Starting phenix.real_space_refine on Thu Jul 2 10:44:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hdo_34676/07_2026/8hdo_34676_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hdo_34676/07_2026/8hdo_34676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hdo_34676/07_2026/8hdo_34676_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hdo_34676/07_2026/8hdo_34676_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hdo_34676/07_2026/8hdo_34676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hdo_34676/07_2026/8hdo_34676.map" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5314 2.51 5 N 1410 2.21 5 O 1498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8277 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1952 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2562 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 432 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2135 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "R" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 223 Unusual residues: {'CLR': 7, 'I5D': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 1.59, per 1000 atoms: 0.19 Number of scatterers: 8277 At special positions: 0 Unit cell: (90.4, 77.6, 129.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1498 8.00 N 1410 7.00 C 5314 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 171 " distance=2.03 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: 0.60 Conformation dependent library (CDL) restraints added in 334.1 milliseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 11 sheets defined 44.0% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.632A pdb=" N ARG A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.545A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 133 through 137 removed outlier: 4.104A pdb=" N THR A 136 " --> pdb=" O TRP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.576A pdb=" N LEU A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.782A pdb=" N PHE A 164 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 4.132A pdb=" N ARG A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 202 removed outlier: 3.665A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 22 removed outlier: 3.570A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.636A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.856A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 112 removed outlier: 4.517A pdb=" N THR N 111 " --> pdb=" O PHE N 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 35 removed outlier: 3.777A pdb=" N LEU R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL R 28 " --> pdb=" O GLY R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 59 removed outlier: 3.557A pdb=" N TYR R 44 " --> pdb=" O THR R 40 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 69 Processing helix chain 'R' and resid 74 through 109 removed outlier: 3.921A pdb=" N LEU R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 117 removed outlier: 4.754A pdb=" N LYS R 114 " --> pdb=" O PRO R 110 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER R 115 " --> pdb=" O LEU R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 138 Processing helix chain 'R' and resid 138 through 143 Processing helix chain 'R' and resid 172 through 177 Processing helix chain 'R' and resid 178 through 184 removed outlier: 3.656A pdb=" N MET R 182 " --> pdb=" O PRO R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 191 Processing helix chain 'R' and resid 191 through 215 Processing helix chain 'R' and resid 225 through 259 removed outlier: 4.279A pdb=" N ILE R 239 " --> pdb=" O SER R 235 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL R 240 " --> pdb=" O LEU R 236 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE R 242 " --> pdb=" O MET R 238 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 270 through 290 removed outlier: 3.723A pdb=" N ASN R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER R 283 " --> pdb=" O SER R 279 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL R 284 " --> pdb=" O HIS R 280 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 294 through 309 removed outlier: 3.524A pdb=" N ARG R 298 " --> pdb=" O ASN R 294 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 removed outlier: 6.181A pdb=" N HIS A 41 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N PHE A 84 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU A 43 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL A 86 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU A 45 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL A 139 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N HIS A 214 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 141 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.948A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.947A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.067A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.623A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.615A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.590A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.662A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.800A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.590A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1316 1.27 - 1.41: 2117 1.41 - 1.55: 4945 1.55 - 1.69: 4 1.69 - 1.83: 77 Bond restraints: 8459 Sorted by residual: bond pdb=" C10 I5D R 408 " pdb=" C5' I5D R 408 " ideal model delta sigma weight residual 1.379 1.536 -0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" C17 I5D R 408 " pdb=" C4' I5D R 408 " ideal model delta sigma weight residual 1.390 1.539 -0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" C11 I5D R 408 " pdb=" C16 I5D R 408 " ideal model delta sigma weight residual 1.395 1.537 -0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" C8 I5D R 408 " pdb=" NAA I5D R 408 " ideal model delta sigma weight residual 1.328 1.461 -0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" C6 I5D R 408 " pdb=" N1 I5D R 408 " ideal model delta sigma weight residual 1.337 1.462 -0.125 2.00e-02 2.50e+03 3.89e+01 ... (remaining 8454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 11333 2.16 - 4.33: 144 4.33 - 6.49: 32 6.49 - 8.65: 2 8.65 - 10.82: 1 Bond angle restraints: 11512 Sorted by residual: angle pdb=" C GLN R 260 " pdb=" N PRO R 261 " pdb=" CA PRO R 261 " ideal model delta sigma weight residual 119.84 114.73 5.11 1.25e+00 6.40e-01 1.67e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 122.61 127.59 -4.98 1.56e+00 4.11e-01 1.02e+01 angle pdb=" C1' I5D R 408 " pdb=" S1 I5D R 408 " pdb=" C5 I5D R 408 " ideal model delta sigma weight residual 101.05 109.28 -8.23 3.00e+00 1.11e-01 7.52e+00 angle pdb=" N VAL R 256 " pdb=" CA VAL R 256 " pdb=" C VAL R 256 " ideal model delta sigma weight residual 113.07 109.44 3.63 1.36e+00 5.41e-01 7.14e+00 angle pdb=" C GLN R 260 " pdb=" N PRO R 261 " pdb=" CD PRO R 261 " ideal model delta sigma weight residual 125.00 135.82 -10.82 4.10e+00 5.95e-02 6.96e+00 ... (remaining 11507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.30: 5138 30.30 - 60.60: 203 60.60 - 90.90: 13 90.90 - 121.20: 0 121.20 - 151.50: 2 Dihedral angle restraints: 5356 sinusoidal: 2361 harmonic: 2995 Sorted by residual: dihedral pdb=" O6 I5D R 408 " pdb=" C5 I5D R 408 " pdb=" C6 I5D R 408 " pdb=" S1 I5D R 408 " ideal model delta sinusoidal sigma weight residual -1.83 -153.33 151.50 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" N1 I5D R 408 " pdb=" C5 I5D R 408 " pdb=" C6 I5D R 408 " pdb=" S1 I5D R 408 " ideal model delta sinusoidal sigma weight residual 178.22 26.73 151.49 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" CB GLU G 58 " pdb=" CG GLU G 58 " pdb=" CD GLU G 58 " pdb=" OE1 GLU G 58 " ideal model delta sinusoidal sigma weight residual 0.00 -87.65 87.65 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 5353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1175 0.064 - 0.129: 134 0.129 - 0.193: 14 0.193 - 0.258: 5 0.258 - 0.322: 1 Chirality restraints: 1329 Sorted by residual: chirality pdb=" C13 I5D R 408 " pdb=" C12 I5D R 408 " pdb=" C14 I5D R 408 " pdb=" C15 I5D R 408 " both_signs ideal model delta sigma weight residual True 2.41 2.74 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C13 CLR R 404 " pdb=" C12 CLR R 404 " pdb=" C14 CLR R 404 " pdb=" C17 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.93 -2.70 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C13 CLR R 403 " pdb=" C12 CLR R 403 " pdb=" C14 CLR R 403 " pdb=" C17 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.93 -2.70 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1326 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 248 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO R 249 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 249 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 249 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 192 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO R 193 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO R 193 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 193 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C THR B 87 " -0.024 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.008 2.00e-02 2.50e+03 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 111 2.64 - 3.20: 7262 3.20 - 3.77: 13165 3.77 - 4.33: 18261 4.33 - 4.90: 30011 Nonbonded interactions: 68810 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.069 3.040 nonbonded pdb=" CD1 LEU R 96 " pdb=" OH TYR R 290 " model vdw 2.134 3.460 nonbonded pdb=" O VAL R 253 " pdb=" OG1 THR R 257 " model vdw 2.244 3.040 nonbonded pdb=" O ILE R 136 " pdb=" OH TYR R 181 " model vdw 2.262 3.040 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.274 3.040 ... (remaining 68805 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.690 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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 : 0.005 0.157 8460 Z= 0.270 Angle : 0.616 10.818 11514 Z= 0.316 Chirality : 0.045 0.322 1329 Planarity : 0.003 0.039 1424 Dihedral : 14.525 151.498 3413 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.12 % Allowed : 22.47 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.24), residues: 1008 helix: -0.07 (0.24), residues: 392 sheet: -0.88 (0.31), residues: 217 loop : -1.56 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.008 0.001 TYR N 95 PHE 0.008 0.001 PHE B 199 TRP 0.009 0.001 TRP B 169 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.27 ( 8459) covalent geometry : angle 0.61630 / 0.32 (11512) SS BOND : bond 0.00231 / 0.12 ( 1) SS BOND : angle 0.87296 / 0.50 ( 2) hydrogen bonds : bond 0.12086 / 8.22 ( 407) hydrogen bonds : angle 5.14307 / 3.54 ( 1155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.281 Fit side-chains REVERT: G 21 MET cc_start: 0.7485 (mpt) cc_final: 0.7200 (mpt) REVERT: N 77 ASN cc_start: 0.7797 (m-40) cc_final: 0.7547 (m-40) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.4407 time to fit residues: 83.0916 Evaluate side-chains 95 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 59 GLN A 82 HIS A 89 GLN A 214 HIS A 239 HIS A 242 GLN B 44 GLN B 75 GLN B 155 ASN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 13 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 251 HIS R 273 ASN R 286 ASN R 294 ASN R 302 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.164514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.129271 restraints weight = 9487.504| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.11 r_work: 0.3587 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8460 Z= 0.108 Angle : 0.499 6.653 11514 Z= 0.258 Chirality : 0.040 0.133 1329 Planarity : 0.004 0.041 1424 Dihedral : 8.349 96.059 1586 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.57 % Allowed : 24.54 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.26), residues: 1008 helix: 1.30 (0.26), residues: 402 sheet: -0.56 (0.31), residues: 226 loop : -0.86 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 117 TYR 0.013 0.001 TYR R 299 PHE 0.009 0.001 PHE B 199 TRP 0.009 0.001 TRP R 247 HIS 0.007 0.001 HIS R 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 8459) covalent geometry : angle 0.49880 / 0.26 (11512) SS BOND : bond 0.00017 / 0.01 ( 1) SS BOND : angle 0.13423 / 0.06 ( 2) hydrogen bonds : bond 0.02725 / 1.80 ( 407) hydrogen bonds : angle 3.99077 / 2.78 ( 1155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 174 GLU cc_start: 0.7857 (pm20) cc_final: 0.7621 (mm-30) REVERT: B 42 ARG cc_start: 0.6787 (tpp-160) cc_final: 0.6540 (tpp-160) REVERT: B 217 MET cc_start: 0.7677 (ppp) cc_final: 0.7462 (ppp) REVERT: B 263 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8652 (m) REVERT: G 21 MET cc_start: 0.7365 (mpt) cc_final: 0.6878 (mmm) REVERT: G 61 PHE cc_start: 0.7493 (m-80) cc_final: 0.7082 (m-80) REVERT: N 77 ASN cc_start: 0.7546 (m-40) cc_final: 0.7297 (m-40) REVERT: N 80 TYR cc_start: 0.7862 (m-80) cc_final: 0.7458 (m-80) REVERT: N 85 SER cc_start: 0.7571 (m) cc_final: 0.7315 (p) outliers start: 31 outliers final: 13 residues processed: 137 average time/residue: 0.3906 time to fit residues: 57.2613 Evaluate side-chains 117 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 42 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 96 optimal weight: 0.0030 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 19 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS B 44 GLN B 88 ASN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 254 ASN R 302 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.156200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.120083 restraints weight = 9601.188| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.12 r_work: 0.3471 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8460 Z= 0.116 Angle : 0.482 6.632 11514 Z= 0.250 Chirality : 0.039 0.141 1329 Planarity : 0.003 0.039 1424 Dihedral : 7.529 74.558 1586 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.69 % Allowed : 25.81 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.27), residues: 1008 helix: 1.66 (0.26), residues: 402 sheet: -0.54 (0.32), residues: 217 loop : -0.60 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 117 TYR 0.016 0.001 TYR R 202 PHE 0.010 0.001 PHE A 74 TRP 0.009 0.001 TRP R 247 HIS 0.006 0.001 HIS R 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 8459) covalent geometry : angle 0.48191 / 0.25 (11512) SS BOND : bond 0.00023 / 0.01 ( 1) SS BOND : angle 0.01919 / 0.01 ( 2) hydrogen bonds : bond 0.02796 / 1.86 ( 407) hydrogen bonds : angle 3.96405 / 2.76 ( 1155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.6004 (mtm-85) REVERT: A 208 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6903 (ptt90) REVERT: B 247 ASP cc_start: 0.8531 (p0) cc_final: 0.8312 (p0) REVERT: B 259 GLN cc_start: 0.8604 (pt0) cc_final: 0.8328 (pt0) REVERT: B 263 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8736 (m) REVERT: G 14 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.6192 (ttmt) REVERT: G 21 MET cc_start: 0.7261 (mpt) cc_final: 0.6713 (mmm) REVERT: G 46 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8682 (mmtt) REVERT: N 38 ARG cc_start: 0.8407 (ptm160) cc_final: 0.8116 (ptt90) REVERT: N 77 ASN cc_start: 0.7677 (m-40) cc_final: 0.7420 (m-40) REVERT: N 80 TYR cc_start: 0.7842 (m-80) cc_final: 0.7411 (m-80) REVERT: N 85 SER cc_start: 0.7676 (m) cc_final: 0.7461 (p) REVERT: R 174 GLU cc_start: 0.7331 (mp0) cc_final: 0.7113 (mp0) outliers start: 32 outliers final: 16 residues processed: 140 average time/residue: 0.3888 time to fit residues: 58.6609 Evaluate side-chains 117 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 192 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN A 31 GLN A 131 ASN B 220 GLN B 230 ASN B 259 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116679 restraints weight = 9730.035| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.12 r_work: 0.3422 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8460 Z= 0.117 Angle : 0.479 6.591 11514 Z= 0.249 Chirality : 0.040 0.131 1329 Planarity : 0.003 0.040 1424 Dihedral : 7.061 63.451 1586 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.49 % Allowed : 26.15 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.27), residues: 1008 helix: 1.83 (0.26), residues: 402 sheet: -0.34 (0.32), residues: 213 loop : -0.42 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.016 0.001 TYR R 202 PHE 0.023 0.001 PHE N 103 TRP 0.010 0.001 TRP R 247 HIS 0.006 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8459) covalent geometry : angle 0.47949 / 0.25 (11512) SS BOND : bond 0.00004 / 0.00 ( 1) SS BOND : angle 0.07302 / 0.04 ( 2) hydrogen bonds : bond 0.02719 / 1.79 ( 407) hydrogen bonds : angle 3.93747 / 2.74 ( 1155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 0.186 Fit side-chains REVERT: A 208 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7188 (mtt90) REVERT: B 172 GLU cc_start: 0.7143 (mp0) cc_final: 0.6893 (pm20) REVERT: B 217 MET cc_start: 0.7955 (ppp) cc_final: 0.7551 (ppp) REVERT: B 228 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: B 247 ASP cc_start: 0.8566 (p0) cc_final: 0.8360 (p0) REVERT: B 259 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: B 263 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8752 (m) REVERT: G 14 LYS cc_start: 0.6641 (OUTLIER) cc_final: 0.6214 (ttmt) REVERT: G 21 MET cc_start: 0.7250 (mpt) cc_final: 0.6696 (mmm) REVERT: N 38 ARG cc_start: 0.8475 (ptm160) cc_final: 0.8155 (ptt90) REVERT: N 80 TYR cc_start: 0.7914 (m-80) cc_final: 0.7414 (m-80) outliers start: 39 outliers final: 15 residues processed: 133 average time/residue: 0.3897 time to fit residues: 55.6026 Evaluate side-chains 116 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 142 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 66 optimal weight: 0.0050 chunk 90 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.152333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115268 restraints weight = 9599.772| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.18 r_work: 0.3406 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8460 Z= 0.117 Angle : 0.478 7.981 11514 Z= 0.246 Chirality : 0.039 0.133 1329 Planarity : 0.003 0.040 1424 Dihedral : 7.091 65.107 1586 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.03 % Allowed : 26.38 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 1008 helix: 1.96 (0.26), residues: 403 sheet: -0.36 (0.32), residues: 225 loop : -0.20 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.014 0.001 TYR R 202 PHE 0.009 0.001 PHE A 74 TRP 0.010 0.001 TRP B 211 HIS 0.005 0.001 HIS R 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8459) covalent geometry : angle 0.47803 / 0.25 (11512) SS BOND : bond 0.00024 / 0.01 ( 1) SS BOND : angle 0.08364 / 0.05 ( 2) hydrogen bonds : bond 0.02752 / 1.81 ( 407) hydrogen bonds : angle 3.93771 / 2.73 ( 1155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7153 (mtt90) REVERT: B 217 MET cc_start: 0.7914 (ppp) cc_final: 0.7458 (ppp) REVERT: B 263 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8758 (m) REVERT: G 14 LYS cc_start: 0.6636 (OUTLIER) cc_final: 0.6210 (ttmt) REVERT: G 21 MET cc_start: 0.7221 (mpt) cc_final: 0.6673 (mmm) REVERT: N 38 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8157 (ptm-80) REVERT: N 80 TYR cc_start: 0.7876 (m-80) cc_final: 0.7414 (m-80) REVERT: N 98 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7960 (tmm160) REVERT: R 296 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.8028 (p0) outliers start: 35 outliers final: 18 residues processed: 125 average time/residue: 0.4171 time to fit residues: 55.7927 Evaluate side-chains 118 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 296 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 70 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 15 optimal weight: 0.0470 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.150607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114618 restraints weight = 9618.563| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.14 r_work: 0.3398 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8460 Z= 0.106 Angle : 0.474 8.570 11514 Z= 0.244 Chirality : 0.039 0.132 1329 Planarity : 0.003 0.040 1424 Dihedral : 6.876 64.662 1586 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.15 % Allowed : 26.04 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.27), residues: 1008 helix: 2.13 (0.26), residues: 403 sheet: -0.31 (0.33), residues: 219 loop : -0.12 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.013 0.001 TYR R 202 PHE 0.009 0.001 PHE A 74 TRP 0.009 0.001 TRP A 96 HIS 0.005 0.001 HIS R 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8459) covalent geometry : angle 0.47371 / 0.24 (11512) SS BOND : bond 0.00066 / 0.03 ( 1) SS BOND : angle 0.20774 / 0.11 ( 2) hydrogen bonds : bond 0.02641 / 1.75 ( 407) hydrogen bonds : angle 3.87166 / 2.68 ( 1155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 136 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8794 (t) REVERT: A 208 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7168 (mtt90) REVERT: B 217 MET cc_start: 0.7989 (ppp) cc_final: 0.7493 (ppp) REVERT: B 260 GLU cc_start: 0.7950 (tt0) cc_final: 0.7669 (tt0) REVERT: B 263 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8671 (m) REVERT: G 14 LYS cc_start: 0.6705 (OUTLIER) cc_final: 0.6254 (ttmt) REVERT: G 21 MET cc_start: 0.7289 (mpt) cc_final: 0.6728 (mmm) REVERT: N 38 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8221 (ptm-80) REVERT: N 80 TYR cc_start: 0.7871 (m-80) cc_final: 0.7380 (m-80) REVERT: R 114 LYS cc_start: 0.8464 (mmmt) cc_final: 0.8046 (mttp) outliers start: 36 outliers final: 20 residues processed: 126 average time/residue: 0.4441 time to fit residues: 59.9590 Evaluate side-chains 125 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.144437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.106867 restraints weight = 9959.712| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.18 r_work: 0.3291 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8460 Z= 0.156 Angle : 0.530 10.047 11514 Z= 0.271 Chirality : 0.041 0.135 1329 Planarity : 0.004 0.039 1424 Dihedral : 6.884 57.882 1586 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.03 % Allowed : 27.07 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.27), residues: 1008 helix: 1.96 (0.26), residues: 410 sheet: -0.44 (0.33), residues: 215 loop : -0.12 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 169 TYR 0.018 0.001 TYR R 202 PHE 0.016 0.001 PHE B 292 TRP 0.011 0.002 TRP B 169 HIS 0.005 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 8459) covalent geometry : angle 0.52997 / 0.27 (11512) SS BOND : bond 0.00019 / 0.01 ( 1) SS BOND : angle 0.14413 / 0.07 ( 2) hydrogen bonds : bond 0.03038 / 2.01 ( 407) hydrogen bonds : angle 4.12503 / 2.86 ( 1155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.300 Fit side-chains REVERT: A 17 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7941 (tppt) REVERT: A 136 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8843 (t) REVERT: A 208 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7081 (mtm-85) REVERT: B 217 MET cc_start: 0.7965 (ppp) cc_final: 0.7735 (ppp) REVERT: G 14 LYS cc_start: 0.6614 (OUTLIER) cc_final: 0.6115 (tptp) REVERT: G 21 MET cc_start: 0.7261 (mpt) cc_final: 0.6885 (mpt) REVERT: N 38 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8210 (ptt90) REVERT: N 80 TYR cc_start: 0.7793 (m-80) cc_final: 0.7539 (m-80) outliers start: 35 outliers final: 19 residues processed: 129 average time/residue: 0.4301 time to fit residues: 59.4918 Evaluate side-chains 120 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.144612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.107300 restraints weight = 9872.132| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.16 r_work: 0.3296 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8460 Z= 0.147 Angle : 0.524 10.027 11514 Z= 0.268 Chirality : 0.041 0.131 1329 Planarity : 0.004 0.041 1424 Dihedral : 6.849 58.414 1586 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.03 % Allowed : 27.19 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.27), residues: 1008 helix: 2.00 (0.26), residues: 410 sheet: -0.46 (0.33), residues: 214 loop : -0.06 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 219 TYR 0.016 0.001 TYR R 202 PHE 0.013 0.001 PHE R 173 TRP 0.011 0.001 TRP A 96 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 8459) covalent geometry : angle 0.52369 / 0.27 (11512) SS BOND : bond 0.00011 / 0.01 ( 1) SS BOND : angle 0.15699 / 0.09 ( 2) hydrogen bonds : bond 0.02968 / 1.96 ( 407) hydrogen bonds : angle 4.10713 / 2.84 ( 1155) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7961 (tppt) REVERT: A 136 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8801 (t) REVERT: A 208 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7099 (mtm-85) REVERT: B 217 MET cc_start: 0.7985 (ppp) cc_final: 0.7769 (ppp) REVERT: G 14 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6263 (ttmt) REVERT: G 21 MET cc_start: 0.7281 (mpt) cc_final: 0.6905 (mpt) REVERT: N 38 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8250 (ptt90) REVERT: N 80 TYR cc_start: 0.7807 (m-80) cc_final: 0.7553 (m-80) REVERT: N 106 ASP cc_start: 0.7701 (p0) cc_final: 0.7456 (p0) REVERT: R 114 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8050 (mttp) outliers start: 35 outliers final: 22 residues processed: 121 average time/residue: 0.5642 time to fit residues: 72.7235 Evaluate side-chains 128 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 182 MET Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 GLN ** 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 = 0.3870 r_free = 0.3870 target = 0.144481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.107266 restraints weight = 9897.794| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.16 r_work: 0.3296 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8460 Z= 0.147 Angle : 0.534 9.970 11514 Z= 0.273 Chirality : 0.041 0.133 1329 Planarity : 0.004 0.040 1424 Dihedral : 6.814 59.440 1586 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.46 % Allowed : 28.57 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.27), residues: 1008 helix: 2.00 (0.26), residues: 410 sheet: -0.51 (0.33), residues: 214 loop : -0.07 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 169 TYR 0.017 0.001 TYR R 202 PHE 0.012 0.001 PHE A 74 TRP 0.010 0.001 TRP A 96 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 8459) covalent geometry : angle 0.53356 / 0.27 (11512) SS BOND : bond 0.00006 / 0.00 ( 1) SS BOND : angle 0.14400 / 0.08 ( 2) hydrogen bonds : bond 0.02994 / 1.98 ( 407) hydrogen bonds : angle 4.12357 / 2.85 ( 1155) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7947 (tppt) REVERT: A 136 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8808 (t) REVERT: A 159 LYS cc_start: 0.8323 (mmmt) cc_final: 0.7891 (mmmm) REVERT: A 208 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7110 (mtm-85) REVERT: B 172 GLU cc_start: 0.7153 (mp0) cc_final: 0.6865 (pm20) REVERT: B 217 MET cc_start: 0.8001 (ppp) cc_final: 0.7774 (ppp) REVERT: B 219 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.7855 (ttm-80) REVERT: G 14 LYS cc_start: 0.6707 (OUTLIER) cc_final: 0.6298 (ttmt) REVERT: G 21 MET cc_start: 0.7288 (mpt) cc_final: 0.6913 (mpt) REVERT: N 38 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8238 (ptt90) outliers start: 30 outliers final: 21 residues processed: 125 average time/residue: 0.5503 time to fit residues: 73.4969 Evaluate side-chains 125 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 0.0060 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111459 restraints weight = 9658.772| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.15 r_work: 0.3349 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8460 Z= 0.114 Angle : 0.516 9.204 11514 Z= 0.266 Chirality : 0.039 0.131 1329 Planarity : 0.003 0.040 1424 Dihedral : 6.632 58.263 1586 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.88 % Allowed : 29.38 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.27), residues: 1008 helix: 2.04 (0.26), residues: 410 sheet: -0.47 (0.33), residues: 212 loop : -0.07 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 169 TYR 0.013 0.001 TYR R 202 PHE 0.009 0.001 PHE A 74 TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 8459) covalent geometry : angle 0.51614 / 0.27 (11512) SS BOND : bond 0.00014 / 0.01 ( 1) SS BOND : angle 0.22487 / 0.13 ( 2) hydrogen bonds : bond 0.02834 / 1.87 ( 407) hydrogen bonds : angle 4.00206 / 2.77 ( 1155) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.324 Fit side-chains REVERT: A 13 ARG cc_start: 0.7072 (tpt170) cc_final: 0.6772 (mmt-90) REVERT: A 17 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8011 (tppt) REVERT: A 136 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8804 (t) REVERT: A 159 LYS cc_start: 0.8281 (mmmt) cc_final: 0.7846 (mmmm) REVERT: A 208 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7058 (mtm-85) REVERT: B 172 GLU cc_start: 0.7155 (mp0) cc_final: 0.6921 (pm20) REVERT: B 217 MET cc_start: 0.8029 (ppp) cc_final: 0.7813 (ppp) REVERT: B 219 ARG cc_start: 0.8458 (ttm-80) cc_final: 0.7878 (ttm-80) REVERT: G 14 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6340 (ttmt) REVERT: G 21 MET cc_start: 0.7274 (mpt) cc_final: 0.6896 (mpt) REVERT: N 38 ARG cc_start: 0.8593 (ptm160) cc_final: 0.8307 (ptt90) outliers start: 25 outliers final: 20 residues processed: 120 average time/residue: 0.5398 time to fit residues: 69.3221 Evaluate side-chains 125 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 GLN ** 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 = 0.3890 r_free = 0.3890 target = 0.146572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.109965 restraints weight = 9766.750| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.15 r_work: 0.3331 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8460 Z= 0.135 Angle : 0.519 9.298 11514 Z= 0.266 Chirality : 0.040 0.132 1329 Planarity : 0.004 0.040 1424 Dihedral : 6.634 59.371 1586 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.23 % Allowed : 28.80 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.27), residues: 1008 helix: 2.00 (0.26), residues: 410 sheet: -0.49 (0.33), residues: 212 loop : -0.07 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 169 TYR 0.015 0.001 TYR R 202 PHE 0.011 0.001 PHE A 74 TRP 0.010 0.001 TRP A 96 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8459) covalent geometry : angle 0.51942 / 0.27 (11512) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 0.17378 / 0.10 ( 2) hydrogen bonds : bond 0.02921 / 1.93 ( 407) hydrogen bonds : angle 4.05494 / 2.80 ( 1155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2811.29 seconds wall clock time: 48 minutes 43.19 seconds (2923.19 seconds total)