Starting phenix.real_space_refine on Thu Mar 5 08:30:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nud_0516/03_2026/6nud_0516.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nud_0516/03_2026/6nud_0516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nud_0516/03_2026/6nud_0516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nud_0516/03_2026/6nud_0516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nud_0516/03_2026/6nud_0516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nud_0516/03_2026/6nud_0516.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 69 5.49 5 S 39 5.16 5 C 13003 2.51 5 N 3532 2.21 5 O 4188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20831 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "B" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "H" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 832 Classifications: {'RNA': 40} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 14, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 19} Chain: "I" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2352 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 283} Chain: "J" Number of atoms: 5997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5997 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 8, 'TRANS': 732} Chain breaks: 1 Chain: "M" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "U" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 602 Classifications: {'RNA': 28} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 5} Link IDs: {'rna2p': 6, 'rna3p': 21} Chain: "C" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1667 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "E" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1667 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "N" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1667 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "O" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1667 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "P" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1667 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.04, per 1000 atoms: 0.24 Number of scatterers: 20831 At special positions: 0 Unit cell: (93.28, 119.78, 212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 69 15.00 O 4188 8.00 N 3532 7.00 C 13003 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: 1.68 Conformation dependent library (CDL) restraints added in 1.0 seconds 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 26 sheets defined 33.7% alpha, 10.0% beta 2 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.760A pdb=" N LEU A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 47 removed outlier: 4.156A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 46 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 71 removed outlier: 3.579A pdb=" N TYR A 63 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 removed outlier: 4.038A pdb=" N LYS A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.884A pdb=" N ALA A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 91 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 94' Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.832A pdb=" N ARG A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU A 108 " --> pdb=" O CYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.709A pdb=" N TYR A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR A 117 " --> pdb=" O TYR A 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 20 removed outlier: 3.547A pdb=" N LEU B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 removed outlier: 4.153A pdb=" N CYS B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 46 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 removed outlier: 3.823A pdb=" N ARG B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 71 " --> pdb=" O GLN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 75 through 86 removed outlier: 4.087A pdb=" N LYS B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 removed outlier: 4.137A pdb=" N ALA B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 91 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 94' Processing helix chain 'B' and resid 96 through 107 removed outlier: 3.771A pdb=" N ARG B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.501A pdb=" N TYR B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 3.947A pdb=" N PHE I 33 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA I 35 " --> pdb=" O ARG I 31 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU I 36 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL I 37 " --> pdb=" O PHE I 33 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS I 42 " --> pdb=" O LEU I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 54 removed outlier: 3.875A pdb=" N LEU I 50 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA I 51 " --> pdb=" O ASP I 47 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU I 52 " --> pdb=" O ALA I 48 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 102 removed outlier: 3.922A pdb=" N ARG I 95 " --> pdb=" O LYS I 91 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS I 98 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU I 99 " --> pdb=" O ARG I 95 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER I 100 " --> pdb=" O GLN I 96 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS I 101 " --> pdb=" O ALA I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 118 removed outlier: 3.534A pdb=" N GLY I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU I 118 " --> pdb=" O TYR I 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 113 through 118' Processing helix chain 'I' and resid 165 through 169 Processing helix chain 'I' and resid 172 through 176 removed outlier: 3.564A pdb=" N TYR I 175 " --> pdb=" O SER I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 230 removed outlier: 3.663A pdb=" N GLU I 230 " --> pdb=" O GLU I 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 12 removed outlier: 3.575A pdb=" N PHE J 9 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR J 10 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA J 12 " --> pdb=" O LEU J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 25 removed outlier: 4.013A pdb=" N ILE J 21 " --> pdb=" O ILE J 17 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA J 24 " --> pdb=" O VAL J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 43 removed outlier: 4.187A pdb=" N GLY J 35 " --> pdb=" O HIS J 31 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP J 37 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU J 41 " --> pdb=" O ASP J 37 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE J 42 " --> pdb=" O TRP J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 54 removed outlier: 3.573A pdb=" N ASP J 50 " --> pdb=" O GLN J 46 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN J 51 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG J 53 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR J 54 " --> pdb=" O ASP J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 81 removed outlier: 3.570A pdb=" N ILE J 79 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER J 81 " --> pdb=" O ASP J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 114 Processing helix chain 'J' and resid 173 through 178 removed outlier: 3.840A pdb=" N GLU J 178 " --> pdb=" O LEU J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 184 removed outlier: 4.170A pdb=" N PHE J 183 " --> pdb=" O ILE J 180 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL J 184 " --> pdb=" O LEU J 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 180 through 184' Processing helix chain 'J' and resid 197 through 219 removed outlier: 3.857A pdb=" N ARG J 203 " --> pdb=" O ALA J 199 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA J 206 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA J 207 " --> pdb=" O ARG J 203 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE J 208 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU J 210 " --> pdb=" O ALA J 206 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR J 213 " --> pdb=" O ALA J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 231 through 238 removed outlier: 3.829A pdb=" N GLU J 237 " --> pdb=" O SER J 233 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU J 238 " --> pdb=" O ALA J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 290 removed outlier: 4.175A pdb=" N LEU J 274 " --> pdb=" O ARG J 270 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP J 275 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE J 276 " --> pdb=" O LEU J 272 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET J 277 " --> pdb=" O TYR J 273 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER J 278 " --> pdb=" O LEU J 274 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU J 279 " --> pdb=" O ASP J 275 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE J 281 " --> pdb=" O MET J 277 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA J 282 " --> pdb=" O SER J 278 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU J 285 " --> pdb=" O ILE J 281 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU J 286 " --> pdb=" O ALA J 282 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY J 290 " --> pdb=" O LEU J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 296 removed outlier: 4.333A pdb=" N ASN J 295 " --> pdb=" O ASN J 292 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU J 296 " --> pdb=" O ARG J 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 292 through 296' Processing helix chain 'J' and resid 312 through 326 removed outlier: 4.123A pdb=" N GLU J 316 " --> pdb=" O GLU J 312 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR J 317 " --> pdb=" O LYS J 313 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU J 318 " --> pdb=" O THR J 314 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL J 319 " --> pdb=" O VAL J 315 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS J 323 " --> pdb=" O VAL J 319 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN J 326 " --> pdb=" O GLU J 322 " (cutoff:3.500A) Processing helix chain 'J' and resid 347 through 351 removed outlier: 3.673A pdb=" N ASP J 350 " --> pdb=" O ALA J 347 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE J 351 " --> pdb=" O ALA J 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 347 through 351' Processing helix chain 'J' and resid 357 through 367 removed outlier: 4.177A pdb=" N TYR J 361 " --> pdb=" O SER J 357 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE J 364 " --> pdb=" O SER J 360 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR J 365 " --> pdb=" O TYR J 361 " (cutoff:3.500A) Processing helix chain 'J' and resid 371 through 376 Processing helix chain 'J' and resid 384 through 388 Processing helix chain 'J' and resid 420 through 428 removed outlier: 4.278A pdb=" N TYR J 424 " --> pdb=" O CYS J 420 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN J 425 " --> pdb=" O ARG J 421 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS J 428 " --> pdb=" O TYR J 424 " (cutoff:3.500A) Processing helix chain 'J' and resid 539 through 552 removed outlier: 3.572A pdb=" N SER J 543 " --> pdb=" O THR J 539 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET J 550 " --> pdb=" O PHE J 546 " (cutoff:3.500A) Processing helix chain 'J' and resid 555 through 561 removed outlier: 3.908A pdb=" N ASN J 559 " --> pdb=" O LYS J 555 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN J 560 " --> pdb=" O VAL J 556 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 601 removed outlier: 3.824A pdb=" N ILE J 586 " --> pdb=" O SER J 582 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE J 587 " --> pdb=" O TRP J 583 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ALA J 588 " --> pdb=" O GLN J 584 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL J 591 " --> pdb=" O ILE J 587 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG J 594 " --> pdb=" O THR J 590 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN J 595 " --> pdb=" O VAL J 591 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN J 596 " --> pdb=" O GLU J 592 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE J 597 " --> pdb=" O LEU J 593 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS J 599 " --> pdb=" O GLN J 595 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 627 removed outlier: 4.304A pdb=" N HIS J 625 " --> pdb=" O SER J 621 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR J 627 " --> pdb=" O MET J 623 " (cutoff:3.500A) Processing helix chain 'J' and resid 628 through 634 removed outlier: 3.830A pdb=" N GLU J 632 " --> pdb=" O GLY J 628 " (cutoff:3.500A) Processing helix chain 'J' and resid 635 through 637 No H-bonds generated for 'chain 'J' and resid 635 through 637' Processing helix chain 'J' and resid 654 through 659 Processing helix chain 'J' and resid 662 through 667 removed outlier: 3.621A pdb=" N GLU J 666 " --> pdb=" O ASP J 662 " (cutoff:3.500A) Processing helix chain 'J' and resid 672 through 676 Processing helix chain 'J' and resid 679 through 682 Processing helix chain 'J' and resid 683 through 690 removed outlier: 3.557A pdb=" N ILE J 687 " --> pdb=" O ILE J 683 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU J 690 " --> pdb=" O LEU J 686 " (cutoff:3.500A) Processing helix chain 'J' and resid 696 through 708 removed outlier: 3.502A pdb=" N VAL J 701 " --> pdb=" O GLU J 697 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA J 702 " --> pdb=" O LYS J 698 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU J 704 " --> pdb=" O ASN J 700 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR J 706 " --> pdb=" O ALA J 702 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR J 707 " --> pdb=" O ARG J 703 " (cutoff:3.500A) Processing helix chain 'J' and resid 709 through 714 removed outlier: 4.302A pdb=" N GLU J 713 " --> pdb=" O THR J 709 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU J 714 " --> pdb=" O ARG J 710 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 709 through 714' Processing helix chain 'J' and resid 719 through 722 removed outlier: 3.527A pdb=" N LYS J 722 " --> pdb=" O GLU J 719 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 719 through 722' Processing helix chain 'J' and resid 723 through 733 removed outlier: 3.668A pdb=" N LEU J 729 " --> pdb=" O GLN J 725 " (cutoff:3.500A) Processing helix chain 'J' and resid 740 through 755 removed outlier: 3.804A pdb=" N ALA J 744 " --> pdb=" O ASP J 740 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR J 751 " --> pdb=" O ALA J 747 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL J 752 " --> pdb=" O LEU J 748 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR J 753 " --> pdb=" O LEU J 749 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE J 755 " --> pdb=" O TYR J 751 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 20 removed outlier: 3.516A pdb=" N LEU M 19 " --> pdb=" O ARG M 15 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU M 20 " --> pdb=" O ALA M 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 15 through 20' Processing helix chain 'M' and resid 39 through 50 removed outlier: 3.764A pdb=" N SER M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER M 44 " --> pdb=" O SER M 40 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR M 46 " --> pdb=" O CYS M 42 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP M 47 " --> pdb=" O SER M 43 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG M 48 " --> pdb=" O SER M 44 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS M 50 " --> pdb=" O TYR M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 71 removed outlier: 4.125A pdb=" N SER M 62 " --> pdb=" O ILE M 58 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG M 65 " --> pdb=" O VAL M 61 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL M 66 " --> pdb=" O SER M 62 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN M 67 " --> pdb=" O TYR M 63 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE M 68 " --> pdb=" O LEU M 64 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL M 69 " --> pdb=" O ARG M 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN M 71 " --> pdb=" O GLN M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 86 removed outlier: 3.991A pdb=" N LYS M 79 " --> pdb=" O GLU M 75 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP M 80 " --> pdb=" O ILE M 76 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU M 81 " --> pdb=" O ALA M 77 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS M 84 " --> pdb=" O ASP M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 94 removed outlier: 4.145A pdb=" N ALA M 90 " --> pdb=" O GLN M 86 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU M 91 " --> pdb=" O ILE M 87 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS M 92 " --> pdb=" O LEU M 88 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU M 93 " --> pdb=" O GLU M 89 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 86 through 94' Processing helix chain 'M' and resid 96 through 108 removed outlier: 3.769A pdb=" N ARG M 102 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE M 103 " --> pdb=" O THR M 99 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG M 105 " --> pdb=" O GLN M 101 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU M 108 " --> pdb=" O CYS M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 113 Processing helix chain 'C' and resid 50 through 61 removed outlier: 3.636A pdb=" N GLY C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 55 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 110 removed outlier: 3.834A pdb=" N ASP C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 179 removed outlier: 3.591A pdb=" N PHE C 167 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 61 removed outlier: 3.629A pdb=" N LYS E 55 " --> pdb=" O SER E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 84 removed outlier: 3.861A pdb=" N PHE E 83 " --> pdb=" O LEU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 110 removed outlier: 4.275A pdb=" N ASP E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 163 through 178 removed outlier: 3.742A pdb=" N LYS E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 61 removed outlier: 3.666A pdb=" N LYS N 53 " --> pdb=" O GLY N 49 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG N 57 " --> pdb=" O LYS N 53 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR N 58 " --> pdb=" O GLY N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.531A pdb=" N LEU N 82 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 79 through 83' Processing helix chain 'N' and resid 105 through 113 removed outlier: 4.166A pdb=" N ASP N 110 " --> pdb=" O ALA N 106 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N SER N 111 " --> pdb=" O ASP N 107 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU N 112 " --> pdb=" O GLU N 108 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY N 113 " --> pdb=" O LEU N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 179 removed outlier: 3.922A pdb=" N LYS N 168 " --> pdb=" O GLU N 164 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL N 169 " --> pdb=" O GLU N 165 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU N 178 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU N 179 " --> pdb=" O LYS N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 189 removed outlier: 4.250A pdb=" N ARG N 188 " --> pdb=" O SER N 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 61 removed outlier: 3.608A pdb=" N GLY O 54 " --> pdb=" O SER O 50 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS O 55 " --> pdb=" O SER O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 84 removed outlier: 3.977A pdb=" N PHE O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 110 removed outlier: 4.449A pdb=" N ASP O 110 " --> pdb=" O ALA O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 113 No H-bonds generated for 'chain 'O' and resid 111 through 113' Processing helix chain 'O' and resid 162 through 178 removed outlier: 4.532A pdb=" N LYS O 168 " --> pdb=" O GLU O 164 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL O 169 " --> pdb=" O GLU O 165 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU O 178 " --> pdb=" O LEU O 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 61 removed outlier: 3.661A pdb=" N LYS P 53 " --> pdb=" O GLY P 49 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET P 56 " --> pdb=" O LEU P 52 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR P 58 " --> pdb=" O GLY P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 84 removed outlier: 3.756A pdb=" N PHE P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 110 removed outlier: 4.585A pdb=" N ASP P 110 " --> pdb=" O ALA P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 113 No H-bonds generated for 'chain 'P' and resid 111 through 113' Processing helix chain 'P' and resid 162 through 178 removed outlier: 3.708A pdb=" N LYS P 168 " --> pdb=" O GLU P 164 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL P 169 " --> pdb=" O GLU P 165 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU P 178 " --> pdb=" O LEU P 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 189 removed outlier: 4.450A pdb=" N ARG P 188 " --> pdb=" O SER P 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 5 through 6 removed outlier: 4.258A pdb=" N PHE I 64 " --> pdb=" O TYR I 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 72 through 73 Processing sheet with id=AA3, first strand: chain 'I' and resid 129 through 132 removed outlier: 3.607A pdb=" N ASP I 129 " --> pdb=" O THR I 147 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL I 145 " --> pdb=" O VAL I 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 204 through 205 removed outlier: 3.726A pdb=" N PHE I 294 " --> pdb=" O THR I 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 303 through 307 removed outlier: 4.465A pdb=" N ALA J 304 " --> pdb=" O PHE J 246 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE J 246 " --> pdb=" O ALA J 304 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA J 340 " --> pdb=" O ASP J 247 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR J 338 " --> pdb=" O SER J 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 303 through 307 removed outlier: 4.465A pdb=" N ALA J 304 " --> pdb=" O PHE J 246 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE J 246 " --> pdb=" O ALA J 304 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE J 241 " --> pdb=" O PHE J 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 434 through 436 removed outlier: 4.315A pdb=" N HIS J 434 " --> pdb=" O VAL J 454 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 568 through 570 removed outlier: 3.745A pdb=" N SER J 568 " --> pdb=" O ILE J 580 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE J 580 " --> pdb=" O SER J 568 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL J 514 " --> pdb=" O ALA J 579 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY J 581 " --> pdb=" O ALA J 512 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA J 512 " --> pdb=" O GLY J 581 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU J 511 " --> pdb=" O PHE J 614 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE J 614 " --> pdb=" O LEU J 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 517 through 518 Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 97 removed outlier: 7.781A pdb=" N LYS C 5 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N THR C 202 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LYS C 7 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA C 200 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER C 9 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU C 198 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 119 through 122 Processing sheet with id=AB3, first strand: chain 'E' and resid 96 through 97 Processing sheet with id=AB4, first strand: chain 'E' and resid 96 through 97 Processing sheet with id=AB5, first strand: chain 'E' and resid 119 through 122 Processing sheet with id=AB6, first strand: chain 'E' and resid 125 through 126 removed outlier: 4.071A pdb=" N THR E 125 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA E 133 " --> pdb=" O THR E 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'N' and resid 96 through 97 removed outlier: 3.503A pdb=" N ILE N 152 " --> pdb=" O ILE N 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 148 through 149 removed outlier: 3.518A pdb=" N PHE N 149 " --> pdb=" O ALA N 10 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA N 10 " --> pdb=" O PHE N 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 119 through 122 Processing sheet with id=AC1, first strand: chain 'N' and resid 125 through 126 removed outlier: 3.517A pdb=" N THR N 125 " --> pdb=" O ALA N 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 148 through 154 Processing sheet with id=AC3, first strand: chain 'O' and resid 148 through 154 Processing sheet with id=AC4, first strand: chain 'O' and resid 118 through 122 Processing sheet with id=AC5, first strand: chain 'P' and resid 96 through 97 Processing sheet with id=AC6, first strand: chain 'P' and resid 96 through 97 Processing sheet with id=AC7, first strand: chain 'P' and resid 119 through 122 removed outlier: 3.531A pdb=" N LYS P 121 " --> pdb=" O ILE P 138 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 125 through 126 removed outlier: 4.356A pdb=" N THR P 125 " --> pdb=" O ALA P 133 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA P 133 " --> pdb=" O THR P 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 380 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5978 1.33 - 1.45: 3663 1.45 - 1.57: 11494 1.57 - 1.69: 137 1.69 - 1.81: 66 Bond restraints: 21338 Sorted by residual: bond pdb=" C4 ATP J 801 " pdb=" C5 ATP J 801 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C5 ATP J 801 " pdb=" C6 ATP J 801 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" C8 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.29e+01 bond pdb=" C5 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.387 1.345 0.042 1.00e-02 1.00e+04 1.74e+01 bond pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 1.374 1.335 0.039 1.00e-02 1.00e+04 1.51e+01 ... (remaining 21333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 29013 3.79 - 7.58: 22 7.58 - 11.38: 3 11.38 - 15.17: 0 15.17 - 18.96: 2 Bond angle restraints: 29040 Sorted by residual: angle pdb=" PB ATP J 801 " pdb=" O3B ATP J 801 " pdb=" PG ATP J 801 " ideal model delta sigma weight residual 139.87 120.91 18.96 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PA ATP J 801 " pdb=" O3A ATP J 801 " pdb=" PB ATP J 801 " ideal model delta sigma weight residual 136.83 120.59 16.24 1.00e+00 1.00e+00 2.64e+02 angle pdb=" C5 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N3 ATP J 801 " ideal model delta sigma weight residual 126.80 118.63 8.17 1.00e+00 1.00e+00 6.67e+01 angle pdb=" N3 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 127.04 135.06 -8.02 1.15e+00 7.59e-01 4.88e+01 angle pdb=" N VAL O 63 " pdb=" CA VAL O 63 " pdb=" C VAL O 63 " ideal model delta sigma weight residual 113.71 108.94 4.77 9.50e-01 1.11e+00 2.52e+01 ... (remaining 29035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 12728 35.48 - 70.97: 213 70.97 - 106.45: 17 106.45 - 141.94: 0 141.94 - 177.42: 13 Dihedral angle restraints: 12971 sinusoidal: 5914 harmonic: 7057 Sorted by residual: dihedral pdb=" O4' U U 21 " pdb=" C1' U U 21 " pdb=" N1 U U 21 " pdb=" C2 U U 21 " ideal model delta sinusoidal sigma weight residual 200.00 50.16 149.84 1 1.50e+01 4.44e-03 7.96e+01 dihedral pdb=" O4' C H 17 " pdb=" C1' C H 17 " pdb=" N1 C H 17 " pdb=" C2 C H 17 " ideal model delta sinusoidal sigma weight residual 200.00 54.59 145.41 1 1.50e+01 4.44e-03 7.78e+01 dihedral pdb=" O4' U U 14 " pdb=" C1' U U 14 " pdb=" N1 U U 14 " pdb=" C2 U U 14 " ideal model delta sinusoidal sigma weight residual 200.00 54.64 145.36 1 1.50e+01 4.44e-03 7.78e+01 ... (remaining 12968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2099 0.028 - 0.056: 881 0.056 - 0.084: 153 0.084 - 0.112: 106 0.112 - 0.140: 24 Chirality restraints: 3263 Sorted by residual: chirality pdb=" CB ILE J 755 " pdb=" CA ILE J 755 " pdb=" CG1 ILE J 755 " pdb=" CG2 ILE J 755 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE N 32 " pdb=" N ILE N 32 " pdb=" C ILE N 32 " pdb=" CB ILE N 32 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" C1' C H 40 " pdb=" O4' C H 40 " pdb=" C2' C H 40 " pdb=" N1 C H 40 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 3260 not shown) Planarity restraints: 3491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE I 196 " -0.015 5.00e-02 4.00e+02 2.30e-02 8.44e-01 pdb=" N PRO I 197 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO I 197 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO I 197 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 71 " -0.014 5.00e-02 4.00e+02 2.09e-02 6.99e-01 pdb=" N PRO E 72 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO E 72 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO E 72 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE O 44 " 0.014 5.00e-02 4.00e+02 2.09e-02 6.96e-01 pdb=" N PRO O 45 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO O 45 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO O 45 " 0.012 5.00e-02 4.00e+02 ... (remaining 3488 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6116 2.81 - 3.33: 17470 3.33 - 3.86: 31472 3.86 - 4.38: 35916 4.38 - 4.90: 61996 Nonbonded interactions: 152970 Sorted by model distance: nonbonded pdb=" O HIS I 233 " pdb=" OG SER I 264 " model vdw 2.290 3.040 nonbonded pdb=" OE2 GLU N 123 " pdb=" OH TYR N 190 " model vdw 2.313 3.040 nonbonded pdb=" O2' G U 20 " pdb=" O2 U U 21 " model vdw 2.315 3.040 nonbonded pdb=" O2' A U 23 " pdb=" OD1 ASN N 134 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR I 130 " pdb=" O VAL I 145 " model vdw 2.322 3.040 ... (remaining 152965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.150 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4507 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 : 0.002 0.083 21338 Z= 0.130 Angle : 0.430 18.961 29040 Z= 0.290 Chirality : 0.035 0.140 3263 Planarity : 0.002 0.023 3491 Dihedral : 13.139 177.424 8427 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 1.54 % Allowed : 14.97 % Favored : 83.49 % Rotamer: Outliers : 0.29 % Allowed : 5.67 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.22 (0.12), residues: 2398 helix: -4.63 (0.08), residues: 528 sheet: -2.72 (0.24), residues: 339 loop : -3.39 (0.12), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 182 TYR 0.005 0.000 TYR J 473 PHE 0.004 0.000 PHE J 246 TRP 0.003 0.000 TRP J 733 HIS 0.001 0.000 HIS I 233 Details of bonding type rmsd covalent geometry : bond 0.00165 (21338) covalent geometry : angle 0.42988 (29040) hydrogen bonds : bond 0.34333 ( 360) hydrogen bonds : angle 10.71875 ( 1060) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 737 time to evaluate : 0.747 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 70 TYR cc_start: 0.2704 (t80) cc_final: 0.2452 (t80) REVERT: J 251 ILE cc_start: 0.7504 (mt) cc_final: 0.7259 (mt) outliers start: 6 outliers final: 0 residues processed: 741 average time/residue: 0.1755 time to fit residues: 191.8235 Evaluate side-chains 320 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.0170 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN I 12 ASN ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 ASN I 284 HIS ** I 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 ASN J 129 ASN ** J 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 ASN J 412 HIS J 489 GLN J 502 ASN J 534 ASN J 559 ASN J 560 GLN J 602 ASN J 700 ASN M 27 ASN C 85 ASN C 105 ASN C 144 ASN E 85 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN N 11 GLN N 213 ASN O 105 ASN O 213 ASN P 85 ASN P 105 ASN ** P 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN P 213 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.196497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.167959 restraints weight = 45833.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.171911 restraints weight = 25310.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.174562 restraints weight = 16945.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.176287 restraints weight = 12823.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.177367 restraints weight = 10591.863| |-----------------------------------------------------------------------------| r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 21338 Z= 0.151 Angle : 0.653 12.844 29040 Z= 0.330 Chirality : 0.042 0.232 3263 Planarity : 0.004 0.048 3491 Dihedral : 14.850 179.964 3681 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.68 % Favored : 89.20 % Rotamer: Outliers : 3.17 % Allowed : 14.76 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.14), residues: 2398 helix: -3.14 (0.15), residues: 582 sheet: -2.17 (0.27), residues: 300 loop : -2.99 (0.13), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 95 TYR 0.033 0.002 TYR J 468 PHE 0.029 0.002 PHE C 102 TRP 0.016 0.002 TRP J 38 HIS 0.005 0.001 HIS J 482 Details of bonding type rmsd covalent geometry : bond 0.00328 (21338) covalent geometry : angle 0.65304 (29040) hydrogen bonds : bond 0.04333 ( 360) hydrogen bonds : angle 5.79764 ( 1060) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 386 time to evaluate : 0.756 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 86 GLN cc_start: 0.7047 (pt0) cc_final: 0.6564 (mp10) REVERT: J 266 GLN cc_start: 0.7960 (pp30) cc_final: 0.7692 (pp30) REVERT: J 561 PHE cc_start: 0.4744 (m-10) cc_final: 0.4361 (m-80) REVERT: C 92 LYS cc_start: 0.5563 (OUTLIER) cc_final: 0.5327 (mmtt) REVERT: E 134 ASN cc_start: 0.7189 (t0) cc_final: 0.6874 (t0) REVERT: E 150 GLU cc_start: 0.6126 (mp0) cc_final: 0.5899 (mp0) REVERT: N 125 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7883 (m) REVERT: O 85 ASN cc_start: 0.8195 (t0) cc_final: 0.7933 (m-40) REVERT: O 144 ASN cc_start: 0.7784 (m-40) cc_final: 0.7469 (m-40) REVERT: P 103 LEU cc_start: 0.6705 (tt) cc_final: 0.4890 (tt) outliers start: 66 outliers final: 28 residues processed: 433 average time/residue: 0.1466 time to fit residues: 99.0495 Evaluate side-chains 305 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 275 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 202 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 237 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 168 optimal weight: 0.4980 chunk 167 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 ASN J 292 ASN J 303 HIS J 389 ASN J 434 HIS J 532 GLN J 536 GLN J 584 GLN J 602 ASN J 675 GLN J 725 GLN C 105 ASN E 11 GLN P 65 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.179905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.148266 restraints weight = 44003.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.151510 restraints weight = 25994.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.153669 restraints weight = 16113.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.154090 restraints weight = 13666.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.154352 restraints weight = 12424.348| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21338 Z= 0.177 Angle : 0.682 9.157 29040 Z= 0.347 Chirality : 0.044 0.188 3263 Planarity : 0.005 0.067 3491 Dihedral : 15.179 179.420 3681 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.97 % Favored : 89.99 % Rotamer: Outliers : 4.23 % Allowed : 15.43 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.15), residues: 2398 helix: -2.31 (0.17), residues: 640 sheet: -1.81 (0.28), residues: 299 loop : -2.79 (0.14), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 203 TYR 0.034 0.002 TYR A 106 PHE 0.026 0.002 PHE P 98 TRP 0.010 0.002 TRP J 600 HIS 0.008 0.002 HIS I 246 Details of bonding type rmsd covalent geometry : bond 0.00397 (21338) covalent geometry : angle 0.68204 (29040) hydrogen bonds : bond 0.03594 ( 360) hydrogen bonds : angle 5.10110 ( 1060) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 300 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7543 (ttp-170) cc_final: 0.7313 (ttm170) REVERT: A 70 TYR cc_start: 0.4675 (t80) cc_final: 0.4383 (t80) REVERT: A 71 GLN cc_start: 0.7902 (mm110) cc_final: 0.7541 (mm110) REVERT: B 35 ILE cc_start: 0.5141 (tp) cc_final: 0.4904 (tp) REVERT: B 106 TYR cc_start: 0.6927 (t80) cc_final: 0.5852 (m-10) REVERT: I 8 MET cc_start: 0.8158 (ptt) cc_final: 0.7783 (ptt) REVERT: J 266 GLN cc_start: 0.8233 (pp30) cc_final: 0.7494 (pp30) REVERT: J 489 GLN cc_start: 0.7052 (mm110) cc_final: 0.6792 (mp10) REVERT: J 516 LEU cc_start: 0.8443 (tt) cc_final: 0.8145 (mt) REVERT: J 571 TYR cc_start: 0.7404 (t80) cc_final: 0.6977 (t80) REVERT: J 602 ASN cc_start: 0.6626 (OUTLIER) cc_final: 0.6205 (t0) REVERT: M 45 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7141 (tt) REVERT: C 143 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7606 (mmm-85) REVERT: E 134 ASN cc_start: 0.7456 (t0) cc_final: 0.7167 (t0) REVERT: N 181 TYR cc_start: 0.8345 (p90) cc_final: 0.8032 (p90) outliers start: 88 outliers final: 46 residues processed: 368 average time/residue: 0.1561 time to fit residues: 88.7867 Evaluate side-chains 276 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 227 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 217 GLU Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 371 MET Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 454 VAL Chi-restraints excluded: chain J residue 482 HIS Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 532 GLN Chi-restraints excluded: chain J residue 541 SER Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 602 ASN Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 202 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 49 optimal weight: 4.9990 chunk 230 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 96 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 4 optimal weight: 0.2980 chunk 60 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 14 HIS ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 HIS J 532 GLN J 602 ASN C 105 ASN C 124 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.173079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.140170 restraints weight = 44219.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.143578 restraints weight = 23660.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.145797 restraints weight = 15956.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.147244 restraints weight = 12389.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.148079 restraints weight = 10479.296| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.7424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21338 Z= 0.161 Angle : 0.623 8.918 29040 Z= 0.318 Chirality : 0.042 0.179 3263 Planarity : 0.004 0.054 3491 Dihedral : 15.300 178.720 3681 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 3.85 % Allowed : 17.16 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.15), residues: 2398 helix: -1.79 (0.19), residues: 668 sheet: -1.66 (0.28), residues: 297 loop : -2.68 (0.14), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 293 TYR 0.019 0.002 TYR P 207 PHE 0.023 0.002 PHE P 98 TRP 0.007 0.001 TRP J 343 HIS 0.010 0.001 HIS J 434 Details of bonding type rmsd covalent geometry : bond 0.00353 (21338) covalent geometry : angle 0.62259 (29040) hydrogen bonds : bond 0.03075 ( 360) hydrogen bonds : angle 4.85165 ( 1060) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 270 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7919 (mm110) cc_final: 0.7700 (mm110) REVERT: A 74 ARG cc_start: 0.5211 (tmt-80) cc_final: 0.4887 (tmt-80) REVERT: B 42 CYS cc_start: 0.6792 (OUTLIER) cc_final: 0.5621 (t) REVERT: B 43 SER cc_start: 0.7825 (p) cc_final: 0.7403 (t) REVERT: I 8 MET cc_start: 0.8528 (ptt) cc_final: 0.8142 (ptt) REVERT: I 244 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: J 516 LEU cc_start: 0.8357 (tt) cc_final: 0.8111 (mp) REVERT: J 571 TYR cc_start: 0.7818 (t80) cc_final: 0.7308 (t80) REVERT: J 602 ASN cc_start: 0.7173 (OUTLIER) cc_final: 0.6557 (t0) REVERT: J 623 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.6499 (tmm) REVERT: M 88 LEU cc_start: 0.8175 (mt) cc_final: 0.7609 (pt) REVERT: C 143 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7443 (mmm-85) REVERT: E 134 ASN cc_start: 0.7714 (t0) cc_final: 0.7385 (t0) REVERT: N 171 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6311 (ptm160) REVERT: N 181 TYR cc_start: 0.8617 (p90) cc_final: 0.8142 (p90) REVERT: O 209 VAL cc_start: 0.8237 (t) cc_final: 0.7921 (m) outliers start: 80 outliers final: 51 residues processed: 329 average time/residue: 0.1510 time to fit residues: 77.6553 Evaluate side-chains 279 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 222 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 244 PHE Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 371 MET Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 454 VAL Chi-restraints excluded: chain J residue 482 HIS Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 541 SER Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 592 GLU Chi-restraints excluded: chain J residue 602 ASN Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 90 ARG Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 202 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 17 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 chunk 222 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 150 optimal weight: 0.0670 chunk 178 optimal weight: 4.9990 chunk 155 optimal weight: 0.0870 chunk 183 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 12 ASN ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 GLN J 602 ASN J 626 GLN J 700 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.171304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.139521 restraints weight = 44732.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.142653 restraints weight = 26445.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.143782 restraints weight = 16535.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.144645 restraints weight = 14386.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.144836 restraints weight = 13320.856| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.7694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21338 Z= 0.111 Angle : 0.570 10.712 29040 Z= 0.286 Chirality : 0.040 0.161 3263 Planarity : 0.003 0.047 3491 Dihedral : 15.239 179.387 3681 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.22 % Allowed : 19.18 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.16), residues: 2398 helix: -1.36 (0.20), residues: 661 sheet: -1.40 (0.29), residues: 297 loop : -2.47 (0.14), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 140 TYR 0.024 0.001 TYR J 298 PHE 0.026 0.001 PHE A 103 TRP 0.007 0.001 TRP J 101 HIS 0.007 0.001 HIS J 434 Details of bonding type rmsd covalent geometry : bond 0.00242 (21338) covalent geometry : angle 0.56973 (29040) hydrogen bonds : bond 0.02678 ( 360) hydrogen bonds : angle 4.55721 ( 1060) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 251 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7654 (ttp-170) cc_final: 0.7391 (ttm170) REVERT: A 70 TYR cc_start: 0.5864 (t80) cc_final: 0.5478 (t80) REVERT: A 74 ARG cc_start: 0.5244 (tmt-80) cc_final: 0.4842 (tmt-80) REVERT: B 42 CYS cc_start: 0.6688 (p) cc_final: 0.5696 (t) REVERT: B 43 SER cc_start: 0.7796 (p) cc_final: 0.7467 (t) REVERT: B 107 MET cc_start: 0.8360 (ppp) cc_final: 0.7933 (ppp) REVERT: I 8 MET cc_start: 0.8439 (ptt) cc_final: 0.8088 (ptt) REVERT: I 244 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: J 571 TYR cc_start: 0.7750 (t80) cc_final: 0.7282 (t80) REVERT: J 590 THR cc_start: 0.8966 (m) cc_final: 0.8740 (p) REVERT: J 623 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.6558 (tmm) REVERT: M 88 LEU cc_start: 0.8146 (mt) cc_final: 0.7593 (pt) REVERT: C 143 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7509 (mmm-85) REVERT: E 134 ASN cc_start: 0.7621 (t0) cc_final: 0.7351 (t0) REVERT: N 171 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6363 (ptm160) REVERT: N 181 TYR cc_start: 0.8451 (p90) cc_final: 0.8003 (p90) REVERT: O 81 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8396 (ptt-90) REVERT: O 199 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8230 (pptt) REVERT: O 209 VAL cc_start: 0.8306 (t) cc_final: 0.8046 (m) outliers start: 67 outliers final: 46 residues processed: 302 average time/residue: 0.1352 time to fit residues: 64.8650 Evaluate side-chains 271 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 219 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 244 PHE Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 371 MET Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 438 THR Chi-restraints excluded: chain J residue 454 VAL Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 749 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 223 optimal weight: 7.9990 chunk 55 optimal weight: 0.3980 chunk 33 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 184 optimal weight: 0.2980 chunk 152 optimal weight: 2.9990 chunk 155 optimal weight: 0.0980 chunk 192 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.158504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.128488 restraints weight = 41443.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.131894 restraints weight = 22565.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.134102 restraints weight = 15331.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.135538 restraints weight = 11948.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.136351 restraints weight = 10168.814| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.8118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21338 Z= 0.117 Angle : 0.570 9.776 29040 Z= 0.286 Chirality : 0.040 0.162 3263 Planarity : 0.003 0.042 3491 Dihedral : 15.288 179.186 3681 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 3.80 % Allowed : 19.04 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.16), residues: 2398 helix: -1.03 (0.20), residues: 661 sheet: -1.47 (0.29), residues: 313 loop : -2.32 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 28 TYR 0.029 0.001 TYR J 298 PHE 0.028 0.001 PHE J 9 TRP 0.006 0.001 TRP J 101 HIS 0.007 0.001 HIS J 434 Details of bonding type rmsd covalent geometry : bond 0.00259 (21338) covalent geometry : angle 0.56976 (29040) hydrogen bonds : bond 0.02648 ( 360) hydrogen bonds : angle 4.35110 ( 1060) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 242 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7567 (ttp-170) cc_final: 0.7338 (ttm170) REVERT: A 74 ARG cc_start: 0.5118 (tmt-80) cc_final: 0.4656 (tmt-80) REVERT: B 42 CYS cc_start: 0.6706 (OUTLIER) cc_final: 0.5756 (t) REVERT: B 43 SER cc_start: 0.7737 (p) cc_final: 0.7404 (t) REVERT: B 107 MET cc_start: 0.8290 (ppp) cc_final: 0.7875 (ppp) REVERT: I 8 MET cc_start: 0.8576 (ptt) cc_final: 0.8273 (ptt) REVERT: I 95 ARG cc_start: 0.6709 (mmt-90) cc_final: 0.6456 (mmp-170) REVERT: J 554 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7889 (t80) REVERT: J 571 TYR cc_start: 0.7868 (t80) cc_final: 0.7254 (t80) REVERT: J 623 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.6532 (tmm) REVERT: J 728 LYS cc_start: 0.8076 (ptpt) cc_final: 0.7778 (pptt) REVERT: M 88 LEU cc_start: 0.8150 (mt) cc_final: 0.7635 (pt) REVERT: C 143 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7268 (mmm-85) REVERT: N 171 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6558 (ptm160) REVERT: N 181 TYR cc_start: 0.8551 (p90) cc_final: 0.8140 (p90) REVERT: O 199 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8230 (pptt) outliers start: 79 outliers final: 51 residues processed: 303 average time/residue: 0.1352 time to fit residues: 65.3368 Evaluate side-chains 270 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 213 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 371 MET Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 482 HIS Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 749 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 20 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 211 optimal weight: 4.9990 chunk 225 optimal weight: 20.0000 chunk 204 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 82 optimal weight: 0.4980 chunk 133 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 461 GLN C 124 ASN E 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.155485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.124767 restraints weight = 42881.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.127899 restraints weight = 24417.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.129940 restraints weight = 17232.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.131298 restraints weight = 13800.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.132083 restraints weight = 11935.620| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.8680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21338 Z= 0.138 Angle : 0.597 10.212 29040 Z= 0.300 Chirality : 0.042 0.171 3263 Planarity : 0.003 0.043 3491 Dihedral : 15.452 178.536 3681 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 3.94 % Allowed : 19.62 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.16), residues: 2398 helix: -0.68 (0.21), residues: 626 sheet: -1.42 (0.28), residues: 322 loop : -2.10 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 756 TYR 0.031 0.001 TYR J 298 PHE 0.025 0.001 PHE O 102 TRP 0.006 0.001 TRP J 101 HIS 0.007 0.001 HIS J 434 Details of bonding type rmsd covalent geometry : bond 0.00309 (21338) covalent geometry : angle 0.59730 (29040) hydrogen bonds : bond 0.02798 ( 360) hydrogen bonds : angle 4.41146 ( 1060) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 232 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 SER cc_start: 0.9013 (t) cc_final: 0.8764 (p) REVERT: A 48 ARG cc_start: 0.7167 (tmm-80) cc_final: 0.6764 (tmm-80) REVERT: A 70 TYR cc_start: 0.4738 (t80) cc_final: 0.4363 (t80) REVERT: A 71 GLN cc_start: 0.8486 (mm110) cc_final: 0.8044 (mm110) REVERT: B 42 CYS cc_start: 0.6661 (OUTLIER) cc_final: 0.5693 (t) REVERT: B 107 MET cc_start: 0.8263 (ppp) cc_final: 0.7862 (ppp) REVERT: I 8 MET cc_start: 0.8637 (ptt) cc_final: 0.8410 (ptt) REVERT: J 487 ASP cc_start: 0.4530 (t0) cc_final: 0.4070 (t0) REVERT: J 554 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7943 (t80) REVERT: J 571 TYR cc_start: 0.7889 (t80) cc_final: 0.7271 (t80) REVERT: J 623 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.6622 (tmm) REVERT: J 728 LYS cc_start: 0.8129 (ptpt) cc_final: 0.7857 (pptt) REVERT: C 143 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7287 (mmm-85) REVERT: N 171 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6553 (ptm160) REVERT: O 199 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8235 (pptt) outliers start: 82 outliers final: 57 residues processed: 300 average time/residue: 0.1458 time to fit residues: 67.9791 Evaluate side-chains 269 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 206 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 371 MET Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 482 HIS Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 657 ILE Chi-restraints excluded: chain J residue 749 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 2 optimal weight: 0.0980 chunk 48 optimal weight: 0.0570 chunk 70 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 189 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 67 GLN ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 GLN ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 471 ASN ** J 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 HIS ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.150908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.120083 restraints weight = 42319.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.123129 restraints weight = 24405.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.125117 restraints weight = 17398.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.126434 restraints weight = 14020.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.127287 restraints weight = 12164.946| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.9316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21338 Z= 0.175 Angle : 0.651 9.918 29040 Z= 0.330 Chirality : 0.043 0.163 3263 Planarity : 0.004 0.050 3491 Dihedral : 15.630 176.248 3681 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 3.80 % Allowed : 20.34 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.31 (0.16), residues: 2398 helix: -0.68 (0.20), residues: 657 sheet: -1.20 (0.33), residues: 253 loop : -2.09 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 57 TYR 0.037 0.002 TYR J 298 PHE 0.023 0.002 PHE A 114 TRP 0.018 0.002 TRP J 343 HIS 0.008 0.001 HIS J 434 Details of bonding type rmsd covalent geometry : bond 0.00395 (21338) covalent geometry : angle 0.65129 (29040) hydrogen bonds : bond 0.03090 ( 360) hydrogen bonds : angle 4.58549 ( 1060) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 222 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 SER cc_start: 0.9125 (t) cc_final: 0.8901 (p) REVERT: B 42 CYS cc_start: 0.6766 (OUTLIER) cc_final: 0.5859 (t) REVERT: B 47 ASP cc_start: 0.7416 (p0) cc_final: 0.7179 (m-30) REVERT: B 107 MET cc_start: 0.8239 (ppp) cc_final: 0.7815 (ppp) REVERT: I 8 MET cc_start: 0.8701 (ptt) cc_final: 0.8483 (ptt) REVERT: J 56 MET cc_start: 0.5872 (pmm) cc_final: 0.5553 (tpt) REVERT: J 554 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7981 (t80) REVERT: J 571 TYR cc_start: 0.8054 (t80) cc_final: 0.7460 (t80) REVERT: J 576 ASP cc_start: 0.7226 (t0) cc_final: 0.6864 (t0) REVERT: J 623 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.6641 (tmm) REVERT: J 716 ASP cc_start: 0.5869 (t70) cc_final: 0.5543 (t0) REVERT: J 728 LYS cc_start: 0.8131 (ptpt) cc_final: 0.7917 (pptt) REVERT: M 88 LEU cc_start: 0.8099 (mp) cc_final: 0.7864 (pt) REVERT: C 143 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7481 (mmm-85) REVERT: N 151 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8107 (tp) REVERT: N 171 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6503 (ptm160) outliers start: 79 outliers final: 59 residues processed: 288 average time/residue: 0.1481 time to fit residues: 66.9105 Evaluate side-chains 266 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 201 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 244 PHE Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 247 ASP Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 371 MET Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 482 HIS Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 592 GLU Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 193 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 53 optimal weight: 0.5980 chunk 167 optimal weight: 0.0170 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 16 optimal weight: 0.0060 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 135 GLN ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 725 GLN C 124 ASN ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.155456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.124872 restraints weight = 42258.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.128261 restraints weight = 23205.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.130408 restraints weight = 16006.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.131794 restraints weight = 12645.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.132607 restraints weight = 10864.434| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.9263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 21338 Z= 0.103 Angle : 0.598 9.576 29040 Z= 0.297 Chirality : 0.041 0.159 3263 Planarity : 0.003 0.053 3491 Dihedral : 15.491 179.812 3681 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.26 % Allowed : 22.16 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.17), residues: 2398 helix: -0.55 (0.20), residues: 672 sheet: -1.20 (0.30), residues: 307 loop : -2.03 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 720 TYR 0.027 0.001 TYR J 298 PHE 0.026 0.001 PHE A 114 TRP 0.009 0.001 TRP J 101 HIS 0.005 0.001 HIS J 31 Details of bonding type rmsd covalent geometry : bond 0.00225 (21338) covalent geometry : angle 0.59815 (29040) hydrogen bonds : bond 0.02503 ( 360) hydrogen bonds : angle 4.35419 ( 1060) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 CYS cc_start: 0.6722 (OUTLIER) cc_final: 0.5903 (t) REVERT: B 107 MET cc_start: 0.8226 (ppp) cc_final: 0.7860 (ppp) REVERT: J 8 LEU cc_start: 0.8633 (tp) cc_final: 0.8405 (tp) REVERT: J 56 MET cc_start: 0.5924 (pmm) cc_final: 0.5707 (tpt) REVERT: J 101 TRP cc_start: 0.5220 (p90) cc_final: 0.4302 (m-10) REVERT: J 382 TYR cc_start: 0.6109 (t80) cc_final: 0.5867 (t80) REVERT: J 554 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7811 (t80) REVERT: J 571 TYR cc_start: 0.7962 (t80) cc_final: 0.7416 (t80) REVERT: J 623 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.6622 (tmm) REVERT: J 671 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.6017 (t80) REVERT: M 36 ARG cc_start: 0.4469 (mmt180) cc_final: 0.4224 (mmt180) REVERT: C 124 ASN cc_start: 0.7107 (OUTLIER) cc_final: 0.6903 (m-40) REVERT: C 143 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7117 (mmm-85) REVERT: C 167 PHE cc_start: 0.8860 (m-80) cc_final: 0.8317 (m-80) REVERT: N 137 GLN cc_start: 0.7176 (tt0) cc_final: 0.6917 (mt0) REVERT: N 171 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6344 (ptm160) REVERT: N 181 TYR cc_start: 0.8473 (p90) cc_final: 0.8102 (p90) REVERT: O 81 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8209 (ptt-90) REVERT: O 119 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6886 (pt0) outliers start: 47 outliers final: 32 residues processed: 263 average time/residue: 0.1595 time to fit residues: 65.6022 Evaluate side-chains 244 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 244 PHE Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 371 MET Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 592 GLU Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 657 ILE Chi-restraints excluded: chain J residue 671 PHE Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain P residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 41 optimal weight: 0.9980 chunk 232 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 206 optimal weight: 0.0570 chunk 203 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.154389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.123764 restraints weight = 42373.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.127025 restraints weight = 23287.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.129194 restraints weight = 16180.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.130589 restraints weight = 12803.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.131505 restraints weight = 10984.127| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.9389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21338 Z= 0.115 Angle : 0.610 12.042 29040 Z= 0.302 Chirality : 0.041 0.269 3263 Planarity : 0.003 0.053 3491 Dihedral : 15.497 179.999 3681 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 2.31 % Allowed : 22.26 % Favored : 75.43 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.17), residues: 2398 helix: -0.40 (0.21), residues: 642 sheet: -1.16 (0.30), residues: 309 loop : -1.88 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 95 TYR 0.030 0.001 TYR J 298 PHE 0.025 0.001 PHE A 114 TRP 0.009 0.001 TRP J 343 HIS 0.005 0.001 HIS J 31 Details of bonding type rmsd covalent geometry : bond 0.00258 (21338) covalent geometry : angle 0.61003 (29040) hydrogen bonds : bond 0.02544 ( 360) hydrogen bonds : angle 4.31350 ( 1060) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 201 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 CYS cc_start: 0.6738 (OUTLIER) cc_final: 0.5915 (t) REVERT: B 107 MET cc_start: 0.8237 (ppp) cc_final: 0.7861 (ppp) REVERT: J 56 MET cc_start: 0.5828 (pmm) cc_final: 0.5616 (tpt) REVERT: J 101 TRP cc_start: 0.5338 (p90) cc_final: 0.4433 (m-10) REVERT: J 386 MET cc_start: 0.7594 (mpp) cc_final: 0.7170 (mpp) REVERT: J 554 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7806 (t80) REVERT: J 571 TYR cc_start: 0.7975 (t80) cc_final: 0.7462 (t80) REVERT: J 623 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.6490 (tmm) REVERT: J 671 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.6141 (t80) REVERT: M 36 ARG cc_start: 0.4594 (mmt180) cc_final: 0.4316 (mmt180) REVERT: C 143 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7114 (mmm-85) REVERT: N 181 TYR cc_start: 0.8511 (p90) cc_final: 0.8080 (p90) REVERT: O 119 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6860 (pt0) REVERT: O 199 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8201 (pptt) REVERT: P 38 LYS cc_start: 0.5754 (tmtt) cc_final: 0.4931 (tmtt) REVERT: P 132 GLU cc_start: 0.6896 (tm-30) cc_final: 0.4746 (pt0) outliers start: 48 outliers final: 36 residues processed: 242 average time/residue: 0.1549 time to fit residues: 58.9563 Evaluate side-chains 234 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 244 PHE Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 371 MET Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 592 GLU Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 657 ILE Chi-restraints excluded: chain J residue 671 PHE Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 58 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 196 optimal weight: 3.9990 chunk 180 optimal weight: 0.1980 chunk 99 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.150542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.119581 restraints weight = 42393.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.122833 restraints weight = 23526.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.124930 restraints weight = 16353.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.126219 restraints weight = 12996.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.127021 restraints weight = 11267.476| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.9775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21338 Z= 0.153 Angle : 0.656 10.143 29040 Z= 0.327 Chirality : 0.043 0.244 3263 Planarity : 0.004 0.052 3491 Dihedral : 15.637 177.569 3681 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 2.55 % Allowed : 22.55 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.17), residues: 2398 helix: -0.58 (0.20), residues: 678 sheet: -1.20 (0.30), residues: 301 loop : -1.91 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 95 TYR 0.025 0.001 TYR J 298 PHE 0.026 0.002 PHE C 167 TRP 0.012 0.002 TRP J 343 HIS 0.005 0.001 HIS J 31 Details of bonding type rmsd covalent geometry : bond 0.00347 (21338) covalent geometry : angle 0.65639 (29040) hydrogen bonds : bond 0.02913 ( 360) hydrogen bonds : angle 4.43875 ( 1060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3907.92 seconds wall clock time: 68 minutes 16.81 seconds (4096.81 seconds total)