 251 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN V 253 " --> pdb=" O VAL R 252 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE V 244 " --> pdb=" O SER Y 243 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY Y 245 " --> pdb=" O ILE V 244 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL V 246 " --> pdb=" O GLY Y 245 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLY Y 247 " --> pdb=" O VAL V 246 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL V 248 " --> pdb=" O GLY Y 247 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N SER Y 249 " --> pdb=" O VAL V 248 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR V 250 " --> pdb=" O SER Y 249 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR Y 251 " --> pdb=" O TYR V 250 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL V 252 " --> pdb=" O THR Y 251 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN Y 253 " --> pdb=" O VAL V 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 159 through 161 removed outlier: 6.587A pdb=" N LEU E 50 " --> pdb=" O VAL E 443 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL E 443 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 81 through 83 removed outlier: 6.663A pdb=" N THR G 55 " --> pdb=" O ASN G 130 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL G 59 " --> pdb=" O THR G 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 89 through 92 Processing sheet with id=AB2, first strand: chain 'G' and resid 148 through 150 removed outlier: 7.958A pdb=" N VAL G 216 " --> pdb=" O THR G 136 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE G 138 " --> pdb=" O VAL G 216 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL G 218 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY G 140 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 159 through 161 removed outlier: 6.587A pdb=" N LEU I 50 " --> pdb=" O VAL I 443 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL I 443 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 81 through 83 removed outlier: 6.663A pdb=" N THR K 55 " --> pdb=" O ASN K 130 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL K 59 " --> pdb=" O THR K 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 89 through 92 Processing sheet with id=AB6, first strand: chain 'K' and resid 148 through 150 removed outlier: 7.958A pdb=" N VAL K 216 " --> pdb=" O THR K 136 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE K 138 " --> pdb=" O VAL K 216 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL K 218 " --> pdb=" O PHE K 138 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY K 140 " --> pdb=" O VAL K 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 81 through 83 removed outlier: 6.664A pdb=" N THR L 55 " --> pdb=" O ASN L 130 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL L 59 " --> pdb=" O THR L 126 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 89 through 92 Processing sheet with id=AB9, first strand: chain 'L' and resid 148 through 150 removed outlier: 7.958A pdb=" N VAL L 216 " --> pdb=" O THR L 136 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE L 138 " --> pdb=" O VAL L 216 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL L 218 " --> pdb=" O PHE L 138 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY L 140 " --> pdb=" O VAL L 218 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.587A pdb=" N LEU M 50 " --> pdb=" O VAL M 443 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL M 443 " --> pdb=" O LEU M 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 81 through 83 removed outlier: 6.663A pdb=" N THR O 55 " --> pdb=" O ASN O 130 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL O 59 " --> pdb=" O THR O 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 89 through 92 Processing sheet with id=AC4, first strand: chain 'O' and resid 148 through 150 removed outlier: 7.958A pdb=" N VAL O 216 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE O 138 " --> pdb=" O VAL O 216 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL O 218 " --> pdb=" O PHE O 138 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY O 140 " --> pdb=" O VAL O 218 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 159 through 161 removed outlier: 6.587A pdb=" N LEU P 50 " --> pdb=" O VAL P 443 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL P 443 " --> pdb=" O LEU P 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 81 through 83 removed outlier: 6.663A pdb=" N THR R 55 " --> pdb=" O ASN R 130 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL R 59 " --> pdb=" O THR R 126 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 89 through 92 Processing sheet with id=AC8, first strand: chain 'R' and resid 148 through 150 removed outlier: 7.959A pdb=" N VAL R 216 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE R 138 " --> pdb=" O VAL R 216 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL R 218 " --> pdb=" O PHE R 138 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY R 140 " --> pdb=" O VAL R 218 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 159 through 161 removed outlier: 6.587A pdb=" N LEU S 50 " --> pdb=" O VAL S 443 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL S 443 " --> pdb=" O LEU S 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 81 through 83 removed outlier: 6.663A pdb=" N THR V 55 " --> pdb=" O ASN V 130 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL V 59 " --> pdb=" O THR V 126 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 89 through 92 Processing sheet with id=AD3, first strand: chain 'V' and resid 148 through 150 removed outlier: 7.958A pdb=" N VAL V 216 " --> pdb=" O THR V 136 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE V 138 " --> pdb=" O VAL V 216 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL V 218 " --> pdb=" O PHE V 138 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY V 140 " --> pdb=" O VAL V 218 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'W' and resid 159 through 161 removed outlier: 6.587A pdb=" N LEU W 50 " --> pdb=" O VAL W 443 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL W 443 " --> pdb=" O LEU W 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Y' and resid 81 through 83 removed outlier: 6.664A pdb=" N THR Y 55 " --> pdb=" O ASN Y 130 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL Y 59 " --> pdb=" O THR Y 126 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 89 through 92 Processing sheet with id=AD7, first strand: chain 'Y' and resid 148 through 150 removed outlier: 7.958A pdb=" N VAL Y 216 " --> pdb=" O THR Y 136 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE Y 138 " --> pdb=" O VAL Y 216 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL Y 218 " --> pdb=" O PHE Y 138 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY Y 140 " --> pdb=" O VAL Y 218 " (cutoff:3.500A) 2627 hydrogen bonds defined for protein. 7683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.66 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8149 1.32 - 1.45: 9442 1.45 - 1.57: 24655 1.57 - 1.69: 8 1.69 - 1.82: 202 Bond restraints: 42456 Sorted by residual: bond pdb=" N PRO W 324 " pdb=" CD PRO W 324 " ideal model delta sigma weight residual 1.473 1.810 -0.337 1.40e-02 5.10e+03 5.78e+02 bond pdb=" N PRO W 323 " pdb=" CD PRO W 323 " ideal model delta sigma weight residual 1.473 1.727 -0.254 1.40e-02 5.10e+03 3.28e+02 bond pdb=" CA TYR P 318 " pdb=" C TYR P 318 " ideal model delta sigma weight residual 1.526 1.433 0.094 1.42e-02 4.96e+03 4.35e+01 bond pdb=" CA TYR W 318 " pdb=" C TYR W 318 " ideal model delta sigma weight residual 1.523 1.441 0.083 1.34e-02 5.57e+03 3.81e+01 bond pdb=" CA PRO W 324 " pdb=" CB PRO W 324 " ideal model delta sigma weight residual 1.533 1.462 0.072 1.42e-02 4.96e+03 2.54e+01 ... (remaining 42451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.82: 57215 7.82 - 15.64: 272 15.64 - 23.46: 37 23.46 - 31.28: 2 31.28 - 39.10: 2 Bond angle restraints: 57528 Sorted by residual: angle pdb=" N PRO W 323 " pdb=" CA PRO W 323 " pdb=" C PRO W 323 " ideal model delta sigma weight residual 110.70 143.29 -32.59 1.22e+00 6.72e-01 7.14e+02 angle pdb=" N PRO W 323 " pdb=" CA PRO W 323 " pdb=" CB PRO W 323 " ideal model delta sigma weight residual 103.08 80.46 22.62 9.70e-01 1.06e+00 5.44e+02 angle pdb=" N ASP A 320 " pdb=" CA ASP A 320 " pdb=" C ASP A 320 " ideal model delta sigma weight residual 113.97 89.17 24.80 1.28e+00 6.10e-01 3.75e+02 angle pdb=" N PRO A 323 " pdb=" CA PRO A 323 " pdb=" C PRO A 323 " ideal model delta sigma weight residual 110.70 130.82 -20.12 1.22e+00 6.72e-01 2.72e+02 angle pdb=" C ASP M 320 " pdb=" CA ASP M 320 " pdb=" CB ASP M 320 " ideal model delta sigma weight residual 109.16 129.87 -20.71 1.29e+00 6.01e-01 2.58e+02 ... (remaining 57523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 22388 17.97 - 35.94: 3145 35.94 - 53.91: 753 53.91 - 71.88: 114 71.88 - 89.85: 88 Dihedral angle restraints: 26488 sinusoidal: 10960 harmonic: 15528 Sorted by residual: dihedral pdb=" CA PRO Y 239 " pdb=" C PRO Y 239 " pdb=" N PHE Y 240 " pdb=" CA PHE Y 240 " ideal model delta harmonic sigma weight residual -180.00 -113.10 -66.90 0 5.00e+00 4.00e-02 1.79e+02 dihedral pdb=" CA PRO K 239 " pdb=" C PRO K 239 " pdb=" N PHE K 240 " pdb=" CA PHE K 240 " ideal model delta harmonic sigma weight residual -180.00 -113.15 -66.85 0 5.00e+00 4.00e-02 1.79e+02 dihedral pdb=" CA PRO G 239 " pdb=" C PRO G 239 " pdb=" N PHE G 240 " pdb=" CA PHE G 240 " ideal model delta harmonic sigma weight residual -180.00 -113.15 -66.85 0 5.00e+00 4.00e-02 1.79e+02 ... (remaining 26485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.207: 6518 0.207 - 0.414: 118 0.414 - 0.621: 5 0.621 - 0.828: 1 0.828 - 1.035: 6 Chirality restraints: 6648 Sorted by residual: chirality pdb=" CA ASP S 320 " pdb=" N ASP S 320 " pdb=" C ASP S 320 " pdb=" CB ASP S 320 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.04 2.00e-01 2.50e+01 2.68e+01 chirality pdb=" CA ASP I 320 " pdb=" N ASP I 320 " pdb=" C ASP I 320 " pdb=" CB ASP I 320 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.11e+01 chirality pdb=" CA ASP M 320 " pdb=" N ASP M 320 " pdb=" C ASP M 320 " pdb=" CB ASP M 320 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.11e+01 ... (remaining 6645 not shown) Planarity restraints: 7576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO W 323 " 0.214 5.00e-02 4.00e+02 2.72e-01 1.18e+02 pdb=" N PRO W 324 " -0.456 5.00e-02 4.00e+02 pdb=" CA PRO W 324 " 0.198 5.00e-02 4.00e+02 pdb=" CD PRO W 324 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG Y 121 " 0.928 9.50e-02 1.11e+02 4.16e-01 1.05e+02 pdb=" NE ARG Y 121 " -0.054 2.00e-02 2.50e+03 pdb=" CZ ARG Y 121 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG Y 121 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG Y 121 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA W 322 " -0.175 5.00e-02 4.00e+02 2.34e-01 8.79e+01 pdb=" N PRO W 323 " 0.401 5.00e-02 4.00e+02 pdb=" CA PRO W 323 " -0.152 5.00e-02 4.00e+02 pdb=" CD PRO W 323 " -0.074 5.00e-02 4.00e+02 ... (remaining 7573 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 944 2.66 - 3.22: 38771 3.22 - 3.78: 74149 3.78 - 4.34: 96074 4.34 - 4.90: 158211 Nonbonded interactions: 368149 Sorted by model distance: nonbonded pdb=" O THR B 319 " pdb=" CG2 THR B 319 " model vdw 2.105 3.460 nonbonded pdb=" N ASP A 320 " pdb=" N ASP A 321 " model vdw 2.112 2.560 nonbonded pdb=" OH TYR M 420 " pdb=" OE2 GLU P 425 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR B 420 " pdb=" OE2 GLU E 425 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR S 420 " pdb=" OE2 GLU W 425 " model vdw 2.163 3.040 ... (remaining 368144 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'V' selection = chain 'Y' } 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: 21.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.510 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.140 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 : 0.009 0.337 42456 Z= 0.418 Angle : 1.556 39.102 57528 Z= 0.845 Chirality : 0.079 1.035 6648 Planarity : 0.016 0.416 7576 Dihedral : 17.896 89.850 16408 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.25 % Favored : 93.28 % Rotamer: Outliers : 0.73 % Allowed : 19.90 % Favored : 79.37 % Cbeta Deviations : 0.75 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.10), residues: 5264 helix: -1.96 (0.08), residues: 2880 sheet: -2.16 (0.23), residues: 344 loop : -2.24 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.082 0.003 ARG B 84 TYR 0.036 0.004 TYR I 318 PHE 0.047 0.005 PHE W 118 TRP 0.031 0.007 TRP W 113 HIS 0.004 0.002 HIS D 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00909 / 0.42 (42456) covalent geometry : angle 1.55647 / 0.85 (57528) hydrogen bonds : bond 0.11129 / 7.49 ( 2627) hydrogen bonds : angle 6.72434 / 4.72 ( 7683) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 682 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: D 179 MET cc_start: 0.7545 (mpp) cc_final: 0.7292 (mpp) REVERT: L 179 MET cc_start: 0.7524 (mpp) cc_final: 0.7261 (mpp) REVERT: P 71 MET cc_start: 0.7340 (mmt) cc_final: 0.6986 (mmt) REVERT: R 179 MET cc_start: 0.7528 (mpp) cc_final: 0.7267 (mpp) REVERT: W 71 MET cc_start: 0.7351 (mmt) cc_final: 0.7009 (mmt) REVERT: Y 179 MET cc_start: 0.7544 (mpp) cc_final: 0.7297 (mpp) outliers start: 33 outliers final: 14 residues processed: 705 average time/residue: 0.2487 time to fit residues: 285.0596 Evaluate side-chains 552 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 538 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain P residue 288 VAL Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain W residue 288 VAL Chi-restraints excluded: chain W residue 319 THR Chi-restraints excluded: chain W residue 321 ASP Chi-restraints excluded: chain W residue 323 PRO Chi-restraints excluded: chain W residue 324 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 394 optimal weight: 0.6980 chunk 430 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 265 optimal weight: 0.5980 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 0.9990 chunk 310 optimal weight: 0.8980 chunk 488 optimal weight: 0.5980 chunk 366 optimal weight: 0.0980 chunk 223 optimal weight: 0.4980 chunk 516 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN A 372 ASN A 440 ASN B 305 ASN B 360 HIS B 372 ASN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN E 372 ASN E 440 ASN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 305 ASN I 360 HIS I 372 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 305 ASN M 372 ASN M 440 ASN ** O 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 305 ASN P 360 HIS P 372 ASN ** S 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 305 ASN S 372 ASN S 440 ASN ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 305 ASN W 360 HIS W 372 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.174399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.147274 restraints weight = 56449.038| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.42 r_work: 0.3756 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 42456 Z= 0.204 Angle : 0.816 12.041 57528 Z= 0.419 Chirality : 0.048 0.222 6648 Planarity : 0.010 0.122 7576 Dihedral : 6.933 53.288 5931 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.09 % Favored : 94.43 % Rotamer: Outliers : 3.61 % Allowed : 19.66 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.11), residues: 5264 helix: -0.63 (0.09), residues: 2832 sheet: -2.10 (0.22), residues: 392 loop : -2.18 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 212 TYR 0.024 0.002 TYR E 318 PHE 0.015 0.001 PHE Y 240 TRP 0.011 0.002 TRP E 113 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (42456) covalent geometry : angle 0.81649 / 0.42 (57528) hydrogen bonds : bond 0.05011 / 3.35 ( 2627) hydrogen bonds : angle 5.49990 / 3.87 ( 7683) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 642 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8024 (mtm) REVERT: A 420 TYR cc_start: 0.8088 (m-10) cc_final: 0.7886 (m-10) REVERT: B 71 MET cc_start: 0.7309 (mmt) cc_final: 0.7034 (mmt) REVERT: E 169 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8041 (mtm) REVERT: E 420 TYR cc_start: 0.8089 (m-10) cc_final: 0.7878 (m-10) REVERT: I 71 MET cc_start: 0.7281 (mmt) cc_final: 0.6997 (mmt) REVERT: M 169 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8039 (mtm) REVERT: M 420 TYR cc_start: 0.8078 (m-10) cc_final: 0.7878 (m-10) REVERT: P 71 MET cc_start: 0.7330 (mmt) cc_final: 0.7069 (mmt) REVERT: S 169 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8027 (mtm) REVERT: S 420 TYR cc_start: 0.8084 (m-10) cc_final: 0.7883 (m-10) REVERT: W 71 MET cc_start: 0.7337 (mmt) cc_final: 0.7086 (mmt) outliers start: 163 outliers final: 74 residues processed: 772 average time/residue: 0.2528 time to fit residues: 312.9050 Evaluate side-chains 632 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 554 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 339 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 230 VAL Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 169 MET Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 245 ASP Chi-restraints excluded: chain P residue 288 VAL Chi-restraints excluded: chain P residue 291 ILE Chi-restraints excluded: chain P residue 339 VAL Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 169 MET Chi-restraints excluded: chain S residue 245 ASP Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 291 ILE Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 234 LEU Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 245 ASP Chi-restraints excluded: chain W residue 288 VAL Chi-restraints excluded: chain W residue 291 ILE Chi-restraints excluded: chain W residue 339 VAL Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain Y residue 104 THR Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 234 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 231 optimal weight: 1.9990 chunk 229 optimal weight: 0.5980 chunk 446 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 395 optimal weight: 0.5980 chunk 512 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 379 optimal weight: 0.4980 chunk 104 optimal weight: 0.5980 chunk 451 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 ASN A 360 HIS A 440 ASN B 212 GLN B 305 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN E 360 HIS E 440 ASN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 GLN I 212 GLN I 305 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 159 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 305 ASN M 360 HIS M 440 ASN ** O 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 159 GLN P 212 GLN P 305 ASN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 305 ASN S 360 HIS S 440 ASN ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 159 GLN W 212 GLN W 305 ASN ** Y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.171615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.145492 restraints weight = 56629.723| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.61 r_work: 0.3697 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 42456 Z= 0.199 Angle : 0.740 12.259 57528 Z= 0.377 Chirality : 0.047 0.222 6648 Planarity : 0.008 0.101 7576 Dihedral : 6.481 49.108 5920 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.13 % Favored : 94.41 % Rotamer: Outliers : 5.08 % Allowed : 19.75 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.11), residues: 5264 helix: -0.02 (0.09), residues: 2824 sheet: -2.34 (0.19), residues: 472 loop : -2.00 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 212 TYR 0.018 0.002 TYR A 318 PHE 0.013 0.001 PHE L 240 TRP 0.009 0.002 TRP M 188 HIS 0.002 0.001 HIS I 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (42456) covalent geometry : angle 0.74029 / 0.38 (57528) hydrogen bonds : bond 0.04839 / 3.24 ( 2627) hydrogen bonds : angle 5.21390 / 3.67 ( 7683) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 617 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ARG cc_start: 0.5854 (OUTLIER) cc_final: 0.5449 (ptt90) REVERT: A 169 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8084 (mtm) REVERT: A 315 MET cc_start: 0.6732 (ptm) cc_final: 0.6390 (ptm) REVERT: A 403 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8177 (tt) REVERT: B 71 MET cc_start: 0.7368 (mmt) cc_final: 0.7086 (mmt) REVERT: B 84 ARG cc_start: 0.5702 (OUTLIER) cc_final: 0.5056 (ptt90) REVERT: B 86 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7312 (mt) REVERT: B 339 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.8045 (t) REVERT: B 363 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6572 (ttm-80) REVERT: D 122 GLU cc_start: 0.7544 (pm20) cc_final: 0.7313 (pm20) REVERT: D 179 MET cc_start: 0.8073 (mpp) cc_final: 0.7827 (mpp) REVERT: D 240 PHE cc_start: 0.2504 (OUTLIER) cc_final: 0.2255 (t80) REVERT: E 84 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5443 (ptt90) REVERT: E 169 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8098 (mtm) REVERT: E 403 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8164 (tt) REVERT: G 43 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7955 (pt) REVERT: G 210 MET cc_start: 0.7866 (mtp) cc_final: 0.7474 (mmm) REVERT: I 71 MET cc_start: 0.7342 (mmt) cc_final: 0.7056 (mmt) REVERT: I 84 ARG cc_start: 0.5712 (OUTLIER) cc_final: 0.5064 (ptt90) REVERT: I 86 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7291 (mt) REVERT: I 339 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.7990 (t) REVERT: I 363 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6555 (ttm-80) REVERT: K 43 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7984 (pt) REVERT: K 210 MET cc_start: 0.7857 (mtp) cc_final: 0.7457 (mmm) REVERT: L 179 MET cc_start: 0.8050 (mpp) cc_final: 0.7806 (mpp) REVERT: M 84 ARG cc_start: 0.5840 (OUTLIER) cc_final: 0.5432 (ptt90) REVERT: M 169 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8088 (mtm) REVERT: M 403 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8163 (tt) REVERT: O 43 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7974 (pt) REVERT: O 210 MET cc_start: 0.7870 (mtp) cc_final: 0.7476 (mmm) REVERT: P 71 MET cc_start: 0.7385 (mmt) cc_final: 0.7110 (mmt) REVERT: P 84 ARG cc_start: 0.5725 (OUTLIER) cc_final: 0.5059 (ptt90) REVERT: P 86 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7313 (mt) REVERT: P 259 ASN cc_start: 0.7858 (m-40) cc_final: 0.7563 (m-40) REVERT: P 339 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.7960 (t) REVERT: P 363 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6560 (ttm-80) REVERT: R 47 MET cc_start: 0.6931 (mmt) cc_final: 0.6618 (mmt) REVERT: R 179 MET cc_start: 0.8083 (mpp) cc_final: 0.7843 (mpp) REVERT: S 84 ARG cc_start: 0.5841 (OUTLIER) cc_final: 0.5438 (ptt90) REVERT: S 169 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8086 (mtm) REVERT: S 403 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8165 (tt) REVERT: V 43 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7961 (pt) REVERT: V 210 MET cc_start: 0.7856 (mtp) cc_final: 0.7456 (mmm) REVERT: W 71 MET cc_start: 0.7402 (mmt) cc_final: 0.7130 (mmt) REVERT: W 84 ARG cc_start: 0.5755 (OUTLIER) cc_final: 0.5094 (ptt90) REVERT: W 86 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7291 (mt) REVERT: W 259 ASN cc_start: 0.7864 (m-40) cc_final: 0.7566 (m-40) REVERT: W 318 TYR cc_start: 0.8043 (m-80) cc_final: 0.7841 (m-80) REVERT: W 339 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.7930 (t) REVERT: W 363 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6561 (ttm-80) REVERT: Y 156 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.8144 (p0) REVERT: Y 179 MET cc_start: 0.8059 (mpp) cc_final: 0.7810 (mpp) outliers start: 229 outliers final: 127 residues processed: 796 average time/residue: 0.2447 time to fit residues: 320.9551 Evaluate side-chains 744 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 583 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 266 SER Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 339 VAL Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 363 ARG Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 230 VAL Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 240 PHE Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 169 MET Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 84 ARG Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain P residue 245 ASP Chi-restraints excluded: chain P residue 266 SER Chi-restraints excluded: chain P residue 288 VAL Chi-restraints excluded: chain P residue 291 ILE Chi-restraints excluded: chain P residue 339 VAL Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 363 ARG Chi-restraints excluded: chain P residue 375 LEU Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 240 PHE Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 169 MET Chi-restraints excluded: chain S residue 245 ASP Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 291 ILE Chi-restraints excluded: chain S residue 358 THR Chi-restraints excluded: chain S residue 403 LEU Chi-restraints excluded: chain V residue 37 LEU Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 234 LEU Chi-restraints excluded: chain V residue 248 VAL Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain W residue 84 ARG Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 147 VAL Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 168 VAL Chi-restraints excluded: chain W residue 245 ASP Chi-restraints excluded: chain W residue 266 SER Chi-restraints excluded: chain W residue 288 VAL Chi-restraints excluded: chain W residue 291 ILE Chi-restraints excluded: chain W residue 339 VAL Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 363 ARG Chi-restraints excluded: chain W residue 375 LEU Chi-restraints excluded: chain Y residue 104 THR Chi-restraints excluded: chain Y residue 156 ASN Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Y residue 240 PHE Chi-restraints excluded: chain Y residue 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 485 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 110 optimal weight: 0.5980 chunk 491 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 chunk 203 optimal weight: 2.9990 chunk 423 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 468 optimal weight: 2.9990 chunk 396 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 212 GLN A 437 GLN A 440 ASN B 298 GLN B 440 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN E 67 GLN E 212 GLN E 297 GLN E 437 GLN E 440 ASN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 GLN I 437 GLN I 440 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 159 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 ASN ** M 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 GLN M 297 GLN M 437 GLN M 440 ASN ** O 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 159 GLN P 440 ASN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 156 ASN ** S 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 212 GLN S 297 GLN S 437 GLN S 440 ASN ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 159 GLN W 298 GLN W 437 GLN W 440 ASN ** Y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 159 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.165332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.139592 restraints weight = 56714.125| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.57 r_work: 0.3603 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 42456 Z= 0.266 Angle : 0.762 12.783 57528 Z= 0.392 Chirality : 0.049 0.199 6648 Planarity : 0.008 0.106 7576 Dihedral : 6.330 46.528 5920 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.36 % Favored : 94.19 % Rotamer: Outliers : 6.32 % Allowed : 19.57 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 1.74 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.11), residues: 5264 helix: 0.15 (0.09), residues: 2856 sheet: -2.43 (0.19), residues: 480 loop : -2.02 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 212 TYR 0.032 0.002 TYR G 91 PHE 0.014 0.002 PHE K 240 TRP 0.009 0.002 TRP A 175 HIS 0.004 0.001 HIS P 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.27 (42456) covalent geometry : angle 0.76221 / 0.39 (57528) hydrogen bonds : bond 0.04875 / 3.26 ( 2627) hydrogen bonds : angle 5.16601 / 3.64 ( 7683) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 285 poor density : 557 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ARG cc_start: 0.6050 (OUTLIER) cc_final: 0.5518 (ptt90) REVERT: A 403 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8191 (tt) REVERT: A 435 LYS cc_start: 0.7238 (mmtp) cc_final: 0.6701 (tppt) REVERT: B 71 MET cc_start: 0.7308 (mmt) cc_final: 0.7034 (mmt) REVERT: B 84 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5433 (ptt90) REVERT: B 315 MET cc_start: 0.8077 (mmt) cc_final: 0.7691 (mmm) REVERT: B 339 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8146 (t) REVERT: B 363 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6498 (ttm-80) REVERT: D 121 ARG cc_start: 0.7463 (ttm170) cc_final: 0.7229 (ttm110) REVERT: E 84 ARG cc_start: 0.6064 (OUTLIER) cc_final: 0.5526 (ptt90) REVERT: E 403 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8183 (tt) REVERT: E 435 LYS cc_start: 0.7246 (mmtp) cc_final: 0.6718 (tppt) REVERT: G 156 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.8137 (p0) REVERT: G 210 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7699 (mmt) REVERT: I 71 MET cc_start: 0.7297 (mmt) cc_final: 0.7031 (mmt) REVERT: I 84 ARG cc_start: 0.6223 (OUTLIER) cc_final: 0.5432 (ptt90) REVERT: I 363 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6480 (ttm-80) REVERT: K 122 GLU cc_start: 0.7559 (pm20) cc_final: 0.7313 (pm20) REVERT: K 156 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8148 (p0) REVERT: K 210 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7711 (mmt) REVERT: M 84 ARG cc_start: 0.6043 (OUTLIER) cc_final: 0.5508 (ptt90) REVERT: M 403 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8194 (tt) REVERT: M 435 LYS cc_start: 0.7229 (mmtp) cc_final: 0.6700 (tppt) REVERT: O 156 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8141 (p0) REVERT: O 210 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7695 (mmt) REVERT: P 71 MET cc_start: 0.7326 (mmt) cc_final: 0.7077 (mmt) REVERT: P 84 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.5407 (ptt90) REVERT: P 259 ASN cc_start: 0.7821 (m-40) cc_final: 0.7534 (m-40) REVERT: P 363 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6495 (ttm-80) REVERT: S 84 ARG cc_start: 0.6033 (OUTLIER) cc_final: 0.5495 (ptt90) REVERT: S 403 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8188 (tt) REVERT: S 435 LYS cc_start: 0.7234 (mmtp) cc_final: 0.6689 (tppt) REVERT: V 156 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8139 (p0) REVERT: V 210 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7712 (mmt) REVERT: W 71 MET cc_start: 0.7339 (mmt) cc_final: 0.7085 (mmt) REVERT: W 84 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5478 (ptt90) REVERT: W 259 ASN cc_start: 0.7811 (m-40) cc_final: 0.7526 (m-40) REVERT: W 363 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6499 (ttm-80) outliers start: 285 outliers final: 180 residues processed: 793 average time/residue: 0.2540 time to fit residues: 331.0892 Evaluate side-chains 716 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 511 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 266 SER Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 363 ARG Chi-restraints excluded: chain I residue 375 LEU Chi-restraints excluded: chain I residue 403 LEU Chi-restraints excluded: chain I residue 429 ILE Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 230 VAL Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain M residue 356 THR Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 429 ILE Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 156 ASN Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 210 MET Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 84 ARG Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 245 ASP Chi-restraints excluded: chain P residue 266 SER Chi-restraints excluded: chain P residue 288 VAL Chi-restraints excluded: chain P residue 291 ILE Chi-restraints excluded: chain P residue 356 THR Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 363 ARG Chi-restraints excluded: chain P residue 375 LEU Chi-restraints excluded: chain P residue 403 LEU Chi-restraints excluded: chain P residue 429 ILE Chi-restraints excluded: chain R residue 37 LEU Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 171 ILE Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 245 ASP Chi-restraints excluded: chain S residue 266 SER Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 356 THR Chi-restraints excluded: chain S residue 358 THR Chi-restraints excluded: chain S residue 403 LEU Chi-restraints excluded: chain S residue 429 ILE Chi-restraints excluded: chain V residue 37 LEU Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 156 ASN Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 210 MET Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 234 LEU Chi-restraints excluded: chain V residue 248 VAL Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain W residue 84 ARG Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 147 VAL Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 168 VAL Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 245 ASP Chi-restraints excluded: chain W residue 266 SER Chi-restraints excluded: chain W residue 288 VAL Chi-restraints excluded: chain W residue 291 ILE Chi-restraints excluded: chain W residue 356 THR Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 363 ARG Chi-restraints excluded: chain W residue 375 LEU Chi-restraints excluded: chain W residue 403 LEU Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 104 THR Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Y residue 248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 464 optimal weight: 3.9990 chunk 434 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 348 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 294 optimal weight: 0.9990 chunk 228 optimal weight: 0.5980 chunk 289 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 485 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 GLN A 440 ASN B 437 GLN B 440 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 GLN E 298 GLN E 440 ASN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 298 GLN I 440 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 297 GLN M 440 ASN ** O 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 298 GLN P 440 ASN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 GLN S 298 GLN S 440 ASN ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 440 ASN ** Y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 159 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.165987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.140490 restraints weight = 56541.140| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.47 r_work: 0.3620 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 42456 Z= 0.219 Angle : 0.736 12.735 57528 Z= 0.373 Chirality : 0.047 0.229 6648 Planarity : 0.008 0.119 7576 Dihedral : 6.098 45.173 5920 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.36 % Favored : 94.19 % Rotamer: Outliers : 5.23 % Allowed : 21.17 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.11), residues: 5264 helix: 0.35 (0.09), residues: 2848 sheet: -2.34 (0.20), residues: 480 loop : -1.85 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 149 TYR 0.035 0.002 TYR K 91 PHE 0.008 0.001 PHE A 118 TRP 0.010 0.002 TRP A 175 HIS 0.003 0.001 HIS P 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (42456) covalent geometry : angle 0.73566 / 0.37 (57528) hydrogen bonds : bond 0.04716 / 3.15 ( 2627) hydrogen bonds : angle 5.07778 / 3.58 ( 7683) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 547 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ARG cc_start: 0.6062 (OUTLIER) cc_final: 0.5502 (ptt90) REVERT: A 403 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8227 (tt) REVERT: B 71 MET cc_start: 0.7334 (mmt) cc_final: 0.7063 (mmt) REVERT: B 84 ARG cc_start: 0.6071 (OUTLIER) cc_final: 0.5453 (ptt90) REVERT: B 315 MET cc_start: 0.7992 (mmt) cc_final: 0.7581 (mmm) REVERT: E 84 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.5503 (ptt90) REVERT: E 403 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8277 (tt) REVERT: G 210 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7710 (mmt) REVERT: I 71 MET cc_start: 0.7301 (mmt) cc_final: 0.7039 (mmt) REVERT: I 84 ARG cc_start: 0.6093 (OUTLIER) cc_final: 0.5480 (ptt90) REVERT: K 210 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7705 (mmt) REVERT: M 84 ARG cc_start: 0.6078 (OUTLIER) cc_final: 0.5519 (ptt90) REVERT: M 403 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8288 (tt) REVERT: O 210 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7678 (mmt) REVERT: P 71 MET cc_start: 0.7347 (mmt) cc_final: 0.7089 (mmt) REVERT: P 84 ARG cc_start: 0.6137 (OUTLIER) cc_final: 0.5504 (ptt90) REVERT: P 259 ASN cc_start: 0.7835 (m-40) cc_final: 0.7514 (m-40) REVERT: P 318 TYR cc_start: 0.8409 (m-80) cc_final: 0.8070 (m-80) REVERT: S 84 ARG cc_start: 0.6052 (OUTLIER) cc_final: 0.5493 (ptt90) REVERT: S 403 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8278 (tt) REVERT: V 210 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7708 (mmt) REVERT: W 71 MET cc_start: 0.7370 (mmt) cc_final: 0.7110 (mmt) REVERT: W 84 ARG cc_start: 0.6131 (OUTLIER) cc_final: 0.5501 (ptt90) REVERT: W 259 ASN cc_start: 0.7875 (m-40) cc_final: 0.7555 (m-40) REVERT: W 339 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8157 (t) REVERT: Y 156 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8255 (p0) outliers start: 236 outliers final: 162 residues processed: 754 average time/residue: 0.2529 time to fit residues: 314.8970 Evaluate side-chains 686 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 506 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 403 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 230 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 356 THR Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 429 ILE Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 210 MET Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 84 ARG Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 245 ASP Chi-restraints excluded: chain P residue 288 VAL Chi-restraints excluded: chain P residue 291 ILE Chi-restraints excluded: chain P residue 356 THR Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 403 LEU Chi-restraints excluded: chain R residue 37 LEU Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 171 ILE Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 245 ASP Chi-restraints excluded: chain S residue 266 SER Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 291 ILE Chi-restraints excluded: chain S residue 356 THR Chi-restraints excluded: chain S residue 358 THR Chi-restraints excluded: chain S residue 403 LEU Chi-restraints excluded: chain S residue 429 ILE Chi-restraints excluded: chain V residue 37 LEU Chi-restraints excluded: chain V residue 125 VAL Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 210 MET Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 248 VAL Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 84 ARG Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 147 VAL Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 168 VAL Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 245 ASP Chi-restraints excluded: chain W residue 288 VAL Chi-restraints excluded: chain W residue 291 ILE Chi-restraints excluded: chain W residue 339 VAL Chi-restraints excluded: chain W residue 356 THR Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 403 LEU Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 104 THR Chi-restraints excluded: chain Y residue 143 VAL Chi-restraints excluded: chain Y residue 156 ASN Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Y residue 248 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 388 optimal weight: 2.9990 chunk 158 optimal weight: 0.2980 chunk 245 optimal weight: 0.0980 chunk 133 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 500 optimal weight: 0.7980 chunk 363 optimal weight: 1.9990 chunk 465 optimal weight: 5.9990 chunk 282 optimal weight: 0.7980 chunk 507 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 440 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 298 GLN M 440 ASN ** O 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 437 GLN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 67 GLN S 440 ASN ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.167409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.142394 restraints weight = 56779.253| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.50 r_work: 0.3639 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 42456 Z= 0.184 Angle : 0.707 12.732 57528 Z= 0.358 Chirality : 0.046 0.187 6648 Planarity : 0.007 0.109 7576 Dihedral : 6.003 39.889 5920 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.51 % Favored : 94.17 % Rotamer: Outliers : 5.34 % Allowed : 20.74 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 3.82 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.11), residues: 5264 helix: 0.51 (0.09), residues: 2848 sheet: -2.38 (0.20), residues: 480 loop : -1.82 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG V 121 TYR 0.030 0.002 TYR O 91 PHE 0.009 0.001 PHE S 118 TRP 0.010 0.002 TRP I 188 HIS 0.012 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (42456) covalent geometry : angle 0.70720 / 0.36 (57528) hydrogen bonds : bond 0.04555 / 3.04 ( 2627) hydrogen bonds : angle 4.95171 / 3.48 ( 7683) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 569 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 ASN cc_start: 0.8195 (m110) cc_final: 0.7931 (m110) REVERT: A 302 ARG cc_start: 0.7825 (mtp-110) cc_final: 0.7069 (mtt90) REVERT: A 403 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8267 (tt) REVERT: B 71 MET cc_start: 0.7418 (mmt) cc_final: 0.7154 (mmt) REVERT: B 84 ARG cc_start: 0.5973 (OUTLIER) cc_final: 0.5214 (ptt90) REVERT: D 43 LEU cc_start: 0.8356 (pp) cc_final: 0.7976 (mp) REVERT: E 259 ASN cc_start: 0.8210 (m110) cc_final: 0.7935 (m110) REVERT: E 403 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8272 (tt) REVERT: G 210 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7693 (mmt) REVERT: I 71 MET cc_start: 0.7379 (mmt) cc_final: 0.7124 (mmt) REVERT: I 84 ARG cc_start: 0.5975 (OUTLIER) cc_final: 0.5209 (ptt90) REVERT: K 210 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7673 (mmt) REVERT: L 43 LEU cc_start: 0.8358 (pp) cc_final: 0.7971 (mp) REVERT: M 171 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8140 (pt) REVERT: M 259 ASN cc_start: 0.8210 (m110) cc_final: 0.7935 (m110) REVERT: M 403 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8279 (tt) REVERT: O 210 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7686 (mmt) REVERT: P 71 MET cc_start: 0.7433 (mmt) cc_final: 0.7174 (mmt) REVERT: P 84 ARG cc_start: 0.6014 (OUTLIER) cc_final: 0.5236 (ptt90) REVERT: P 259 ASN cc_start: 0.7870 (m-40) cc_final: 0.7563 (m-40) REVERT: P 318 TYR cc_start: 0.8393 (m-80) cc_final: 0.8052 (m-80) REVERT: R 43 LEU cc_start: 0.8374 (pp) cc_final: 0.7979 (mp) REVERT: S 67 GLN cc_start: 0.8167 (tt0) cc_final: 0.7935 (tt0) REVERT: S 259 ASN cc_start: 0.8217 (m110) cc_final: 0.7946 (m110) REVERT: S 403 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8269 (tt) REVERT: V 210 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7692 (mmt) REVERT: W 71 MET cc_start: 0.7401 (mmt) cc_final: 0.7150 (mmt) REVERT: W 84 ARG cc_start: 0.6012 (OUTLIER) cc_final: 0.5226 (ptt90) REVERT: W 259 ASN cc_start: 0.7898 (m-40) cc_final: 0.7591 (m-40) REVERT: W 339 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8183 (t) REVERT: Y 43 LEU cc_start: 0.8372 (pp) cc_final: 0.8000 (mp) outliers start: 241 outliers final: 165 residues processed: 765 average time/residue: 0.2545 time to fit residues: 321.3867 Evaluate side-chains 689 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 510 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 403 LEU Chi-restraints excluded: chain I residue 429 ILE Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 230 VAL Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 210 MET Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 84 ARG Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain P residue 171 ILE Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 245 ASP Chi-restraints excluded: chain P residue 288 VAL Chi-restraints excluded: chain P residue 291 ILE Chi-restraints excluded: chain P residue 356 THR Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 403 LEU Chi-restraints excluded: chain P residue 429 ILE Chi-restraints excluded: chain R residue 37 LEU Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 171 ILE Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 245 ASP Chi-restraints excluded: chain S residue 266 SER Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 291 ILE Chi-restraints excluded: chain S residue 358 THR Chi-restraints excluded: chain S residue 403 LEU Chi-restraints excluded: chain S residue 429 ILE Chi-restraints excluded: chain V residue 37 LEU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 210 MET Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 248 VAL Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain W residue 84 ARG Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 147 VAL Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 168 VAL Chi-restraints excluded: chain W residue 171 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 245 ASP Chi-restraints excluded: chain W residue 288 VAL Chi-restraints excluded: chain W residue 339 VAL Chi-restraints excluded: chain W residue 356 THR Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 403 LEU Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 104 THR Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Y residue 248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 190 optimal weight: 0.0870 chunk 403 optimal weight: 0.0970 chunk 401 optimal weight: 7.9990 chunk 405 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 133 optimal weight: 0.2980 chunk 379 optimal weight: 0.2980 chunk 212 optimal weight: 0.6980 chunk 496 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 330 optimal weight: 0.8980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 ASN ** M 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 440 ASN ** O 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 ASN S 440 ASN ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 440 ASN ** Y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 159 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.170098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.145512 restraints weight = 56423.716| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.48 r_work: 0.3681 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 42456 Z= 0.154 Angle : 0.686 12.385 57528 Z= 0.349 Chirality : 0.045 0.190 6648 Planarity : 0.007 0.106 7576 Dihedral : 5.853 36.576 5920 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.51 % Favored : 94.19 % Rotamer: Outliers : 4.41 % Allowed : 21.48 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.11), residues: 5264 helix: 0.62 (0.09), residues: 2848 sheet: -2.36 (0.20), residues: 480 loop : -1.79 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 121 TYR 0.031 0.002 TYR O 91 PHE 0.007 0.001 PHE M 118 TRP 0.013 0.002 TRP W 188 HIS 0.008 0.001 HIS M 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (42456) covalent geometry : angle 0.68591 / 0.35 (57528) hydrogen bonds : bond 0.04373 / 2.92 ( 2627) hydrogen bonds : angle 4.85439 / 3.42 ( 7683) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 583 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8118 (pt) REVERT: A 259 ASN cc_start: 0.8161 (m110) cc_final: 0.7900 (m110) REVERT: A 302 ARG cc_start: 0.7779 (mtp-110) cc_final: 0.7037 (mtt90) REVERT: A 403 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8247 (tt) REVERT: A 461 MET cc_start: -0.0371 (ptm) cc_final: -0.1275 (mtm) REVERT: B 71 MET cc_start: 0.7394 (mmt) cc_final: 0.7136 (mmt) REVERT: B 259 ASN cc_start: 0.8035 (m-40) cc_final: 0.7539 (m-40) REVERT: B 339 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8155 (t) REVERT: B 448 THR cc_start: 0.7297 (p) cc_final: 0.7068 (p) REVERT: D 43 LEU cc_start: 0.8225 (pp) cc_final: 0.7833 (mp) REVERT: D 156 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8388 (p0) REVERT: E 171 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8133 (pt) REVERT: E 259 ASN cc_start: 0.8185 (m110) cc_final: 0.7932 (m110) REVERT: E 403 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8242 (tt) REVERT: G 210 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7628 (mmt) REVERT: I 71 MET cc_start: 0.7354 (mmt) cc_final: 0.7109 (mmt) REVERT: I 259 ASN cc_start: 0.8009 (m-40) cc_final: 0.7518 (m-40) REVERT: I 448 THR cc_start: 0.7300 (p) cc_final: 0.7061 (p) REVERT: K 210 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7603 (mmt) REVERT: L 43 LEU cc_start: 0.8245 (pp) cc_final: 0.7841 (mp) REVERT: L 156 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8379 (p0) REVERT: M 171 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8127 (pt) REVERT: M 259 ASN cc_start: 0.8187 (m110) cc_final: 0.7930 (m110) REVERT: M 403 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8249 (tt) REVERT: O 210 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7603 (mmt) REVERT: P 71 MET cc_start: 0.7400 (mmt) cc_final: 0.7142 (mmt) REVERT: P 84 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.5088 (ptt90) REVERT: P 259 ASN cc_start: 0.7862 (m-40) cc_final: 0.7576 (m-40) REVERT: R 43 LEU cc_start: 0.8253 (pp) cc_final: 0.7843 (mp) REVERT: R 156 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8396 (p0) REVERT: S 67 GLN cc_start: 0.8090 (tt0) cc_final: 0.7884 (tt0) REVERT: S 171 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8100 (pt) REVERT: S 259 ASN cc_start: 0.8185 (m110) cc_final: 0.7917 (m110) REVERT: S 403 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8252 (tt) REVERT: V 210 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7581 (mmt) REVERT: W 71 MET cc_start: 0.7409 (mmt) cc_final: 0.7170 (mmt) REVERT: W 259 ASN cc_start: 0.7878 (m-40) cc_final: 0.7591 (m-40) REVERT: W 339 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8182 (t) REVERT: Y 43 LEU cc_start: 0.8238 (pp) cc_final: 0.7838 (mp) REVERT: Y 156 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.8202 (p0) outliers start: 199 outliers final: 141 residues processed: 744 average time/residue: 0.2286 time to fit residues: 286.3603 Evaluate side-chains 686 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 526 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 266 SER Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 349 SER Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 403 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 156 ASN Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 349 SER Chi-restraints excluded: chain M residue 356 THR Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 429 ILE Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 210 MET Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 84 ARG Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 171 ILE Chi-restraints excluded: chain P residue 245 ASP Chi-restraints excluded: chain P residue 288 VAL Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 403 LEU Chi-restraints excluded: chain R residue 37 LEU Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 156 ASN Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 171 ILE Chi-restraints excluded: chain S residue 245 ASP Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 291 ILE Chi-restraints excluded: chain S residue 349 SER Chi-restraints excluded: chain S residue 356 THR Chi-restraints excluded: chain S residue 358 THR Chi-restraints excluded: chain S residue 403 LEU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 210 MET Chi-restraints excluded: chain V residue 234 LEU Chi-restraints excluded: chain V residue 248 VAL Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 147 VAL Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 171 ILE Chi-restraints excluded: chain W residue 245 ASP Chi-restraints excluded: chain W residue 288 VAL Chi-restraints excluded: chain W residue 291 ILE Chi-restraints excluded: chain W residue 339 VAL Chi-restraints excluded: chain W residue 349 SER Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 403 LEU Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain W residue 440 ASN Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 104 THR Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 156 ASN Chi-restraints excluded: chain Y residue 248 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 381 optimal weight: 0.9980 chunk 165 optimal weight: 0.5980 chunk 264 optimal weight: 2.9990 chunk 372 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 290 optimal weight: 0.9980 chunk 445 optimal weight: 0.0070 chunk 173 optimal weight: 1.9990 chunk 229 optimal weight: 0.5980 chunk 351 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN D 156 ASN D 159 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 GLN I 440 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 159 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 ASN L 159 GLN ** M 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 440 ASN ** O 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 159 GLN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 156 ASN R 159 GLN S 440 ASN ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 159 GLN W 440 ASN ** Y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 128 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.167519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.142772 restraints weight = 56696.253| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.53 r_work: 0.3648 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 42456 Z= 0.186 Angle : 0.691 12.520 57528 Z= 0.353 Chirality : 0.046 0.194 6648 Planarity : 0.006 0.101 7576 Dihedral : 5.797 35.699 5920 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.57 % Favored : 94.13 % Rotamer: Outliers : 5.14 % Allowed : 21.05 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.11), residues: 5264 helix: 0.70 (0.09), residues: 2848 sheet: -2.28 (0.20), residues: 480 loop : -1.79 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 93 TYR 0.035 0.002 TYR G 91 PHE 0.008 0.001 PHE A 118 TRP 0.010 0.002 TRP B 188 HIS 0.006 0.001 HIS E 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (42456) covalent geometry : angle 0.69070 / 0.35 (57528) hydrogen bonds : bond 0.04459 / 2.98 ( 2627) hydrogen bonds : angle 4.81959 / 3.39 ( 7683) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 500 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8063 (pt) REVERT: A 259 ASN cc_start: 0.8170 (m110) cc_final: 0.7903 (m110) REVERT: A 403 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8255 (tt) REVERT: B 71 MET cc_start: 0.7314 (mmt) cc_final: 0.7064 (mmt) REVERT: B 169 MET cc_start: 0.8636 (ptp) cc_final: 0.8281 (ptp) REVERT: B 259 ASN cc_start: 0.8048 (m-40) cc_final: 0.7562 (m-40) REVERT: B 318 TYR cc_start: 0.8367 (m-80) cc_final: 0.8100 (m-80) REVERT: B 339 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8179 (t) REVERT: D 43 LEU cc_start: 0.8315 (pp) cc_final: 0.7934 (mp) REVERT: E 171 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8023 (pt) REVERT: E 259 ASN cc_start: 0.8182 (m110) cc_final: 0.7917 (m110) REVERT: E 403 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8258 (tt) REVERT: E 461 MET cc_start: -0.0436 (ptm) cc_final: -0.1252 (mtm) REVERT: G 210 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7666 (mmt) REVERT: I 71 MET cc_start: 0.7302 (mmt) cc_final: 0.7049 (mmt) REVERT: I 259 ASN cc_start: 0.8057 (m-40) cc_final: 0.7569 (m-40) REVERT: K 210 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7673 (mmt) REVERT: L 43 LEU cc_start: 0.8329 (pp) cc_final: 0.7939 (mp) REVERT: M 171 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8014 (pt) REVERT: M 259 ASN cc_start: 0.8198 (m110) cc_final: 0.7930 (m110) REVERT: M 403 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8263 (tt) REVERT: M 461 MET cc_start: -0.0429 (ptm) cc_final: -0.1242 (mtm) REVERT: O 210 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7649 (mmt) REVERT: P 71 MET cc_start: 0.7346 (mmt) cc_final: 0.7084 (mmt) REVERT: P 173 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.6687 (p90) REVERT: P 259 ASN cc_start: 0.7840 (m-40) cc_final: 0.7568 (m-40) REVERT: P 318 TYR cc_start: 0.8517 (m-80) cc_final: 0.8174 (m-80) REVERT: R 43 LEU cc_start: 0.8328 (pp) cc_final: 0.7937 (mp) REVERT: S 171 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8032 (pt) REVERT: S 259 ASN cc_start: 0.8193 (m110) cc_final: 0.7919 (m110) REVERT: S 403 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8261 (tt) REVERT: S 461 MET cc_start: -0.0436 (ptm) cc_final: -0.1250 (mtm) REVERT: V 156 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8089 (p0) REVERT: V 210 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7660 (mmt) REVERT: W 71 MET cc_start: 0.7366 (mmt) cc_final: 0.7111 (mmt) REVERT: W 173 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.6697 (p90) REVERT: W 259 ASN cc_start: 0.7860 (m-40) cc_final: 0.7592 (m-40) REVERT: W 339 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8198 (t) REVERT: Y 43 LEU cc_start: 0.8245 (pp) cc_final: 0.7849 (mp) REVERT: Y 156 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.8197 (p0) outliers start: 232 outliers final: 182 residues processed: 693 average time/residue: 0.2366 time to fit residues: 279.3210 Evaluate side-chains 677 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 477 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 266 SER Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 349 SER Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 403 LEU Chi-restraints excluded: chain I residue 429 ILE Chi-restraints excluded: chain I residue 440 ASN Chi-restraints excluded: chain I residue 445 GLU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 230 VAL Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 349 SER Chi-restraints excluded: chain M residue 356 THR Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 429 ILE Chi-restraints excluded: chain M residue 440 ASN Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 210 MET Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 171 ILE Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 245 ASP Chi-restraints excluded: chain P residue 266 SER Chi-restraints excluded: chain P residue 288 VAL Chi-restraints excluded: chain P residue 291 ILE Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain P residue 356 THR Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 403 LEU Chi-restraints excluded: chain P residue 429 ILE Chi-restraints excluded: chain R residue 37 LEU Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 171 ILE Chi-restraints excluded: chain S residue 245 ASP Chi-restraints excluded: chain S residue 266 SER Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 291 ILE Chi-restraints excluded: chain S residue 349 SER Chi-restraints excluded: chain S residue 356 THR Chi-restraints excluded: chain S residue 358 THR Chi-restraints excluded: chain S residue 403 LEU Chi-restraints excluded: chain S residue 440 ASN Chi-restraints excluded: chain V residue 37 LEU Chi-restraints excluded: chain V residue 125 VAL Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 156 ASN Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 197 LEU Chi-restraints excluded: chain V residue 210 MET Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 234 LEU Chi-restraints excluded: chain V residue 248 VAL Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 100 LEU Chi-restraints excluded: chain W residue 147 VAL Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 171 ILE Chi-restraints excluded: chain W residue 173 PHE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 245 ASP Chi-restraints excluded: chain W residue 266 SER Chi-restraints excluded: chain W residue 288 VAL Chi-restraints excluded: chain W residue 291 ILE Chi-restraints excluded: chain W residue 339 VAL Chi-restraints excluded: chain W residue 349 SER Chi-restraints excluded: chain W residue 356 THR Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 403 LEU Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 104 THR Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 156 ASN Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 248 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 335 optimal weight: 7.9990 chunk 478 optimal weight: 0.5980 chunk 371 optimal weight: 1.9990 chunk 465 optimal weight: 2.9990 chunk 273 optimal weight: 0.9980 chunk 333 optimal weight: 7.9990 chunk 445 optimal weight: 0.9990 chunk 269 optimal weight: 6.9990 chunk 185 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 359 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 440 ASN K 86 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 GLN ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 GLN ** Y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.167376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.139485 restraints weight = 56140.145| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.78 r_work: 0.3596 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 42456 Z= 0.214 Angle : 0.704 12.640 57528 Z= 0.360 Chirality : 0.046 0.205 6648 Planarity : 0.006 0.099 7576 Dihedral : 5.828 34.397 5920 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.49 % Favored : 94.21 % Rotamer: Outliers : 5.43 % Allowed : 20.94 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.11), residues: 5264 helix: 0.70 (0.09), residues: 2848 sheet: -2.24 (0.20), residues: 480 loop : -1.81 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 302 TYR 0.038 0.002 TYR G 91 PHE 0.022 0.001 PHE M 173 TRP 0.011 0.002 TRP S 175 HIS 0.005 0.001 HIS E 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (42456) covalent geometry : angle 0.70401 / 0.36 (57528) hydrogen bonds : bond 0.04544 / 3.03 ( 2627) hydrogen bonds : angle 4.85336 / 3.41 ( 7683) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 487 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7819 (pt) REVERT: A 259 ASN cc_start: 0.8361 (m110) cc_final: 0.8006 (m110) REVERT: A 302 ARG cc_start: 0.7970 (mtp-110) cc_final: 0.6823 (mtt90) REVERT: A 403 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8205 (tt) REVERT: A 461 MET cc_start: 0.1146 (ptp) cc_final: 0.0457 (mtm) REVERT: B 169 MET cc_start: 0.8849 (ptp) cc_final: 0.8529 (ptp) REVERT: B 173 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6549 (p90) REVERT: B 259 ASN cc_start: 0.8206 (m-40) cc_final: 0.7554 (m-40) REVERT: B 318 TYR cc_start: 0.8500 (m-80) cc_final: 0.8153 (m-80) REVERT: B 448 THR cc_start: 0.7695 (p) cc_final: 0.7490 (p) REVERT: D 43 LEU cc_start: 0.8379 (pp) cc_final: 0.8009 (mp) REVERT: E 259 ASN cc_start: 0.8365 (m110) cc_final: 0.8007 (m110) REVERT: E 403 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8213 (tt) REVERT: G 156 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8263 (p0) REVERT: G 186 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.6407 (mtp-110) REVERT: G 210 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7893 (mmt) REVERT: I 169 MET cc_start: 0.8859 (ptp) cc_final: 0.8548 (ptp) REVERT: I 173 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6553 (p90) REVERT: I 259 ASN cc_start: 0.8211 (m-40) cc_final: 0.7558 (m-40) REVERT: I 448 THR cc_start: 0.7685 (p) cc_final: 0.7468 (p) REVERT: K 156 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8257 (p0) REVERT: K 210 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7906 (mmt) REVERT: L 43 LEU cc_start: 0.8373 (pp) cc_final: 0.7989 (mp) REVERT: M 259 ASN cc_start: 0.8360 (m110) cc_final: 0.8006 (m110) REVERT: M 403 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8194 (tt) REVERT: O 156 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8252 (p0) REVERT: O 186 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.6402 (mtp-110) REVERT: O 210 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7894 (mmt) REVERT: P 169 MET cc_start: 0.8825 (ptp) cc_final: 0.8483 (ptp) REVERT: P 173 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6648 (p90) REVERT: P 259 ASN cc_start: 0.7978 (m-40) cc_final: 0.7666 (m-40) REVERT: P 318 TYR cc_start: 0.8591 (m-80) cc_final: 0.8090 (m-80) REVERT: R 43 LEU cc_start: 0.8364 (pp) cc_final: 0.7980 (mp) REVERT: S 171 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7851 (pt) REVERT: S 259 ASN cc_start: 0.8363 (m110) cc_final: 0.8003 (m110) REVERT: S 403 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8189 (tt) REVERT: V 156 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8246 (p0) REVERT: V 186 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.6370 (mtp-110) REVERT: V 210 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7897 (mmt) REVERT: W 169 MET cc_start: 0.8838 (ptp) cc_final: 0.8525 (ptp) REVERT: W 173 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.6644 (p90) REVERT: W 259 ASN cc_start: 0.7983 (m-40) cc_final: 0.7679 (m-40) REVERT: W 339 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7898 (t) REVERT: Y 43 LEU cc_start: 0.8351 (pp) cc_final: 0.7964 (mp) REVERT: Y 156 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8340 (p0) REVERT: Y 196 GLN cc_start: 0.7974 (mp10) cc_final: 0.7770 (mp10) outliers start: 245 outliers final: 184 residues processed: 696 average time/residue: 0.2254 time to fit residues: 265.5749 Evaluate side-chains 690 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 483 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 186 ARG Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 173 PHE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 266 SER Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 349 SER Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 403 LEU Chi-restraints excluded: chain I residue 429 ILE Chi-restraints excluded: chain I residue 440 ASN Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 42 ARG Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 230 VAL Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 349 SER Chi-restraints excluded: chain M residue 356 THR Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 429 ILE Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 156 ASN Chi-restraints excluded: chain O residue 186 ARG Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 210 MET Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 171 ILE Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 245 ASP Chi-restraints excluded: chain P residue 266 SER Chi-restraints excluded: chain P residue 288 VAL Chi-restraints excluded: chain P residue 291 ILE Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain P residue 356 THR Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 403 LEU Chi-restraints excluded: chain P residue 429 ILE Chi-restraints excluded: chain R residue 37 LEU Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 171 ILE Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 245 ASP Chi-restraints excluded: chain S residue 266 SER Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 291 ILE Chi-restraints excluded: chain S residue 349 SER Chi-restraints excluded: chain S residue 356 THR Chi-restraints excluded: chain S residue 358 THR Chi-restraints excluded: chain S residue 403 LEU Chi-restraints excluded: chain S residue 429 ILE Chi-restraints excluded: chain V residue 37 LEU Chi-restraints excluded: chain V residue 125 VAL Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 156 ASN Chi-restraints excluded: chain V residue 186 ARG Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 210 MET Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 234 LEU Chi-restraints excluded: chain V residue 248 VAL Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 147 VAL Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 171 ILE Chi-restraints excluded: chain W residue 173 PHE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 245 ASP Chi-restraints excluded: chain W residue 266 SER Chi-restraints excluded: chain W residue 288 VAL Chi-restraints excluded: chain W residue 291 ILE Chi-restraints excluded: chain W residue 339 VAL Chi-restraints excluded: chain W residue 349 SER Chi-restraints excluded: chain W residue 356 THR Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 403 LEU Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 104 THR Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 143 VAL Chi-restraints excluded: chain Y residue 156 ASN Chi-restraints excluded: chain Y residue 212 ARG Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 347 optimal weight: 1.9990 chunk 335 optimal weight: 8.9990 chunk 297 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 272 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 332 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 476 optimal weight: 0.9990 chunk 315 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN E 440 ASN G 86 ASN G 196 GLN K 196 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 GLN M 440 ASN O 86 ASN O 196 GLN P 440 ASN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 GLN V 86 ASN V 196 GLN ** Y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.166363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.138321 restraints weight = 56191.458| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.76 r_work: 0.3590 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 42456 Z= 0.217 Angle : 0.712 12.713 57528 Z= 0.364 Chirality : 0.047 0.211 6648 Planarity : 0.006 0.098 7576 Dihedral : 5.869 32.802 5920 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.49 % Favored : 94.21 % Rotamer: Outliers : 5.03 % Allowed : 21.21 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.11), residues: 5264 helix: 0.69 (0.09), residues: 2848 sheet: -1.70 (0.22), residues: 400 loop : -1.88 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 212 TYR 0.039 0.002 TYR G 91 PHE 0.020 0.001 PHE E 173 TRP 0.013 0.002 TRP E 175 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (42456) covalent geometry : angle 0.71234 / 0.36 (57528) hydrogen bonds : bond 0.04600 / 3.08 ( 2627) hydrogen bonds : angle 4.87428 / 3.43 ( 7683) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10528 Ramachandran restraints generated. 5264 Oldfield, 0 Emsley, 5264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 508 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLU cc_start: 0.7339 (tm-30) cc_final: 0.7114 (tm-30) REVERT: A 171 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7691 (pt) REVERT: A 259 ASN cc_start: 0.8354 (m110) cc_final: 0.8125 (m110) REVERT: A 302 ARG cc_start: 0.7964 (mtp-110) cc_final: 0.6846 (mtt90) REVERT: A 403 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8192 (tt) REVERT: A 461 MET cc_start: 0.1037 (ptp) cc_final: 0.0572 (mtm) REVERT: B 169 MET cc_start: 0.8874 (ptp) cc_final: 0.8610 (ptp) REVERT: B 173 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6518 (p90) REVERT: B 318 TYR cc_start: 0.8491 (m-80) cc_final: 0.8186 (m-80) REVERT: B 448 THR cc_start: 0.7726 (p) cc_final: 0.7449 (p) REVERT: D 43 LEU cc_start: 0.8375 (pp) cc_final: 0.8032 (mp) REVERT: E 259 ASN cc_start: 0.8374 (m110) cc_final: 0.8141 (m110) REVERT: E 403 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8201 (tt) REVERT: E 461 MET cc_start: 0.1027 (ptp) cc_final: 0.0585 (mtm) REVERT: G 156 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8249 (p0) REVERT: G 186 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.6361 (mtp-110) REVERT: G 210 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7891 (mmt) REVERT: I 169 MET cc_start: 0.8861 (ptp) cc_final: 0.8602 (ptp) REVERT: I 173 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6537 (p90) REVERT: I 193 MET cc_start: 0.8417 (mmp) cc_final: 0.8157 (mmp) REVERT: I 318 TYR cc_start: 0.8409 (m-80) cc_final: 0.8137 (m-80) REVERT: I 448 THR cc_start: 0.7729 (p) cc_final: 0.7445 (p) REVERT: K 156 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8250 (p0) REVERT: K 210 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7890 (mmt) REVERT: L 43 LEU cc_start: 0.8380 (pp) cc_final: 0.8020 (mp) REVERT: M 259 ASN cc_start: 0.8341 (m110) cc_final: 0.8107 (m110) REVERT: M 403 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8172 (tt) REVERT: M 461 MET cc_start: 0.1043 (ptp) cc_final: 0.0592 (mtm) REVERT: O 156 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8234 (p0) REVERT: O 186 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.6359 (mtp-110) REVERT: O 210 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7882 (mmt) REVERT: P 169 MET cc_start: 0.8855 (ptp) cc_final: 0.8570 (ptp) REVERT: P 173 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6548 (p90) REVERT: P 193 MET cc_start: 0.8419 (mmp) cc_final: 0.8162 (mmp) REVERT: P 259 ASN cc_start: 0.7976 (m-40) cc_final: 0.7617 (m-40) REVERT: P 318 TYR cc_start: 0.8567 (m-80) cc_final: 0.8199 (m-80) REVERT: R 43 LEU cc_start: 0.8374 (pp) cc_final: 0.8018 (mp) REVERT: S 170 GLU cc_start: 0.7314 (tm-30) cc_final: 0.7106 (tm-30) REVERT: S 171 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7729 (pt) REVERT: S 259 ASN cc_start: 0.8360 (m110) cc_final: 0.8129 (m110) REVERT: S 403 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8177 (tt) REVERT: S 461 MET cc_start: 0.1035 (ptp) cc_final: 0.0582 (mtm) REVERT: V 156 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8231 (p0) REVERT: V 186 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.6355 (mtp-110) REVERT: V 210 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7876 (mmt) REVERT: W 169 MET cc_start: 0.8851 (ptp) cc_final: 0.8594 (ptp) REVERT: W 173 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6540 (p90) REVERT: W 193 MET cc_start: 0.8409 (mmp) cc_final: 0.8174 (mmp) REVERT: W 259 ASN cc_start: 0.7991 (m-40) cc_final: 0.7631 (m-40) REVERT: Y 43 LEU cc_start: 0.8372 (pp) cc_final: 0.8052 (mp) REVERT: Y 47 MET cc_start: 0.7241 (mmt) cc_final: 0.6889 (mmt) REVERT: Y 156 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8317 (p0) REVERT: Y 197 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7801 (tp) outliers start: 227 outliers final: 184 residues processed: 703 average time/residue: 0.2346 time to fit residues: 276.3885 Evaluate side-chains 688 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 481 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 186 ARG Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 173 PHE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 266 SER Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 349 SER Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 403 LEU Chi-restraints excluded: chain I residue 445 GLU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 42 ARG Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 230 VAL Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 349 SER Chi-restraints excluded: chain M residue 356 THR Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 429 ILE Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 156 ASN Chi-restraints excluded: chain O residue 186 ARG Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 210 MET Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 171 ILE Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 245 ASP Chi-restraints excluded: chain P residue 288 VAL Chi-restraints excluded: chain P residue 291 ILE Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain P residue 356 THR Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 403 LEU Chi-restraints excluded: chain P residue 429 ILE Chi-restraints excluded: chain P residue 440 ASN Chi-restraints excluded: chain R residue 37 LEU Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 171 ILE Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 245 ASP Chi-restraints excluded: chain S residue 266 SER Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 291 ILE Chi-restraints excluded: chain S residue 349 SER Chi-restraints excluded: chain S residue 356 THR Chi-restraints excluded: chain S residue 358 THR Chi-restraints excluded: chain S residue 403 LEU Chi-restraints excluded: chain S residue 429 ILE Chi-restraints excluded: chain V residue 37 LEU Chi-restraints excluded: chain V residue 125 VAL Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 156 ASN Chi-restraints excluded: chain V residue 186 ARG Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 210 MET Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 234 LEU Chi-restraints excluded: chain V residue 248 VAL Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 147 VAL Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 171 ILE Chi-restraints excluded: chain W residue 173 PHE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 245 ASP Chi-restraints excluded: chain W residue 288 VAL Chi-restraints excluded: chain W residue 291 ILE Chi-restraints excluded: chain W residue 349 SER Chi-restraints excluded: chain W residue 356 THR Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 403 LEU Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 104 THR Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain Y residue 143 VAL Chi-restraints excluded: chain Y residue 156 ASN Chi-restraints excluded: chain Y residue 197 LEU Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 351 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 457 optimal weight: 0.2980 chunk 275 optimal weight: 1.9990 chunk 416 optimal weight: 1.9990 chunk 497 optimal weight: 0.9990 chunk 382 optimal weight: 2.9990 chunk 308 optimal weight: 0.7980 chunk 511 optimal weight: 0.5980 chunk 297 optimal weight: 0.8980 chunk 386 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 259 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN E 259 ASN G 196 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 GLN M 259 ASN O 196 GLN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 259 ASN S 297 GLN V 196 GLN ** Y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.166889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.138651 restraints weight = 56358.051| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.77 r_work: 0.3591 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 42456 Z= 0.198 Angle : 0.707 12.684 57528 Z= 0.360 Chirality : 0.046 0.411 6648 Planarity : 0.007 0.094 7576 Dihedral : 5.842 32.087 5920 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.78 % Favored : 93.92 % Rotamer: Outliers : 4.79 % Allowed : 21.56 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.11), residues: 5264 helix: 0.69 (0.09), residues: 2848 sheet: -1.76 (0.22), residues: 400 loop : -1.88 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 48 TYR 0.038 0.002 TYR O 91 PHE 0.020 0.001 PHE E 173 TRP 0.012 0.002 TRP M 175 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (42456) covalent geometry : angle 0.70674 / 0.36 (57528) hydrogen bonds : bond 0.04539 / 3.03 ( 2627) hydrogen bonds : angle 4.85194 / 3.42 ( 7683) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13186.35 seconds wall clock time: 225 minutes 52.25 seconds (13552.25 seconds total)