Starting phenix.real_space_refine on Wed Feb 4 05:55:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jed_61413/02_2026/9jed_61413.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jed_61413/02_2026/9jed_61413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jed_61413/02_2026/9jed_61413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jed_61413/02_2026/9jed_61413.map" model { file = "/net/cci-nas-00/data/ceres_data/9jed_61413/02_2026/9jed_61413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jed_61413/02_2026/9jed_61413.cif" } resolution = 2.58 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= 0.093 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 1 5.49 5 S 59 5.16 5 C 5714 2.51 5 N 1501 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8941 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "D" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2276 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 9, 'TRANS': 267} Chain breaks: 1 Chain: "S" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1787 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 16 Unusual residues: {'HSM': 1, 'PO4': 1} Classifications: {'undetermined': 2, 'water': 3} Link IDs: {None: 4} Time building chain proxies: 2.21, per 1000 atoms: 0.25 Number of scatterers: 8941 At special positions: 0 Unit cell: (89.856, 122.304, 124.8, 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 59 16.00 P 1 15.00 O 1666 8.00 N 1501 7.00 C 5714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " distance=2.04 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: 0.77 Conformation dependent library (CDL) restraints added in 353.7 milliseconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 39.3% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.749A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.811A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.784A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.119A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.517A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'D' and resid 3 through 25 removed outlier: 3.604A pdb=" N CYS D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 25 Processing helix chain 'G' and resid 29 through 46 removed outlier: 4.331A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 43 removed outlier: 4.558A pdb=" N THR R 17 " --> pdb=" O SER R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 67 removed outlier: 3.502A pdb=" N PHE R 63 " --> pdb=" O ILE R 59 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL R 64 " --> pdb=" O SER R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 78 removed outlier: 3.996A pdb=" N LEU R 71 " --> pdb=" O ILE R 67 " (cutoff:3.500A) Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 83 through 118 Processing helix chain 'R' and resid 118 through 125 Processing helix chain 'R' and resid 128 through 153 removed outlier: 3.977A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 171 through 183 Processing helix chain 'R' and resid 183 through 204 removed outlier: 3.676A pdb=" N LEU R 201 " --> pdb=" O ILE R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 330 Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 337 through 362 removed outlier: 3.554A pdb=" N GLN R 347 " --> pdb=" O ALA R 343 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) Proline residue: R 355 - end of helix Proline residue: R 359 - end of helix removed outlier: 3.566A pdb=" N HIS R 362 " --> pdb=" O TYR R 358 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 374 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.545A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.542A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.674A pdb=" N ARG D 49 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS D 317 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.602A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.919A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY D 116 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE D 120 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 134 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 151 removed outlier: 6.627A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N PHE D 151 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLN D 156 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.958A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.408A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.754A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.531A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 7.015A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.694A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL S 226 " --> pdb=" O GLN S 179 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.694A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR S 238 " --> pdb=" O GLN S 231 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1248 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: 1.63 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2100 1.33 - 1.45: 2019 1.45 - 1.57: 4931 1.57 - 1.69: 3 1.69 - 1.81: 85 Bond restraints: 9138 Sorted by residual: bond pdb=" O4 PO4 R 402 " pdb=" P PO4 R 402 " ideal model delta sigma weight residual 1.568 1.480 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CA HSM R 401 " pdb=" CB HSM R 401 " ideal model delta sigma weight residual 1.533 1.469 0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" CA THR G 52 " pdb=" C THR G 52 " ideal model delta sigma weight residual 1.521 1.556 -0.035 1.14e-02 7.69e+03 9.58e+00 bond pdb=" CG HSM R 401 " pdb=" ND1 HSM R 401 " ideal model delta sigma weight residual 1.383 1.327 0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" CA PRO G 49 " pdb=" C PRO G 49 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.10e-02 8.26e+03 7.02e+00 ... (remaining 9133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 12234 2.95 - 5.90: 121 5.90 - 8.84: 17 8.84 - 11.79: 8 11.79 - 14.74: 2 Bond angle restraints: 12382 Sorted by residual: angle pdb=" N TRP R 316 " pdb=" CA TRP R 316 " pdb=" C TRP R 316 " ideal model delta sigma weight residual 111.36 120.46 -9.10 1.09e+00 8.42e-01 6.97e+01 angle pdb=" N SER R 154 " pdb=" CA SER R 154 " pdb=" C SER R 154 " ideal model delta sigma weight residual 111.90 101.78 10.12 1.32e+00 5.74e-01 5.88e+01 angle pdb=" C CYS R 361 " pdb=" N HIS R 362 " pdb=" CA HIS R 362 " ideal model delta sigma weight residual 121.42 111.77 9.65 1.43e+00 4.89e-01 4.56e+01 angle pdb=" N LEU R 152 " pdb=" CA LEU R 152 " pdb=" C LEU R 152 " ideal model delta sigma weight residual 111.14 118.06 -6.92 1.08e+00 8.57e-01 4.11e+01 angle pdb=" N SER R 156 " pdb=" CA SER R 156 " pdb=" C SER R 156 " ideal model delta sigma weight residual 111.28 102.85 8.43 1.35e+00 5.49e-01 3.90e+01 ... (remaining 12377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 5100 14.88 - 29.76: 217 29.76 - 44.63: 45 44.63 - 59.51: 10 59.51 - 74.39: 4 Dihedral angle restraints: 5376 sinusoidal: 2083 harmonic: 3293 Sorted by residual: dihedral pdb=" CB CYS R 87 " pdb=" SG CYS R 87 " pdb=" SG CYS R 164 " pdb=" CB CYS R 164 " ideal model delta sinusoidal sigma weight residual -86.00 -156.12 70.12 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CA TYR S 235 " pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta harmonic sigma weight residual 0.00 28.99 -28.99 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" C TYR R 358 " pdb=" N TYR R 358 " pdb=" CA TYR R 358 " pdb=" CB TYR R 358 " ideal model delta harmonic sigma weight residual -122.60 -134.04 11.44 0 2.50e+00 1.60e-01 2.09e+01 ... (remaining 5373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1264 0.108 - 0.216: 110 0.216 - 0.324: 12 0.324 - 0.432: 3 0.432 - 0.541: 2 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CG LEU R 201 " pdb=" CB LEU R 201 " pdb=" CD1 LEU R 201 " pdb=" CD2 LEU R 201 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.30e+00 chirality pdb=" CA TYR R 358 " pdb=" N TYR R 358 " pdb=" C TYR R 358 " pdb=" CB TYR R 358 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA TRP R 316 " pdb=" N TRP R 316 " pdb=" C TRP R 316 " pdb=" CB TRP R 316 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 1388 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " 0.107 5.00e-02 4.00e+02 1.65e-01 4.33e+01 pdb=" N PRO G 53 " -0.285 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.095 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 358 " -0.077 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO R 359 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO R 359 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO R 359 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 317 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO R 318 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO R 318 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO R 318 " -0.042 5.00e-02 4.00e+02 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 861 2.74 - 3.28: 8941 3.28 - 3.82: 14646 3.82 - 4.36: 18292 4.36 - 4.90: 31649 Nonbonded interactions: 74389 Sorted by model distance: nonbonded pdb=" N HSM R 401 " pdb=" O1 PO4 R 402 " model vdw 2.202 3.120 nonbonded pdb=" NE2 GLN S 142 " pdb=" OG1 THR S 243 " model vdw 2.212 3.120 nonbonded pdb=" O THR D 86 " pdb=" OG1 THR D 87 " model vdw 2.213 3.040 nonbonded pdb=" OE1 GLU A 318 " pdb=" NZ LYS A 345 " model vdw 2.214 3.120 nonbonded pdb=" O THR A 262 " pdb=" NZ LYS A 317 " model vdw 2.217 3.120 ... (remaining 74384 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.210 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 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 0.088 9139 Z= 0.331 Angle : 0.797 14.738 12384 Z= 0.528 Chirality : 0.063 0.541 1391 Planarity : 0.007 0.165 1557 Dihedral : 8.984 74.389 3247 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.72 % Allowed : 2.36 % Favored : 96.92 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.33 % 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: -0.22 (0.24), residues: 1116 helix: 1.64 (0.26), residues: 402 sheet: -0.39 (0.31), residues: 254 loop : -1.64 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 364 TYR 0.012 0.001 TYR R 113 PHE 0.016 0.001 PHE R 168 TRP 0.012 0.001 TRP R 345 HIS 0.002 0.001 HIS R 292 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 9138) covalent geometry : angle 0.79632 (12382) SS BOND : bond 0.01388 ( 1) SS BOND : angle 2.67316 ( 2) hydrogen bonds : bond 0.22133 ( 439) hydrogen bonds : angle 6.69063 ( 1248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 238 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7904 (mttt) cc_final: 0.7645 (mmtp) REVERT: A 269 ASN cc_start: 0.8610 (m110) cc_final: 0.8219 (m-40) REVERT: A 349 LYS cc_start: 0.7333 (mtpt) cc_final: 0.7035 (mtmt) REVERT: D 46 ARG cc_start: 0.7110 (mtt-85) cc_final: 0.6782 (mtm-85) REVERT: D 175 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7350 (mm110) REVERT: D 188 MET cc_start: 0.8647 (mmm) cc_final: 0.8405 (mmm) REVERT: D 226 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7300 (mp0) REVERT: D 254 ASP cc_start: 0.7770 (t70) cc_final: 0.7385 (t0) REVERT: R 22 MET cc_start: 0.7167 (mtt) cc_final: 0.6933 (mtt) REVERT: R 92 THR cc_start: 0.7438 (m) cc_final: 0.7197 (p) REVERT: R 121 SER cc_start: 0.7811 (t) cc_final: 0.7586 (m) REVERT: R 363 LYS cc_start: 0.7668 (mmtt) cc_final: 0.7400 (mptt) REVERT: S 73 ASP cc_start: 0.7622 (t0) cc_final: 0.7025 (t0) REVERT: S 76 LYS cc_start: 0.7208 (mtpp) cc_final: 0.6868 (mtmm) REVERT: S 244 LYS cc_start: 0.7507 (ttpt) cc_final: 0.7083 (ttpp) outliers start: 7 outliers final: 0 residues processed: 243 average time/residue: 0.6641 time to fit residues: 170.5520 Evaluate side-chains 160 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 0.0670 overall best weight: 1.3460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 269 ASN A 322 HIS A 346 ASN D 32 GLN D 44 GLN D 75 GLN D 176 GLN G 24 ASN ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 HIS R 347 GLN R 362 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.150603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.107001 restraints weight = 10656.372| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.27 r_work: 0.3122 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9139 Z= 0.163 Angle : 0.575 10.847 12384 Z= 0.311 Chirality : 0.043 0.220 1391 Planarity : 0.005 0.089 1557 Dihedral : 4.352 27.715 1226 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.67 % Allowed : 10.07 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.60 (0.24), residues: 1116 helix: 1.88 (0.26), residues: 406 sheet: 0.29 (0.31), residues: 256 loop : -0.90 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 313 TYR 0.012 0.002 TYR S 50 PHE 0.017 0.002 PHE D 278 TRP 0.016 0.002 TRP D 169 HIS 0.005 0.002 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9138) covalent geometry : angle 0.57468 (12382) SS BOND : bond 0.00171 ( 1) SS BOND : angle 0.91949 ( 2) hydrogen bonds : bond 0.05473 ( 439) hydrogen bonds : angle 4.81001 ( 1248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 349 LYS cc_start: 0.8358 (mtpt) cc_final: 0.8083 (mtmt) REVERT: D 19 ARG cc_start: 0.7678 (ttp80) cc_final: 0.7458 (ttp80) REVERT: D 46 ARG cc_start: 0.8611 (mtt-85) cc_final: 0.8035 (mtp-110) REVERT: D 96 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8168 (mtt180) REVERT: D 175 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7949 (mm110) REVERT: D 188 MET cc_start: 0.9052 (mmm) cc_final: 0.8788 (mmm) REVERT: D 217 MET cc_start: 0.8377 (pmm) cc_final: 0.8079 (pmt) REVERT: D 226 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8293 (mp0) REVERT: D 263 THR cc_start: 0.9107 (t) cc_final: 0.8819 (m) REVERT: R 121 SER cc_start: 0.8517 (t) cc_final: 0.8174 (m) REVERT: R 150 MET cc_start: 0.7081 (mmp) cc_final: 0.6718 (mmt) REVERT: S 34 MET cc_start: 0.8554 (mmp) cc_final: 0.8131 (mmt) REVERT: S 73 ASP cc_start: 0.8226 (t0) cc_final: 0.7781 (t0) REVERT: S 76 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7462 (mtmm) REVERT: S 87 ARG cc_start: 0.7476 (mpt-90) cc_final: 0.7196 (mpt-90) outliers start: 26 outliers final: 12 residues processed: 178 average time/residue: 0.7193 time to fit residues: 135.1283 Evaluate side-chains 164 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 331 ASN A 347 ASN D 75 GLN D 259 GLN D 340 ASN R 75 HIS S 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.104610 restraints weight = 10503.296| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.33 r_work: 0.3104 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9139 Z= 0.127 Angle : 0.513 9.553 12384 Z= 0.277 Chirality : 0.041 0.182 1391 Planarity : 0.005 0.078 1557 Dihedral : 4.235 20.672 1226 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.98 % Allowed : 12.64 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.87 (0.25), residues: 1116 helix: 2.05 (0.26), residues: 406 sheet: 0.31 (0.29), residues: 282 loop : -0.65 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 160 TYR 0.009 0.001 TYR R 173 PHE 0.013 0.001 PHE D 151 TRP 0.016 0.001 TRP D 169 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9138) covalent geometry : angle 0.51269 (12382) SS BOND : bond 0.00061 ( 1) SS BOND : angle 0.61944 ( 2) hydrogen bonds : bond 0.04734 ( 439) hydrogen bonds : angle 4.50679 ( 1248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.372 Fit side-chains REVERT: A 330 LYS cc_start: 0.7220 (mtpt) cc_final: 0.6907 (mttp) REVERT: A 349 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7938 (mtmt) REVERT: D 19 ARG cc_start: 0.7562 (ttp80) cc_final: 0.7329 (ttp80) REVERT: D 46 ARG cc_start: 0.8457 (mtt-85) cc_final: 0.7862 (mtp-110) REVERT: D 96 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7964 (mtt180) REVERT: D 175 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7825 (mm110) REVERT: D 217 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8095 (pmt) REVERT: D 226 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8213 (mp0) REVERT: R 121 SER cc_start: 0.8293 (t) cc_final: 0.7881 (m) REVERT: R 150 MET cc_start: 0.7012 (mmp) cc_final: 0.6631 (mmt) REVERT: R 372 ILE cc_start: 0.6269 (OUTLIER) cc_final: 0.6052 (mp) REVERT: S 34 MET cc_start: 0.8614 (mmp) cc_final: 0.8182 (mmt) REVERT: S 73 ASP cc_start: 0.8070 (t0) cc_final: 0.7690 (t70) REVERT: S 76 LYS cc_start: 0.7686 (mtpp) cc_final: 0.7323 (mtmm) REVERT: S 206 SER cc_start: 0.7770 (OUTLIER) cc_final: 0.7244 (p) REVERT: S 246 GLU cc_start: 0.8010 (pm20) cc_final: 0.7785 (pm20) outliers start: 29 outliers final: 14 residues processed: 182 average time/residue: 0.6679 time to fit residues: 128.7729 Evaluate side-chains 175 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 372 ILE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 103 optimal weight: 0.0980 chunk 19 optimal weight: 0.0970 chunk 35 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 195 HIS A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN D 44 GLN D 237 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 ASN R 75 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.103030 restraints weight = 10726.468| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.33 r_work: 0.3080 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9139 Z= 0.129 Angle : 0.509 9.394 12384 Z= 0.274 Chirality : 0.041 0.191 1391 Planarity : 0.005 0.071 1557 Dihedral : 4.281 20.318 1226 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.19 % Allowed : 13.67 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.07 (0.25), residues: 1116 helix: 2.17 (0.25), residues: 408 sheet: 0.37 (0.28), residues: 291 loop : -0.46 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 160 TYR 0.012 0.001 TYR A 287 PHE 0.014 0.001 PHE D 151 TRP 0.014 0.001 TRP D 169 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9138) covalent geometry : angle 0.50919 (12382) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.62473 ( 2) hydrogen bonds : bond 0.04441 ( 439) hydrogen bonds : angle 4.35507 ( 1248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.364 Fit side-chains REVERT: A 17 LYS cc_start: 0.7892 (mttt) cc_final: 0.7417 (mtpt) REVERT: A 330 LYS cc_start: 0.7205 (mtpt) cc_final: 0.6935 (mttp) REVERT: A 349 LYS cc_start: 0.8308 (mtpt) cc_final: 0.7966 (mtmt) REVERT: D 19 ARG cc_start: 0.7601 (ttp80) cc_final: 0.7358 (ttp80) REVERT: D 46 ARG cc_start: 0.8421 (mtt-85) cc_final: 0.7835 (mtp180) REVERT: D 96 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7854 (mtt180) REVERT: D 175 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7844 (mm110) REVERT: D 217 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8199 (pmt) REVERT: D 226 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8246 (mp0) REVERT: D 325 MET cc_start: 0.8725 (tpp) cc_final: 0.8413 (mmm) REVERT: R 121 SER cc_start: 0.8298 (t) cc_final: 0.7875 (m) REVERT: R 150 MET cc_start: 0.7020 (mmp) cc_final: 0.6709 (mmt) REVERT: S 19 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8295 (tppp) REVERT: S 34 MET cc_start: 0.8655 (mmp) cc_final: 0.8097 (mmt) REVERT: S 76 LYS cc_start: 0.7667 (mtpp) cc_final: 0.7360 (mtmm) REVERT: S 87 ARG cc_start: 0.7591 (mpt-90) cc_final: 0.7286 (mpt-90) REVERT: S 206 SER cc_start: 0.7786 (OUTLIER) cc_final: 0.7282 (p) REVERT: S 246 GLU cc_start: 0.8124 (pm20) cc_final: 0.7851 (pm20) outliers start: 31 outliers final: 17 residues processed: 175 average time/residue: 0.6784 time to fit residues: 125.5846 Evaluate side-chains 173 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 306 GLN A 331 ASN A 347 ASN D 237 ASN D 259 GLN R 75 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.103000 restraints weight = 10664.198| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.33 r_work: 0.3083 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9139 Z= 0.121 Angle : 0.492 8.429 12384 Z= 0.265 Chirality : 0.041 0.175 1391 Planarity : 0.004 0.074 1557 Dihedral : 4.198 20.047 1226 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.60 % Allowed : 14.39 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.24 (0.25), residues: 1116 helix: 2.25 (0.26), residues: 408 sheet: 0.62 (0.29), residues: 278 loop : -0.40 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 160 TYR 0.009 0.001 TYR R 173 PHE 0.012 0.001 PHE D 151 TRP 0.014 0.001 TRP D 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9138) covalent geometry : angle 0.49222 (12382) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.30397 ( 2) hydrogen bonds : bond 0.04271 ( 439) hydrogen bonds : angle 4.25818 ( 1248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.359 Fit side-chains REVERT: A 17 LYS cc_start: 0.7887 (mttt) cc_final: 0.7408 (mtpt) REVERT: A 330 LYS cc_start: 0.7226 (mtpt) cc_final: 0.6975 (mttp) REVERT: A 349 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7982 (mtmt) REVERT: D 19 ARG cc_start: 0.7542 (ttp80) cc_final: 0.7300 (ttp80) REVERT: D 46 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.7775 (mtp180) REVERT: D 96 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7869 (mtt180) REVERT: D 175 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7864 (mm110) REVERT: D 217 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8230 (pmt) REVERT: D 226 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8247 (mp0) REVERT: R 121 SER cc_start: 0.8299 (t) cc_final: 0.7859 (m) REVERT: R 150 MET cc_start: 0.7121 (mmp) cc_final: 0.6844 (mmt) REVERT: S 19 LYS cc_start: 0.8561 (tttt) cc_final: 0.8326 (tppp) REVERT: S 34 MET cc_start: 0.8640 (mmp) cc_final: 0.8084 (mmt) REVERT: S 73 ASP cc_start: 0.8055 (t0) cc_final: 0.7552 (t70) REVERT: S 76 LYS cc_start: 0.7723 (mtpp) cc_final: 0.7284 (mtmm) REVERT: S 109 ASP cc_start: 0.7935 (p0) cc_final: 0.7718 (p0) REVERT: S 246 GLU cc_start: 0.8185 (pm20) cc_final: 0.7942 (pm20) outliers start: 35 outliers final: 19 residues processed: 168 average time/residue: 0.7441 time to fit residues: 131.8359 Evaluate side-chains 166 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 195 MET Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 223 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 105 optimal weight: 0.1980 chunk 106 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN D 237 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.148645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.104513 restraints weight = 10572.043| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.31 r_work: 0.3106 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9139 Z= 0.102 Angle : 0.473 7.588 12384 Z= 0.254 Chirality : 0.040 0.174 1391 Planarity : 0.004 0.073 1557 Dihedral : 4.017 19.222 1226 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.67 % Allowed : 16.14 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.41 (0.25), residues: 1116 helix: 2.38 (0.26), residues: 407 sheet: 0.85 (0.29), residues: 275 loop : -0.40 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 313 TYR 0.009 0.001 TYR R 173 PHE 0.010 0.001 PHE D 151 TRP 0.014 0.001 TRP D 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 9138) covalent geometry : angle 0.47257 (12382) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.36026 ( 2) hydrogen bonds : bond 0.03901 ( 439) hydrogen bonds : angle 4.08850 ( 1248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.357 Fit side-chains REVERT: A 17 LYS cc_start: 0.7870 (mttt) cc_final: 0.7395 (mtpt) REVERT: A 330 LYS cc_start: 0.7221 (mtpt) cc_final: 0.6956 (mttp) REVERT: A 349 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7938 (mtmt) REVERT: D 19 ARG cc_start: 0.7544 (ttp80) cc_final: 0.7208 (ttp80) REVERT: D 46 ARG cc_start: 0.8365 (mtt-85) cc_final: 0.7770 (mtp180) REVERT: D 175 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7820 (mm110) REVERT: D 217 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8257 (pmt) REVERT: D 226 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8202 (mp0) REVERT: G 20 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7826 (mtmm) REVERT: R 47 ARG cc_start: 0.7704 (mmp80) cc_final: 0.7436 (mmp-170) REVERT: R 121 SER cc_start: 0.8244 (t) cc_final: 0.7795 (m) REVERT: R 150 MET cc_start: 0.6964 (mmp) cc_final: 0.6749 (mmt) REVERT: S 19 LYS cc_start: 0.8514 (tttt) cc_final: 0.8281 (tppp) REVERT: S 31 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8398 (t) REVERT: S 34 MET cc_start: 0.8610 (mmp) cc_final: 0.8136 (mmt) REVERT: S 73 ASP cc_start: 0.8028 (t0) cc_final: 0.7495 (t70) REVERT: S 76 LYS cc_start: 0.7718 (mtpp) cc_final: 0.7295 (mtmm) REVERT: S 206 SER cc_start: 0.7769 (OUTLIER) cc_final: 0.7245 (p) REVERT: S 244 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7293 (ttmt) REVERT: S 246 GLU cc_start: 0.8167 (pm20) cc_final: 0.7912 (pm20) outliers start: 26 outliers final: 13 residues processed: 159 average time/residue: 0.6414 time to fit residues: 107.5891 Evaluate side-chains 160 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 109 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 HIS ** 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 = 0.3760 r_free = 0.3760 target = 0.146899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102391 restraints weight = 10680.089| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.32 r_work: 0.3074 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9139 Z= 0.127 Angle : 0.499 9.558 12384 Z= 0.268 Chirality : 0.041 0.182 1391 Planarity : 0.004 0.080 1557 Dihedral : 4.142 19.800 1226 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.49 % Allowed : 15.83 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.38 (0.25), residues: 1116 helix: 2.29 (0.25), residues: 410 sheet: 0.81 (0.29), residues: 281 loop : -0.36 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.009 0.001 TYR R 173 PHE 0.012 0.001 PHE D 151 TRP 0.015 0.001 TRP R 80 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9138) covalent geometry : angle 0.49936 (12382) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.41365 ( 2) hydrogen bonds : bond 0.04192 ( 439) hydrogen bonds : angle 4.19104 ( 1248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.278 Fit side-chains REVERT: A 17 LYS cc_start: 0.7966 (mttt) cc_final: 0.7486 (mtpt) REVERT: A 330 LYS cc_start: 0.7247 (mtpt) cc_final: 0.6952 (mttp) REVERT: A 349 LYS cc_start: 0.8299 (mtpt) cc_final: 0.7959 (mtmt) REVERT: D 19 ARG cc_start: 0.7564 (ttp80) cc_final: 0.7344 (ttp80) REVERT: D 46 ARG cc_start: 0.8375 (mtt-85) cc_final: 0.7768 (mtp180) REVERT: D 175 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7864 (mm110) REVERT: D 217 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8266 (pmt) REVERT: D 226 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8215 (mp0) REVERT: G 20 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7877 (mtmm) REVERT: R 47 ARG cc_start: 0.7768 (mmp80) cc_final: 0.7386 (mmp-170) REVERT: R 80 TRP cc_start: 0.7041 (t60) cc_final: 0.6501 (t60) REVERT: R 121 SER cc_start: 0.8294 (t) cc_final: 0.7862 (m) REVERT: R 150 MET cc_start: 0.7132 (mmp) cc_final: 0.6909 (mmt) REVERT: S 19 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8304 (tppp) REVERT: S 31 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8421 (t) REVERT: S 34 MET cc_start: 0.8700 (mmp) cc_final: 0.8104 (mmt) REVERT: S 76 LYS cc_start: 0.7751 (mtpp) cc_final: 0.7430 (mtmm) REVERT: S 191 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.6677 (mtp180) REVERT: S 206 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7284 (p) REVERT: S 246 GLU cc_start: 0.8164 (pm20) cc_final: 0.7938 (pm20) outliers start: 34 outliers final: 21 residues processed: 161 average time/residue: 0.6382 time to fit residues: 108.6834 Evaluate side-chains 166 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 195 MET Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 223 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 102 optimal weight: 0.0170 chunk 37 optimal weight: 0.6980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN D 237 ASN ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.104498 restraints weight = 10663.209| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.32 r_work: 0.3107 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9139 Z= 0.099 Angle : 0.471 8.187 12384 Z= 0.253 Chirality : 0.039 0.173 1391 Planarity : 0.004 0.078 1557 Dihedral : 3.965 18.764 1226 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.36 % Allowed : 17.37 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.50 (0.25), residues: 1116 helix: 2.43 (0.26), residues: 408 sheet: 0.96 (0.30), residues: 275 loop : -0.38 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 313 TYR 0.014 0.001 TYR A 287 PHE 0.010 0.001 PHE D 151 TRP 0.014 0.001 TRP D 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 9138) covalent geometry : angle 0.47090 (12382) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.45681 ( 2) hydrogen bonds : bond 0.03776 ( 439) hydrogen bonds : angle 4.05494 ( 1248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.258 Fit side-chains REVERT: A 17 LYS cc_start: 0.7910 (mttt) cc_final: 0.7427 (mtpt) REVERT: A 330 LYS cc_start: 0.7206 (mtpt) cc_final: 0.6951 (mttp) REVERT: A 349 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7936 (mtmt) REVERT: D 19 ARG cc_start: 0.7556 (ttp80) cc_final: 0.7342 (ttp80) REVERT: D 46 ARG cc_start: 0.8374 (mtt-85) cc_final: 0.7766 (mtp180) REVERT: D 175 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7815 (mm110) REVERT: D 217 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8227 (pmt) REVERT: D 226 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8198 (mp0) REVERT: R 47 ARG cc_start: 0.7781 (mmp80) cc_final: 0.7389 (mmp-170) REVERT: R 80 TRP cc_start: 0.7097 (t60) cc_final: 0.6626 (t60) REVERT: R 121 SER cc_start: 0.8241 (t) cc_final: 0.7792 (m) REVERT: S 19 LYS cc_start: 0.8501 (tttt) cc_final: 0.8274 (tppp) REVERT: S 31 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8405 (t) REVERT: S 34 MET cc_start: 0.8616 (mmp) cc_final: 0.8144 (mmt) REVERT: S 73 ASP cc_start: 0.7984 (t0) cc_final: 0.7473 (t70) REVERT: S 76 LYS cc_start: 0.7735 (mtpp) cc_final: 0.7336 (mtmm) REVERT: S 109 ASP cc_start: 0.8046 (p0) cc_final: 0.7787 (p0) REVERT: S 206 SER cc_start: 0.7705 (OUTLIER) cc_final: 0.7258 (p) REVERT: S 246 GLU cc_start: 0.8150 (pm20) cc_final: 0.7924 (pm20) outliers start: 23 outliers final: 14 residues processed: 158 average time/residue: 0.5817 time to fit residues: 97.1428 Evaluate side-chains 156 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 223 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 0.0470 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN D 237 ASN D 259 GLN ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 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 = 0.3760 r_free = 0.3760 target = 0.146999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102482 restraints weight = 10627.430| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.31 r_work: 0.3077 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9139 Z= 0.124 Angle : 0.505 8.988 12384 Z= 0.271 Chirality : 0.040 0.179 1391 Planarity : 0.004 0.083 1557 Dihedral : 4.108 19.540 1226 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.47 % Allowed : 17.37 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.47 (0.25), residues: 1116 helix: 2.37 (0.25), residues: 409 sheet: 0.97 (0.30), residues: 275 loop : -0.37 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 313 TYR 0.016 0.001 TYR A 287 PHE 0.012 0.001 PHE D 151 TRP 0.011 0.001 TRP R 80 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9138) covalent geometry : angle 0.50507 (12382) SS BOND : bond 0.00021 ( 1) SS BOND : angle 0.27062 ( 2) hydrogen bonds : bond 0.04117 ( 439) hydrogen bonds : angle 4.17048 ( 1248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.240 Fit side-chains REVERT: A 9 ASP cc_start: 0.8058 (m-30) cc_final: 0.7770 (m-30) REVERT: A 17 LYS cc_start: 0.7954 (mttt) cc_final: 0.7470 (mtpt) REVERT: A 330 LYS cc_start: 0.7270 (mtpt) cc_final: 0.6979 (mttp) REVERT: A 349 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7937 (mtmt) REVERT: D 19 ARG cc_start: 0.7568 (ttp80) cc_final: 0.7351 (ttp80) REVERT: D 46 ARG cc_start: 0.8353 (mtt-85) cc_final: 0.7693 (mtp180) REVERT: D 175 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7871 (mm110) REVERT: D 217 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8217 (pmt) REVERT: D 226 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8218 (mp0) REVERT: R 80 TRP cc_start: 0.7120 (t60) cc_final: 0.6660 (t60) REVERT: R 121 SER cc_start: 0.8283 (t) cc_final: 0.7847 (m) REVERT: S 19 LYS cc_start: 0.8530 (tttt) cc_final: 0.8313 (tppp) REVERT: S 31 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8418 (t) REVERT: S 34 MET cc_start: 0.8700 (mmp) cc_final: 0.8091 (mmt) REVERT: S 73 ASP cc_start: 0.8017 (t0) cc_final: 0.7491 (t70) REVERT: S 76 LYS cc_start: 0.7770 (mtpp) cc_final: 0.7369 (mtmm) REVERT: S 109 ASP cc_start: 0.8049 (p0) cc_final: 0.7815 (p0) REVERT: S 206 SER cc_start: 0.7737 (OUTLIER) cc_final: 0.7277 (p) REVERT: S 244 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7308 (ttmt) REVERT: S 246 GLU cc_start: 0.8166 (pm20) cc_final: 0.7930 (pm20) outliers start: 24 outliers final: 18 residues processed: 155 average time/residue: 0.5513 time to fit residues: 90.4016 Evaluate side-chains 160 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 ASN ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 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 = 0.3752 r_free = 0.3752 target = 0.146200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.101530 restraints weight = 10580.874| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.32 r_work: 0.3061 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9139 Z= 0.141 Angle : 0.530 9.822 12384 Z= 0.283 Chirality : 0.041 0.186 1391 Planarity : 0.004 0.086 1557 Dihedral : 4.242 19.754 1226 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.77 % Allowed : 17.27 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.46 (0.25), residues: 1116 helix: 2.38 (0.25), residues: 403 sheet: 0.89 (0.30), residues: 276 loop : -0.31 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.015 0.001 TYR A 287 PHE 0.013 0.001 PHE D 151 TRP 0.010 0.001 TRP D 169 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9138) covalent geometry : angle 0.52992 (12382) SS BOND : bond 0.00021 ( 1) SS BOND : angle 0.18645 ( 2) hydrogen bonds : bond 0.04373 ( 439) hydrogen bonds : angle 4.29427 ( 1248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.211 Fit side-chains REVERT: A 9 ASP cc_start: 0.8074 (m-30) cc_final: 0.7811 (m-30) REVERT: A 17 LYS cc_start: 0.8012 (mttt) cc_final: 0.7536 (mtpt) REVERT: A 330 LYS cc_start: 0.7219 (mtpt) cc_final: 0.6963 (mttp) REVERT: A 349 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7943 (mtmt) REVERT: D 19 ARG cc_start: 0.7559 (ttp80) cc_final: 0.7217 (ttp80) REVERT: D 46 ARG cc_start: 0.8375 (mtt-85) cc_final: 0.7716 (mtp180) REVERT: D 175 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7871 (mm110) REVERT: D 217 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8207 (pmt) REVERT: D 226 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8230 (mp0) REVERT: R 80 TRP cc_start: 0.7116 (t60) cc_final: 0.6720 (t60) REVERT: R 121 SER cc_start: 0.8277 (t) cc_final: 0.7838 (m) REVERT: S 19 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8363 (tppp) REVERT: S 34 MET cc_start: 0.8712 (mmp) cc_final: 0.8057 (mmt) REVERT: S 73 ASP cc_start: 0.8029 (t0) cc_final: 0.7506 (t70) REVERT: S 76 LYS cc_start: 0.7748 (mtpp) cc_final: 0.7362 (mtmm) REVERT: S 109 ASP cc_start: 0.8044 (p0) cc_final: 0.7806 (p0) REVERT: S 191 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.6695 (mtp180) REVERT: S 206 SER cc_start: 0.7750 (OUTLIER) cc_final: 0.7290 (p) REVERT: S 244 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7318 (ttmt) REVERT: S 246 GLU cc_start: 0.8155 (pm20) cc_final: 0.7934 (pm20) outliers start: 27 outliers final: 21 residues processed: 158 average time/residue: 0.5815 time to fit residues: 96.8690 Evaluate side-chains 165 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 102 optimal weight: 0.0470 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 ASN ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 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 = 0.3767 r_free = 0.3767 target = 0.147518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.104274 restraints weight = 10547.393| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.26 r_work: 0.3104 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9139 Z= 0.106 Angle : 0.499 10.422 12384 Z= 0.266 Chirality : 0.040 0.176 1391 Planarity : 0.004 0.083 1557 Dihedral : 3.989 18.630 1226 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.47 % Allowed : 17.68 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.56 (0.25), residues: 1116 helix: 2.48 (0.26), residues: 402 sheet: 0.99 (0.30), residues: 275 loop : -0.29 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 313 TYR 0.013 0.001 TYR A 287 PHE 0.011 0.001 PHE D 151 TRP 0.014 0.001 TRP D 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9138) covalent geometry : angle 0.49862 (12382) SS BOND : bond 0.00016 ( 1) SS BOND : angle 0.46235 ( 2) hydrogen bonds : bond 0.03882 ( 439) hydrogen bonds : angle 4.12504 ( 1248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4150.65 seconds wall clock time: 71 minutes 20.66 seconds (4280.66 seconds total)