Starting phenix.real_space_refine on Sun Sep 13 04:18:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nud_0516/09_2026/6nud_0516.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nud_0516/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6nud_0516/09_2026/6nud_0516.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nud_0516/09_2026/6nud_0516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nud_0516/09_2026/6nud_0516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nud_0516/09_2026/6nud_0516.map" model { file = "/net/cci-nas-00/data/ceres_data/6nud_0516/09_2026/6nud_0516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nud_0516/09_2026/6nud_0516.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 40} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 14, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 19} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: {'RNAv2': 28} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 5} Link IDs: {'rna2p': 6, 'rna3p': 21} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 4.62, per 1000 atoms: 0.22 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: 1.63 Conformation dependent library (CDL) restraints added in 904.7 milliseconds 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: 2.27 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: 3.46 Time building geometry restraints manager: 2.22 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: 28959 3.79 - 7.58: 76 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 - 34.02: 12449 34.02 - 68.05: 256 68.05 - 102.07: 41 102.07 - 136.09: 0 136.09 - 170.11: 2 Dihedral angle restraints: 12748 sinusoidal: 5691 harmonic: 7057 Sorted by residual: dihedral pdb=" C4' G H 13 " pdb=" C3' G H 13 " pdb=" C2' G H 13 " pdb=" C1' G H 13 " ideal model delta sinusoidal sigma weight residual 36.34 -35.92 72.26 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" C4' U H 21 " pdb=" C3' U H 21 " pdb=" C2' U H 21 " pdb=" C1' U H 21 " ideal model delta sinusoidal sigma weight residual 36.35 -35.83 72.17 1 3.10e+00 1.04e-01 6.93e+02 dihedral pdb=" C4' U H 9 " pdb=" C3' U H 9 " pdb=" C2' U H 9 " pdb=" C1' U H 9 " ideal model delta sinusoidal sigma weight residual 36.35 -35.78 72.13 1 3.10e+00 1.04e-01 6.92e+02 ... (remaining 12745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2870 0.057 - 0.114: 257 0.114 - 0.171: 18 0.171 - 0.228: 1 0.228 - 0.285: 117 Chirality restraints: 3263 Sorted by residual: chirality pdb=" P A U 26 " pdb=" OP1 A U 26 " pdb=" OP2 A U 26 " pdb=" O5' A U 26 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" P G H 13 " pdb=" OP1 G H 13 " pdb=" OP2 G H 13 " pdb=" O5' G H 13 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C2' U H 28 " pdb=" C3' U H 28 " pdb=" O2' U H 28 " pdb=" C1' U H 28 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (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: 4.170 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.240 Find NCS groups from input model: 0.240 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4591 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= 0.136 Angle : 0.539 18.961 29040 Z= 0.314 Chirality : 0.059 0.285 3263 Planarity : 0.002 0.023 3491 Dihedral : 12.693 170.115 8204 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/Z covalent geometry : bond 0.00185 / 0.14 (21338) covalent geometry : angle 0.53903 / 0.31 (29040) hydrogen bonds : bond 0.34333 / 21.69 ( 360) hydrogen bonds : angle 10.71875 / 7.28 ( 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 : 0.814 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: 0.1731 time to fit residues: 189.8009 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 : 0.726 ------------------------------------------------------------------------------- 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: 3.9990 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: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN B 27 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 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 ASN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 602 ASN J 675 GLN 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 213 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.190742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.161966 restraints weight = 45556.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.165653 restraints weight = 25424.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 78)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.168114 restraints weight = 17123.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.169678 restraints weight = 13121.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.170817 restraints weight = 10990.486| |-----------------------------------------------------------------------------| r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.4948 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= 0.201 Angle : 0.976 18.205 29040 Z= 0.432 Chirality : 0.076 1.184 3263 Planarity : 0.005 0.050 3491 Dihedral : 11.392 168.410 3458 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.55 % Favored : 89.37 % Rotamer: Outliers : 3.51 % Allowed : 14.23 % Favored : 82.26 % 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: -4.29 (0.14), residues: 2398 helix: -3.21 (0.15), residues: 605 sheet: -2.50 (0.26), residues: 326 loop : -2.89 (0.13), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 390 TYR 0.028 0.002 TYR J 468 PHE 0.030 0.002 PHE C 102 TRP 0.016 0.002 TRP J 38 HIS 0.007 0.001 HIS J 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (21338) covalent geometry : angle 0.97649 / 0.43 (29040) hydrogen bonds : bond 0.03888 / 2.45 ( 360) hydrogen bonds : angle 5.74609 / 3.80 ( 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 458 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 385 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7203 (pt0) cc_final: 0.6728 (mp10) REVERT: A 88 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7624 (mt) REVERT: J 243 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8150 (tt) REVERT: J 266 GLN cc_start: 0.7996 (pp30) cc_final: 0.7698 (pp30) REVERT: J 602 ASN cc_start: 0.6393 (OUTLIER) cc_final: 0.5609 (t0) REVERT: J 639 LYS cc_start: 0.6684 (mtmt) cc_final: 0.6311 (mttm) REVERT: C 92 LYS cc_start: 0.5618 (OUTLIER) cc_final: 0.5399 (mmtt) REVERT: C 124 ASN cc_start: 0.7382 (p0) cc_final: 0.7073 (t0) REVERT: C 196 GLU cc_start: 0.7213 (tt0) cc_final: 0.6765 (tt0) REVERT: E 118 THR cc_start: 0.8259 (p) cc_final: 0.7854 (t) REVERT: E 124 ASN cc_start: 0.8187 (p0) cc_final: 0.7960 (p0) REVERT: E 134 ASN cc_start: 0.7392 (t0) cc_final: 0.7022 (t0) REVERT: E 150 GLU cc_start: 0.6358 (mp0) cc_final: 0.6149 (mp0) REVERT: N 178 GLU cc_start: 0.7426 (pt0) cc_final: 0.7201 (pt0) REVERT: N 181 TYR cc_start: 0.8163 (p90) cc_final: 0.7927 (p90) REVERT: O 85 ASN cc_start: 0.8399 (t0) cc_final: 0.8137 (m-40) REVERT: P 103 LEU cc_start: 0.6719 (tt) cc_final: 0.4900 (tt) outliers start: 73 outliers final: 34 residues processed: 438 average time/residue: 0.1434 time to fit residues: 98.2900 Evaluate side-chains 314 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 276 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain I residue 60 LEU 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 243 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 434 HIS Chi-restraints excluded: chain J residue 454 VAL 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 J residue 541 SER Chi-restraints excluded: chain J residue 549 SER 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 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 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 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 201 THR 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: 0.5980 chunk 42 optimal weight: 0.0060 chunk 39 optimal weight: 0.9980 chunk 168 optimal weight: 0.6980 chunk 167 optimal weight: 8.9990 chunk 172 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 ASN J 292 ASN J 303 HIS J 389 ASN J 532 GLN ** J 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 584 GLN J 602 ASN J 725 GLN C 105 ASN E 11 GLN O 159 ASN P 65 ASN ** P 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.182529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.151244 restraints weight = 45371.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.154855 restraints weight = 25532.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.157262 restraints weight = 17490.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.158851 restraints weight = 13614.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.159851 restraints weight = 11489.332| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.6133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21338 Z= 0.143 Angle : 0.747 11.957 29040 Z= 0.343 Chirality : 0.061 0.750 3263 Planarity : 0.004 0.042 3491 Dihedral : 11.499 163.042 3458 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.76 % Favored : 90.20 % Rotamer: Outliers : 3.65 % Allowed : 16.06 % Favored : 80.29 % 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: -3.63 (0.15), residues: 2398 helix: -2.27 (0.18), residues: 625 sheet: -1.76 (0.29), residues: 290 loop : -2.75 (0.14), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 121 TYR 0.017 0.001 TYR J 488 PHE 0.021 0.002 PHE J 554 TRP 0.007 0.001 TRP J 38 HIS 0.007 0.001 HIS J 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (21338) covalent geometry : angle 0.74694 / 0.34 (29040) hydrogen bonds : bond 0.03514 / 2.26 ( 360) hydrogen bonds : angle 4.89047 / 3.22 ( 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 376 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 300 time to evaluate : 0.788 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: A 65 ARG cc_start: 0.7516 (ttp-170) cc_final: 0.7284 (ttp-170) REVERT: A 84 LYS cc_start: 0.6442 (OUTLIER) cc_final: 0.5236 (ptmt) REVERT: A 86 GLN cc_start: 0.7356 (pt0) cc_final: 0.6870 (mp10) REVERT: A 103 PHE cc_start: 0.8788 (t80) cc_final: 0.8575 (t80) REVERT: B 35 ILE cc_start: 0.4923 (tp) cc_final: 0.4580 (tp) REVERT: J 266 GLN cc_start: 0.8139 (pp30) cc_final: 0.7576 (pp30) REVERT: J 489 GLN cc_start: 0.6956 (mm110) cc_final: 0.6693 (mp10) REVERT: J 602 ASN cc_start: 0.6454 (OUTLIER) cc_final: 0.6031 (t0) REVERT: M 88 LEU cc_start: 0.7989 (mt) cc_final: 0.7494 (pt) REVERT: C 124 ASN cc_start: 0.7645 (p0) cc_final: 0.7381 (m-40) REVERT: E 81 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7544 (pmt100) REVERT: E 118 THR cc_start: 0.8440 (p) cc_final: 0.8001 (t) REVERT: E 124 ASN cc_start: 0.8155 (p0) cc_final: 0.7776 (p0) REVERT: E 134 ASN cc_start: 0.7832 (t0) cc_final: 0.7352 (t0) REVERT: E 150 GLU cc_start: 0.6475 (mp0) cc_final: 0.6266 (mp0) REVERT: N 181 TYR cc_start: 0.8334 (p90) cc_final: 0.8038 (p90) REVERT: N 198 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7909 (tp) REVERT: P 108 GLU cc_start: 0.5992 (OUTLIER) cc_final: 0.5718 (pm20) outliers start: 76 outliers final: 44 residues processed: 356 average time/residue: 0.1435 time to fit residues: 81.1720 Evaluate side-chains 297 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 248 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 111 VAL 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 60 LEU Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 217 GLU Chi-restraints excluded: chain J residue 242 LEU 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 384 THR Chi-restraints excluded: chain J residue 409 VAL 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 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 532 GLN Chi-restraints excluded: chain J residue 541 SER Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 602 ASN 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 E residue 12 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 81 ARG 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 47 ILE Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain P residue 108 GLU Chi-restraints excluded: chain P residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 49 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 226 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 146 optimal weight: 0.0970 chunk 70 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 60 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 12 ASN ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 602 ASN C 105 ASN E 162 GLN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN P 206 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.181135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.150000 restraints weight = 45505.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.153575 restraints weight = 25296.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.155964 restraints weight = 17240.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.157539 restraints weight = 13366.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.158621 restraints weight = 11250.730| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.6568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21338 Z= 0.109 Angle : 0.678 10.027 29040 Z= 0.311 Chirality : 0.056 0.620 3263 Planarity : 0.003 0.048 3491 Dihedral : 11.234 161.935 3458 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.67 % Favored : 91.28 % Rotamer: Outliers : 2.93 % Allowed : 17.98 % Favored : 79.09 % 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: -3.19 (0.15), residues: 2398 helix: -1.76 (0.19), residues: 633 sheet: -1.62 (0.28), residues: 308 loop : -2.50 (0.14), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 182 TYR 0.021 0.001 TYR P 207 PHE 0.027 0.001 PHE J 9 TRP 0.007 0.001 TRP J 101 HIS 0.005 0.001 HIS J 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (21338) covalent geometry : angle 0.67835 / 0.31 (29040) hydrogen bonds : bond 0.02940 / 1.89 ( 360) hydrogen bonds : angle 4.57566 / 3.02 ( 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 325 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 264 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7489 (ttp-170) cc_final: 0.7261 (ttp-170) REVERT: A 84 LYS cc_start: 0.6568 (OUTLIER) cc_final: 0.5433 (ptmt) REVERT: A 86 GLN cc_start: 0.7424 (pt0) cc_final: 0.6943 (mp10) REVERT: B 42 CYS cc_start: 0.6937 (OUTLIER) cc_final: 0.5799 (t) REVERT: B 43 SER cc_start: 0.7763 (p) cc_final: 0.7342 (t) REVERT: J 266 GLN cc_start: 0.8152 (pp30) cc_final: 0.7486 (pp30) REVERT: J 623 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.6699 (tmm) REVERT: J 639 LYS cc_start: 0.6464 (mttp) cc_final: 0.6095 (mttm) REVERT: M 88 LEU cc_start: 0.8083 (mt) cc_final: 0.7540 (pt) REVERT: E 118 THR cc_start: 0.8460 (p) cc_final: 0.8076 (t) REVERT: E 124 ASN cc_start: 0.8140 (p0) cc_final: 0.7828 (p0) REVERT: E 134 ASN cc_start: 0.7816 (t0) cc_final: 0.7366 (t0) REVERT: N 181 TYR cc_start: 0.8341 (p90) cc_final: 0.8042 (p90) REVERT: N 198 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7907 (tp) outliers start: 61 outliers final: 36 residues processed: 309 average time/residue: 0.1467 time to fit residues: 72.6634 Evaluate side-chains 274 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 111 VAL 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 28 SER Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 217 GLU Chi-restraints excluded: chain J residue 311 THR 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 438 THR 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 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 E residue 12 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 206 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 17 optimal weight: 0.3980 chunk 201 optimal weight: 1.9990 chunk 222 optimal weight: 0.0000 chunk 42 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 183 optimal weight: 20.0000 chunk 51 optimal weight: 0.0570 chunk 86 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 overall best weight: 0.6504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 12 ASN ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 532 GLN J 536 GLN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.176243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.146041 restraints weight = 45413.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.149197 restraints weight = 26052.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.151262 restraints weight = 16439.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.151805 restraints weight = 13964.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.152505 restraints weight = 12325.384| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.6975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21338 Z= 0.108 Angle : 0.654 9.748 29040 Z= 0.300 Chirality : 0.054 0.549 3263 Planarity : 0.003 0.044 3491 Dihedral : 11.271 162.993 3458 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 2.88 % Allowed : 18.85 % Favored : 78.27 % 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: -1.43 (0.20), residues: 633 sheet: -1.64 (0.29), residues: 313 loop : -2.36 (0.14), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 95 TYR 0.024 0.001 TYR J 706 PHE 0.027 0.001 PHE A 103 TRP 0.008 0.001 TRP J 101 HIS 0.005 0.001 HIS J 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (21338) covalent geometry : angle 0.65372 / 0.30 (29040) hydrogen bonds : bond 0.02902 / 1.91 ( 360) hydrogen bonds : angle 4.40595 / 2.90 ( 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: 60 poor density : 258 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.6498 (OUTLIER) cc_final: 0.5367 (ptmt) REVERT: A 86 GLN cc_start: 0.7485 (pt0) cc_final: 0.6871 (mp10) REVERT: A 88 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7446 (mt) REVERT: B 42 CYS cc_start: 0.6961 (p) cc_final: 0.5954 (t) REVERT: B 43 SER cc_start: 0.7835 (p) cc_final: 0.7451 (t) REVERT: B 107 MET cc_start: 0.8387 (ppp) cc_final: 0.7965 (ppp) REVERT: J 266 GLN cc_start: 0.8246 (pp30) cc_final: 0.7475 (pp30) REVERT: J 623 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.6629 (tmm) REVERT: M 88 LEU cc_start: 0.8111 (mt) cc_final: 0.7557 (pt) REVERT: E 34 SER cc_start: 0.8656 (m) cc_final: 0.8083 (p) REVERT: E 118 THR cc_start: 0.8471 (p) cc_final: 0.8057 (t) REVERT: E 124 ASN cc_start: 0.8185 (p0) cc_final: 0.7806 (p0) REVERT: E 134 ASN cc_start: 0.7860 (t0) cc_final: 0.7393 (t0) REVERT: N 122 PHE cc_start: 0.7535 (m-80) cc_final: 0.7331 (m-80) REVERT: N 181 TYR cc_start: 0.8369 (p90) cc_final: 0.8060 (p90) REVERT: N 198 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7949 (tp) REVERT: O 81 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8189 (ptt-90) REVERT: O 209 VAL cc_start: 0.7961 (t) cc_final: 0.7621 (m) REVERT: P 119 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5821 (tp30) outliers start: 60 outliers final: 35 residues processed: 301 average time/residue: 0.1457 time to fit residues: 70.4475 Evaluate side-chains 270 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 311 THR 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 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 589 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 E residue 12 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 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 169 VAL Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain O residue 207 TYR Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 202 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: 0.7980 chunk 33 optimal weight: 0.5980 chunk 221 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 31 optimal weight: 0.0070 chunk 184 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 GLN ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 532 GLN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.176751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.145663 restraints weight = 45284.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.148307 restraints weight = 27975.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.150330 restraints weight = 17712.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.150949 restraints weight = 14696.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.151162 restraints weight = 13476.796| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.7415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21338 Z= 0.110 Angle : 0.650 10.173 29040 Z= 0.300 Chirality : 0.053 0.459 3263 Planarity : 0.003 0.044 3491 Dihedral : 11.265 162.448 3458 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.03 % Allowed : 19.62 % Favored : 77.36 % 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: -2.58 (0.16), residues: 2398 helix: -0.99 (0.21), residues: 605 sheet: -1.50 (0.29), residues: 313 loop : -2.16 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 182 TYR 0.025 0.001 TYR J 149 PHE 0.035 0.001 PHE J 9 TRP 0.006 0.001 TRP J 343 HIS 0.005 0.001 HIS J 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (21338) covalent geometry : angle 0.65027 / 0.30 (29040) hydrogen bonds : bond 0.02952 / 1.96 ( 360) hydrogen bonds : angle 4.29452 / 2.83 ( 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 326 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 263 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7517 (pt0) cc_final: 0.6838 (mp10) REVERT: A 108 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: B 42 CYS cc_start: 0.6843 (OUTLIER) cc_final: 0.6015 (t) REVERT: B 43 SER cc_start: 0.7866 (p) cc_final: 0.7528 (t) REVERT: B 107 MET cc_start: 0.8338 (ppp) cc_final: 0.7934 (ppp) REVERT: J 283 ASP cc_start: 0.5664 (t0) cc_final: 0.5202 (t0) REVERT: J 554 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.7368 (t80) REVERT: J 623 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.6662 (tmm) REVERT: J 728 LYS cc_start: 0.8068 (ptpt) cc_final: 0.7682 (pptt) REVERT: M 88 LEU cc_start: 0.8130 (mt) cc_final: 0.7609 (pt) REVERT: E 34 SER cc_start: 0.8608 (m) cc_final: 0.8091 (p) REVERT: E 81 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7736 (pmt100) REVERT: E 118 THR cc_start: 0.8496 (p) cc_final: 0.8160 (t) REVERT: E 124 ASN cc_start: 0.8115 (p0) cc_final: 0.7724 (p0) REVERT: E 134 ASN cc_start: 0.7984 (t0) cc_final: 0.7513 (t0) REVERT: N 181 TYR cc_start: 0.8357 (p90) cc_final: 0.8034 (p90) REVERT: N 198 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7989 (tp) REVERT: O 81 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8256 (ptt-90) REVERT: O 209 VAL cc_start: 0.8142 (t) cc_final: 0.7832 (m) REVERT: P 119 GLU cc_start: 0.6292 (pm20) cc_final: 0.5930 (tp30) outliers start: 63 outliers final: 41 residues processed: 310 average time/residue: 0.1429 time to fit residues: 71.2590 Evaluate side-chains 273 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 225 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 108 GLU 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 212 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 292 ASN Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 371 MET Chi-restraints excluded: chain J residue 382 TYR 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 648 ASP Chi-restraints excluded: chain J residue 749 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 64 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 E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain N residue 37 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 169 VAL Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain O residue 207 TYR Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 202 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 20 optimal weight: 5.9990 chunk 161 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 103 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 14 HIS ** 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 596 ASN J 626 GLN C 19 HIS N 11 GLN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** P 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.168462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.135554 restraints weight = 44198.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.138798 restraints weight = 23843.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.140960 restraints weight = 16149.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.142361 restraints weight = 12516.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.143283 restraints weight = 10584.178| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.8420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21338 Z= 0.171 Angle : 0.758 11.916 29040 Z= 0.353 Chirality : 0.059 0.677 3263 Planarity : 0.004 0.054 3491 Dihedral : 11.506 161.171 3458 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.05 % Favored : 90.91 % Rotamer: Outliers : 3.61 % Allowed : 20.48 % Favored : 75.91 % 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: -2.65 (0.16), residues: 2398 helix: -1.05 (0.20), residues: 667 sheet: -1.53 (0.29), residues: 322 loop : -2.24 (0.15), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 383 TYR 0.023 0.002 TYR A 106 PHE 0.031 0.002 PHE J 9 TRP 0.010 0.002 TRP J 343 HIS 0.011 0.001 HIS J 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (21338) covalent geometry : angle 0.75801 / 0.35 (29040) hydrogen bonds : bond 0.03934 / 2.60 ( 360) hydrogen bonds : angle 4.53509 / 3.00 ( 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 326 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 251 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6173 (ptmt) REVERT: A 86 GLN cc_start: 0.7726 (pt0) cc_final: 0.6680 (mp10) REVERT: B 42 CYS cc_start: 0.6766 (OUTLIER) cc_final: 0.5852 (t) REVERT: B 43 SER cc_start: 0.7678 (p) cc_final: 0.7363 (t) REVERT: B 107 MET cc_start: 0.8328 (ppp) cc_final: 0.7843 (ppp) REVERT: J 554 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7883 (t80) REVERT: J 623 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.6499 (tmm) REVERT: J 728 LYS cc_start: 0.8132 (ptpt) cc_final: 0.7830 (pptt) REVERT: M 88 LEU cc_start: 0.8094 (mt) cc_final: 0.7641 (pt) REVERT: C 85 ASN cc_start: 0.5531 (t0) cc_final: 0.5265 (t0) REVERT: E 34 SER cc_start: 0.8775 (m) cc_final: 0.8079 (p) REVERT: E 81 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7740 (pmt100) REVERT: E 118 THR cc_start: 0.8872 (p) cc_final: 0.8634 (p) REVERT: E 124 ASN cc_start: 0.8658 (p0) cc_final: 0.8258 (p0) REVERT: N 154 GLU cc_start: 0.7857 (pm20) cc_final: 0.7528 (pm20) REVERT: N 198 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8192 (tp) REVERT: P 119 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6347 (tp30) REVERT: P 138 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7740 (mt) outliers start: 75 outliers final: 42 residues processed: 309 average time/residue: 0.1416 time to fit residues: 70.9781 Evaluate side-chains 275 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 225 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 84 LYS 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 60 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 215 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 242 LEU Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 382 TYR 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 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 M residue 81 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG 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 11 GLN 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 120 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 202 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 131 optimal weight: 0.0270 chunk 189 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 162 optimal weight: 0.1980 chunk 81 optimal weight: 0.0050 overall best weight: 1.0456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 GLN P 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.169034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.136628 restraints weight = 43840.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.139929 restraints weight = 23413.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.142063 restraints weight = 15734.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.143388 restraints weight = 12205.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.144178 restraints weight = 10379.791| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.8672 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= 0.133 Angle : 0.702 10.446 29040 Z= 0.326 Chirality : 0.056 0.559 3263 Planarity : 0.003 0.045 3491 Dihedral : 11.508 162.511 3458 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.09 % Favored : 91.87 % Rotamer: Outliers : 2.74 % Allowed : 21.83 % Favored : 75.43 % 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: -2.38 (0.16), residues: 2398 helix: -0.70 (0.21), residues: 645 sheet: -1.56 (0.29), residues: 324 loop : -2.08 (0.15), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 466 TYR 0.017 0.001 TYR J 149 PHE 0.033 0.001 PHE J 9 TRP 0.012 0.001 TRP J 343 HIS 0.004 0.001 HIS J 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (21338) covalent geometry : angle 0.70209 / 0.33 (29040) hydrogen bonds : bond 0.03722 / 2.47 ( 360) hydrogen bonds : angle 4.40368 / 2.89 ( 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 287 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 CYS cc_start: 0.6652 (OUTLIER) cc_final: 0.5646 (t) REVERT: B 43 SER cc_start: 0.7692 (p) cc_final: 0.7331 (t) REVERT: B 107 MET cc_start: 0.8245 (ppp) cc_final: 0.7837 (ppp) REVERT: I 132 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8416 (p) REVERT: J 386 MET cc_start: 0.8062 (mpp) cc_final: 0.7862 (mpp) REVERT: J 554 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7752 (t80) REVERT: J 623 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.6536 (tmm) REVERT: J 728 LYS cc_start: 0.8154 (ptpt) cc_final: 0.7855 (pptt) REVERT: C 66 GLU cc_start: 0.5668 (pm20) cc_final: 0.5435 (pm20) REVERT: C 124 ASN cc_start: 0.7785 (p0) cc_final: 0.7328 (m-40) REVERT: E 34 SER cc_start: 0.8592 (m) cc_final: 0.7918 (p) REVERT: E 81 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7489 (pmt100) REVERT: E 93 MET cc_start: 0.8160 (mmt) cc_final: 0.7834 (mmt) REVERT: E 118 THR cc_start: 0.8819 (p) cc_final: 0.8396 (t) REVERT: N 198 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8295 (tp) REVERT: P 138 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7599 (mt) outliers start: 57 outliers final: 33 residues processed: 278 average time/residue: 0.1412 time to fit residues: 63.4519 Evaluate side-chains 246 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 ASP 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 60 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 382 TYR 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 648 ASP Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG 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 198 LEU Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 138 ILE 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: 4.9990 chunk 58 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 532 GLN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 HIS P 65 ASN ** P 105 ASN ** 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 = 0.4369 r_free = 0.4369 target = 0.168401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.136147 restraints weight = 43879.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.139446 restraints weight = 23221.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.141611 restraints weight = 15505.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.142999 restraints weight = 11962.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.143913 restraints weight = 10089.572| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.8951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21338 Z= 0.131 Angle : 0.715 10.303 29040 Z= 0.331 Chirality : 0.055 0.550 3263 Planarity : 0.004 0.052 3491 Dihedral : 11.527 164.119 3458 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.80 % Favored : 91.16 % Rotamer: Outliers : 2.40 % Allowed : 22.69 % 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: -2.30 (0.16), residues: 2398 helix: -0.72 (0.20), residues: 661 sheet: -1.47 (0.29), residues: 322 loop : -2.00 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 57 TYR 0.022 0.001 TYR J 224 PHE 0.032 0.001 PHE J 9 TRP 0.013 0.001 TRP J 343 HIS 0.006 0.001 HIS J 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (21338) covalent geometry : angle 0.71521 / 0.33 (29040) hydrogen bonds : bond 0.03824 / 2.55 ( 360) hydrogen bonds : angle 4.35739 / 2.88 ( 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 270 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 CYS cc_start: 0.6606 (OUTLIER) cc_final: 0.5628 (t) REVERT: B 43 SER cc_start: 0.7714 (p) cc_final: 0.7500 (t) REVERT: B 107 MET cc_start: 0.8279 (ppp) cc_final: 0.7892 (ppp) REVERT: I 132 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8480 (p) REVERT: J 554 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7832 (t80) REVERT: J 623 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6506 (tmm) REVERT: J 728 LYS cc_start: 0.8145 (ptpt) cc_final: 0.7900 (pptt) REVERT: M 88 LEU cc_start: 0.8138 (mp) cc_final: 0.7846 (pt) REVERT: E 81 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7579 (pmt100) REVERT: E 93 MET cc_start: 0.8151 (mmt) cc_final: 0.7886 (mmt) REVERT: E 118 THR cc_start: 0.8857 (p) cc_final: 0.8445 (t) REVERT: N 198 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8172 (tp) REVERT: P 138 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7665 (mt) outliers start: 50 outliers final: 34 residues processed: 262 average time/residue: 0.1433 time to fit residues: 59.4974 Evaluate side-chains 241 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 60 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 382 TYR 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 648 ASP Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG 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 120 VAL Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 41 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 155 optimal weight: 0.0050 chunk 10 optimal weight: 10.0000 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 GLN ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 GLN ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 532 GLN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 GLN O 19 HIS ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.151898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.121258 restraints weight = 42679.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.124341 restraints weight = 24400.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.126381 restraints weight = 17293.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.127689 restraints weight = 13900.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.128503 restraints weight = 12061.287| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.9625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21338 Z= 0.205 Angle : 0.820 12.419 29040 Z= 0.385 Chirality : 0.063 0.770 3263 Planarity : 0.004 0.053 3491 Dihedral : 11.842 166.322 3458 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.84 % Favored : 90.12 % Rotamer: Outliers : 2.45 % Allowed : 23.03 % Favored : 74.52 % 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: -2.34 (0.16), residues: 2398 helix: -0.73 (0.19), residues: 718 sheet: -1.20 (0.33), residues: 263 loop : -2.15 (0.15), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 57 TYR 0.024 0.002 TYR J 54 PHE 0.033 0.002 PHE J 9 TRP 0.016 0.002 TRP J 343 HIS 0.007 0.002 HIS J 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (21338) covalent geometry : angle 0.82028 / 0.38 (29040) hydrogen bonds : bond 0.04847 / 3.16 ( 360) hydrogen bonds : angle 4.55609 / 3.03 ( 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 274 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 223 time to evaluate : 0.739 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: B 42 CYS cc_start: 0.6656 (OUTLIER) cc_final: 0.5728 (t) REVERT: B 107 MET cc_start: 0.8272 (ppp) cc_final: 0.7847 (ppp) REVERT: I 132 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8470 (p) REVERT: J 101 TRP cc_start: 0.5304 (p90) cc_final: 0.4343 (m-10) REVERT: J 554 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8131 (t80) REVERT: J 623 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.6702 (tmm) REVERT: J 728 LYS cc_start: 0.8199 (ptpt) cc_final: 0.7921 (pptt) REVERT: C 93 MET cc_start: 0.7748 (mmt) cc_final: 0.7419 (mmt) REVERT: E 81 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7576 (pmt100) REVERT: N 154 GLU cc_start: 0.7736 (pm20) cc_final: 0.7278 (pm20) outliers start: 51 outliers final: 34 residues processed: 263 average time/residue: 0.1438 time to fit residues: 59.7245 Evaluate side-chains 239 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER 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 132 THR Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 9 PHE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 382 TYR 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 513 VAL Chi-restraints excluded: chain J residue 532 GLN 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 E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG 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 120 VAL Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain P residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 58 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 60 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 31 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 180 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 242 optimal weight: 8.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 532 GLN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** P 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.164497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.131698 restraints weight = 43896.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.134837 restraints weight = 23678.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.136908 restraints weight = 16069.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.138267 restraints weight = 12495.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.139068 restraints weight = 10598.219| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.9681 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= 0.135 Angle : 0.749 10.655 29040 Z= 0.348 Chirality : 0.058 0.604 3263 Planarity : 0.004 0.051 3491 Dihedral : 11.760 170.063 3458 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 1.92 % Allowed : 24.23 % Favored : 73.85 % 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: -0.65 (0.20), residues: 712 sheet: -1.29 (0.30), residues: 306 loop : -1.99 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.028 0.002 TYR J 54 PHE 0.031 0.001 PHE J 9 TRP 0.012 0.001 TRP J 343 HIS 0.006 0.001 HIS P 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (21338) covalent geometry : angle 0.74860 / 0.35 (29040) hydrogen bonds : bond 0.04283 / 2.84 ( 360) hydrogen bonds : angle 4.40423 / 2.93 ( 1060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3977.18 seconds wall clock time: 69 minutes 34.41 seconds (4174.41 seconds total)