Starting phenix.real_space_refine on Thu Feb 13 12:50:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vab_31836/02_2025/7vab_31836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vab_31836/02_2025/7vab_31836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vab_31836/02_2025/7vab_31836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vab_31836/02_2025/7vab_31836.map" model { file = "/net/cci-nas-00/data/ceres_data/7vab_31836/02_2025/7vab_31836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vab_31836/02_2025/7vab_31836.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5616 2.51 5 N 1525 2.21 5 O 1583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8772 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2399 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain breaks: 4 Chain: "P" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 220 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.31, per 1000 atoms: 0.61 Number of scatterers: 8772 At special positions: 0 Unit cell: (81.396, 101.745, 160.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1583 8.00 N 1525 7.00 C 5616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 216 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 994.4 milliseconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.4% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'R' and resid 31 through 48 Processing helix chain 'R' and resid 128 through 162 removed outlier: 3.806A pdb=" N ALA R 150 " --> pdb=" O SER R 146 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE R 162 " --> pdb=" O ILE R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 166 removed outlier: 3.526A pdb=" N HIS R 166 " --> pdb=" O ARG R 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 163 through 166' Processing helix chain 'R' and resid 167 through 193 removed outlier: 3.549A pdb=" N ILE R 172 " --> pdb=" O THR R 168 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG R 192 " --> pdb=" O LEU R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 246 removed outlier: 3.739A pdb=" N ILE R 221 " --> pdb=" O ARG R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 281 removed outlier: 3.890A pdb=" N TYR R 259 " --> pdb=" O HIS R 255 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU R 260 " --> pdb=" O PHE R 256 " (cutoff:3.500A) Proline residue: R 267 - end of helix Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 296 through 328 Proline residue: R 302 - end of helix removed outlier: 4.271A pdb=" N THR R 306 " --> pdb=" O PRO R 302 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU R 318 " --> pdb=" O PHE R 314 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU R 325 " --> pdb=" O LEU R 321 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR R 327 " --> pdb=" O SER R 323 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG R 328 " --> pdb=" O LYS R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 351 removed outlier: 3.959A pdb=" N LEU R 339 " --> pdb=" O TYR R 335 " (cutoff:3.500A) Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 368 through 383 removed outlier: 3.621A pdb=" N ALA R 372 " --> pdb=" O ALA R 368 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE R 378 " --> pdb=" O LEU R 374 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU R 380 " --> pdb=" O PHE R 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE R 383 " --> pdb=" O PHE R 379 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 394 Processing helix chain 'R' and resid 396 through 411 removed outlier: 3.581A pdb=" N GLY R 406 " --> pdb=" O GLU R 402 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.956A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.508A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 removed outlier: 3.605A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A 218 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.502A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.445A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.646A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.786A pdb=" N THR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.755A pdb=" N PHE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.753A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.717A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.813A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.756A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.037A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.868A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.922A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.757A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.563A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.583A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.586A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.591A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.556A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.272A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1242 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: 2.46 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2839 1.34 - 1.46: 2008 1.46 - 1.58: 4052 1.58 - 1.70: 0 1.70 - 1.81: 66 Bond restraints: 8965 Sorted by residual: bond pdb=" C5 CLR R 603 " pdb=" C6 CLR R 603 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C5 CLR R 605 " pdb=" C6 CLR R 605 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C5 CLR R 602 " pdb=" C6 CLR R 602 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C5 CLR R 601 " pdb=" C6 CLR R 601 " ideal model delta sigma weight residual 1.332 1.302 0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C ALA R 266 " pdb=" N PRO R 267 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.30e+00 ... (remaining 8960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 12040 3.11 - 6.22: 115 6.22 - 9.33: 13 9.33 - 12.44: 1 12.44 - 15.55: 1 Bond angle restraints: 12170 Sorted by residual: angle pdb=" C ASP A 229 " pdb=" N TYR A 230 " pdb=" CA TYR A 230 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 angle pdb=" CA TYR R 141 " pdb=" CB TYR R 141 " pdb=" CG TYR R 141 " ideal model delta sigma weight residual 113.90 119.75 -5.85 1.80e+00 3.09e-01 1.06e+01 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 122.40 126.93 -4.53 1.45e+00 4.76e-01 9.77e+00 angle pdb=" C MET R 140 " pdb=" N TYR R 141 " pdb=" CA TYR R 141 " ideal model delta sigma weight residual 121.14 116.04 5.10 1.75e+00 3.27e-01 8.49e+00 angle pdb=" CA LYS B 127 " pdb=" CB LYS B 127 " pdb=" CG LYS B 127 " ideal model delta sigma weight residual 114.10 119.77 -5.67 2.00e+00 2.50e-01 8.05e+00 ... (remaining 12165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 5379 14.99 - 29.98: 158 29.98 - 44.98: 52 44.98 - 59.97: 16 59.97 - 74.96: 6 Dihedral angle restraints: 5611 sinusoidal: 2484 harmonic: 3127 Sorted by residual: dihedral pdb=" CB CYS R 216 " pdb=" SG CYS R 216 " pdb=" SG CYS R 286 " pdb=" CB CYS R 286 " ideal model delta sinusoidal sigma weight residual 93.00 142.34 -49.34 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -117.55 31.55 1 1.00e+01 1.00e-02 1.42e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1223 0.085 - 0.169: 123 0.169 - 0.254: 11 0.254 - 0.338: 6 0.338 - 0.423: 6 Chirality restraints: 1369 Sorted by residual: chirality pdb=" C14 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C15 CLR R 602 " pdb=" C8 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C14 CLR R 604 " pdb=" C13 CLR R 604 " pdb=" C15 CLR R 604 " pdb=" C8 CLR R 604 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 1366 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 298 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 299 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 309 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C ILE R 309 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE R 309 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN R 310 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO N 88 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.025 5.00e-02 4.00e+02 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2016 2.80 - 3.32: 7579 3.32 - 3.85: 13849 3.85 - 4.37: 15977 4.37 - 4.90: 28255 Nonbonded interactions: 67676 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.270 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.307 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.313 3.040 nonbonded pdb=" NH1 ARG A 209 " pdb=" OD2 ASP N 109 " model vdw 2.360 3.120 ... (remaining 67671 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: 0.920 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.430 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 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 : 0.004 0.052 8965 Z= 0.223 Angle : 0.800 15.553 12170 Z= 0.416 Chirality : 0.062 0.423 1369 Planarity : 0.006 0.049 1514 Dihedral : 9.193 74.961 3582 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.21), residues: 1050 helix: -1.67 (0.18), residues: 409 sheet: -0.85 (0.33), residues: 224 loop : -1.80 (0.25), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 248 HIS 0.004 0.001 HIS R 173 PHE 0.021 0.002 PHE B 199 TYR 0.022 0.002 TYR B 264 ARG 0.007 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 137 LEU cc_start: 0.8137 (mt) cc_final: 0.7863 (mt) REVERT: R 181 MET cc_start: 0.7377 (ttm) cc_final: 0.7058 (mtt) REVERT: R 192 ARG cc_start: 0.7505 (mmt-90) cc_final: 0.6621 (mmp-170) REVERT: R 193 LEU cc_start: 0.7916 (mt) cc_final: 0.7613 (tt) REVERT: R 194 LEU cc_start: 0.6093 (tp) cc_final: 0.5861 (tp) REVERT: R 217 ARG cc_start: 0.7523 (mtt180) cc_final: 0.7108 (ttm110) REVERT: R 252 GLU cc_start: 0.4957 (mp0) cc_final: 0.4501 (pt0) REVERT: R 253 GLU cc_start: 0.4555 (pm20) cc_final: 0.3975 (mm-30) REVERT: R 327 THR cc_start: 0.6131 (m) cc_final: 0.5836 (p) REVERT: R 402 GLU cc_start: 0.7518 (tp30) cc_final: 0.7311 (tp30) REVERT: A 15 ARG cc_start: 0.6827 (ttt180) cc_final: 0.6540 (ttt-90) REVERT: A 274 LYS cc_start: 0.7881 (ptmt) cc_final: 0.7597 (ptpp) REVERT: A 310 ASP cc_start: 0.7029 (t70) cc_final: 0.6614 (t0) REVERT: A 311 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7251 (mm-30) REVERT: B 44 GLN cc_start: 0.7858 (mt0) cc_final: 0.7558 (mm-40) REVERT: B 135 VAL cc_start: 0.8096 (t) cc_final: 0.7832 (t) REVERT: B 156 GLN cc_start: 0.7924 (mt0) cc_final: 0.7715 (mt0) REVERT: B 217 MET cc_start: 0.7128 (mtm) cc_final: 0.6456 (mmt) REVERT: B 262 MET cc_start: 0.6874 (ttm) cc_final: 0.6607 (tpt) REVERT: B 280 LYS cc_start: 0.9014 (tttp) cc_final: 0.8766 (ttmm) REVERT: G 21 MET cc_start: 0.8139 (mmt) cc_final: 0.7898 (ttt) REVERT: N 21 SER cc_start: 0.8550 (m) cc_final: 0.8325 (t) REVERT: N 28 THR cc_start: 0.8087 (m) cc_final: 0.7708 (p) REVERT: N 87 LYS cc_start: 0.8100 (mttt) cc_final: 0.7617 (ttmt) REVERT: N 90 ASP cc_start: 0.8245 (t0) cc_final: 0.7937 (m-30) REVERT: N 117 TYR cc_start: 0.8123 (m-10) cc_final: 0.7381 (m-80) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.3093 time to fit residues: 106.4857 Evaluate side-chains 170 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 0.0010 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 173 HIS R 224 GLN R 408 HIS A 204 GLN A 324 HIS A 329 HIS B 62 HIS B 88 ASN B 91 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 266 HIS N 31 ASN N 35 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.211192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.153408 restraints weight = 8916.420| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.17 r_work: 0.3528 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8965 Z= 0.331 Angle : 0.604 14.598 12170 Z= 0.310 Chirality : 0.043 0.144 1369 Planarity : 0.005 0.054 1514 Dihedral : 6.755 57.650 1582 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.52 % Allowed : 8.23 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1050 helix: 0.88 (0.24), residues: 432 sheet: -0.66 (0.33), residues: 224 loop : -1.41 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.011 0.002 HIS A 324 PHE 0.022 0.002 PHE R 376 TYR 0.026 0.002 TYR R 141 ARG 0.006 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7950 (mm-30) REVERT: R 181 MET cc_start: 0.8315 (ttm) cc_final: 0.8007 (mtt) REVERT: R 192 ARG cc_start: 0.7293 (mmt-90) cc_final: 0.6590 (mmp-170) REVERT: R 193 LEU cc_start: 0.7679 (mt) cc_final: 0.7352 (tt) REVERT: R 252 GLU cc_start: 0.5307 (mp0) cc_final: 0.4676 (pm20) REVERT: R 253 GLU cc_start: 0.4782 (pm20) cc_final: 0.3884 (mm-30) REVERT: R 289 ARG cc_start: 0.7903 (mtp180) cc_final: 0.7307 (mtm180) REVERT: R 336 ARG cc_start: 0.6078 (mtt180) cc_final: 0.5365 (tpt170) REVERT: R 345 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7250 (t80) REVERT: A 31 ARG cc_start: 0.8354 (mtm110) cc_final: 0.7921 (mtt-85) REVERT: A 47 SER cc_start: 0.8545 (m) cc_final: 0.8246 (p) REVERT: A 53 MET cc_start: 0.8029 (mmt) cc_final: 0.7821 (mmt) REVERT: A 193 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7940 (mtmm) REVERT: A 274 LYS cc_start: 0.8214 (ptmt) cc_final: 0.8009 (ptpp) REVERT: A 310 ASP cc_start: 0.8136 (t70) cc_final: 0.7800 (t0) REVERT: A 323 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.7191 (mtm110) REVERT: B 13 GLN cc_start: 0.8783 (pt0) cc_final: 0.8542 (pt0) REVERT: B 44 GLN cc_start: 0.8450 (mt0) cc_final: 0.8049 (mm-40) REVERT: B 215 GLU cc_start: 0.7942 (mp0) cc_final: 0.7609 (mp0) REVERT: N 67 ARG cc_start: 0.6728 (mtp85) cc_final: 0.6525 (mtm180) REVERT: N 87 LYS cc_start: 0.7992 (mttt) cc_final: 0.7627 (ttmt) REVERT: N 90 ASP cc_start: 0.8535 (t0) cc_final: 0.8272 (t0) outliers start: 14 outliers final: 6 residues processed: 191 average time/residue: 0.2775 time to fit residues: 68.2826 Evaluate side-chains 163 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 60 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 55 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 ASN R 242 HIS A 197 HIS B 239 ASN B 259 GLN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.210948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.163975 restraints weight = 9004.447| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 3.33 r_work: 0.3443 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8965 Z= 0.190 Angle : 0.513 12.615 12170 Z= 0.260 Chirality : 0.040 0.137 1369 Planarity : 0.003 0.036 1514 Dihedral : 6.101 47.252 1582 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.38 % Allowed : 11.04 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1050 helix: 1.71 (0.25), residues: 433 sheet: -0.50 (0.33), residues: 228 loop : -1.17 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.004 0.001 HIS B 142 PHE 0.020 0.002 PHE R 386 TYR 0.022 0.001 TYR R 392 ARG 0.004 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7958 (mm-30) REVERT: R 174 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7517 (mm) REVERT: R 181 MET cc_start: 0.8241 (ttm) cc_final: 0.7719 (mtp) REVERT: R 192 ARG cc_start: 0.7371 (mmt-90) cc_final: 0.6610 (mmp-170) REVERT: R 193 LEU cc_start: 0.7616 (mt) cc_final: 0.7279 (tt) REVERT: R 237 GLU cc_start: 0.7991 (tt0) cc_final: 0.7747 (tt0) REVERT: R 252 GLU cc_start: 0.5222 (mp0) cc_final: 0.4812 (mp0) REVERT: R 289 ARG cc_start: 0.7752 (mtp180) cc_final: 0.7259 (mtm180) REVERT: R 336 ARG cc_start: 0.6019 (mtt180) cc_final: 0.5273 (tpt170) REVERT: R 345 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7438 (t80) REVERT: A 15 ARG cc_start: 0.7251 (ttt90) cc_final: 0.6813 (ttt-90) REVERT: A 47 SER cc_start: 0.8542 (m) cc_final: 0.8250 (p) REVERT: A 182 SER cc_start: 0.8384 (OUTLIER) cc_final: 0.8076 (p) REVERT: A 193 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7954 (mtmm) REVERT: A 310 ASP cc_start: 0.8090 (t70) cc_final: 0.7821 (t0) REVERT: A 323 ARG cc_start: 0.7537 (mtm-85) cc_final: 0.7183 (mtm110) REVERT: B 262 MET cc_start: 0.7298 (tpt) cc_final: 0.7061 (tpt) REVERT: N 67 ARG cc_start: 0.6756 (mtp85) cc_final: 0.6555 (mtm180) REVERT: N 90 ASP cc_start: 0.8473 (t0) cc_final: 0.8258 (t0) REVERT: N 114 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7716 (t) outliers start: 22 outliers final: 12 residues processed: 180 average time/residue: 0.2803 time to fit residues: 64.8365 Evaluate side-chains 162 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 62 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 0.0270 chunk 77 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.211302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.157786 restraints weight = 8884.776| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.85 r_work: 0.3580 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8965 Z= 0.144 Angle : 0.491 11.227 12170 Z= 0.248 Chirality : 0.039 0.152 1369 Planarity : 0.003 0.033 1514 Dihedral : 5.720 43.272 1582 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.49 % Allowed : 11.90 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.26), residues: 1050 helix: 2.13 (0.25), residues: 433 sheet: -0.40 (0.33), residues: 228 loop : -1.13 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.001 PHE R 386 TYR 0.017 0.001 TYR R 141 ARG 0.005 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 MET cc_start: 0.8273 (ttm) cc_final: 0.7828 (mtp) REVERT: R 192 ARG cc_start: 0.7446 (mmt-90) cc_final: 0.6647 (mmp-170) REVERT: R 193 LEU cc_start: 0.7728 (mt) cc_final: 0.7447 (tt) REVERT: R 237 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: R 289 ARG cc_start: 0.7680 (mtp180) cc_final: 0.7253 (mtm180) REVERT: R 336 ARG cc_start: 0.6124 (mtt180) cc_final: 0.5462 (tpt170) REVERT: R 345 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7563 (t80) REVERT: A 15 ARG cc_start: 0.7326 (ttt90) cc_final: 0.6973 (ttt-90) REVERT: A 47 SER cc_start: 0.8528 (m) cc_final: 0.8264 (p) REVERT: A 187 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8759 (p) REVERT: A 310 ASP cc_start: 0.8276 (t70) cc_final: 0.8022 (t0) REVERT: A 323 ARG cc_start: 0.7584 (mtm-85) cc_final: 0.7292 (mtm110) REVERT: N 87 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7619 (mttt) REVERT: N 90 ASP cc_start: 0.8535 (t0) cc_final: 0.8276 (t0) REVERT: N 114 THR cc_start: 0.8072 (OUTLIER) cc_final: 0.7866 (t) REVERT: N 117 TYR cc_start: 0.8577 (m-10) cc_final: 0.8010 (m-80) outliers start: 23 outliers final: 11 residues processed: 175 average time/residue: 0.2696 time to fit residues: 61.2505 Evaluate side-chains 168 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 374 LEU Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 16 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 54 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 268 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.210871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.150235 restraints weight = 8845.075| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.91 r_work: 0.3444 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8965 Z= 0.177 Angle : 0.494 10.044 12170 Z= 0.252 Chirality : 0.040 0.135 1369 Planarity : 0.003 0.037 1514 Dihedral : 5.524 41.653 1582 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.60 % Allowed : 12.12 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1050 helix: 2.25 (0.25), residues: 437 sheet: -0.43 (0.33), residues: 223 loop : -1.10 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.004 0.001 HIS A 354 PHE 0.019 0.001 PHE R 379 TYR 0.017 0.001 TYR R 141 ARG 0.007 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8466 (tmm) cc_final: 0.7066 (mmm) REVERT: R 181 MET cc_start: 0.8166 (ttm) cc_final: 0.7608 (mtp) REVERT: R 183 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6450 (ttm-80) REVERT: R 192 ARG cc_start: 0.7365 (mmt-90) cc_final: 0.6595 (mmp-170) REVERT: R 237 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: R 289 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7149 (mtm180) REVERT: R 336 ARG cc_start: 0.6034 (mtt180) cc_final: 0.5281 (tpt170) REVERT: R 345 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7405 (t80) REVERT: A 15 ARG cc_start: 0.7154 (ttt90) cc_final: 0.6836 (ttt-90) REVERT: A 31 ARG cc_start: 0.8300 (mtm110) cc_final: 0.7895 (mtt-85) REVERT: A 47 SER cc_start: 0.8474 (m) cc_final: 0.8104 (p) REVERT: A 187 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8733 (p) REVERT: A 274 LYS cc_start: 0.8035 (ptpt) cc_final: 0.7525 (ptpp) REVERT: A 310 ASP cc_start: 0.8091 (t70) cc_final: 0.7805 (t0) REVERT: A 323 ARG cc_start: 0.7620 (mtm-85) cc_final: 0.7215 (mtm110) REVERT: B 226 GLU cc_start: 0.8667 (mt-10) cc_final: 0.7911 (mt-10) REVERT: B 264 TYR cc_start: 0.9139 (m-80) cc_final: 0.8740 (m-80) REVERT: N 90 ASP cc_start: 0.8455 (t0) cc_final: 0.7753 (t0) REVERT: N 114 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7816 (t) REVERT: N 117 TYR cc_start: 0.8524 (m-10) cc_final: 0.7855 (m-80) outliers start: 24 outliers final: 14 residues processed: 177 average time/residue: 0.2870 time to fit residues: 64.4894 Evaluate side-chains 171 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 374 LEU Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 56 optimal weight: 0.0050 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.210367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3794 r_free = 0.3794 target = 0.155937 restraints weight = 8824.518| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.88 r_work: 0.3530 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8965 Z= 0.172 Angle : 0.493 10.831 12170 Z= 0.250 Chirality : 0.039 0.134 1369 Planarity : 0.003 0.036 1514 Dihedral : 5.335 39.764 1582 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.27 % Allowed : 12.99 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1050 helix: 2.32 (0.25), residues: 437 sheet: -0.41 (0.33), residues: 223 loop : -1.04 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.004 0.001 HIS A 354 PHE 0.013 0.001 PHE A 189 TYR 0.017 0.001 TYR R 141 ARG 0.007 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8410 (tmm) cc_final: 0.7098 (mmm) REVERT: R 181 MET cc_start: 0.8388 (ttm) cc_final: 0.7932 (mtp) REVERT: R 183 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6826 (ttm-80) REVERT: R 192 ARG cc_start: 0.7570 (mmt-90) cc_final: 0.6817 (mmp-170) REVERT: R 237 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: R 289 ARG cc_start: 0.7550 (mtp180) cc_final: 0.7196 (mtm180) REVERT: R 336 ARG cc_start: 0.6163 (mtt180) cc_final: 0.5551 (tpt170) REVERT: R 345 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7704 (t80) REVERT: A 15 ARG cc_start: 0.7314 (ttt90) cc_final: 0.7051 (ttt-90) REVERT: A 47 SER cc_start: 0.8558 (m) cc_final: 0.8194 (p) REVERT: A 187 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8785 (p) REVERT: A 274 LYS cc_start: 0.8121 (ptpt) cc_final: 0.7632 (ptpp) REVERT: A 310 ASP cc_start: 0.8370 (t70) cc_final: 0.8169 (t0) REVERT: A 323 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7357 (mtm110) REVERT: B 226 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8049 (mt-10) REVERT: B 255 LEU cc_start: 0.8925 (mp) cc_final: 0.8706 (mt) REVERT: B 264 TYR cc_start: 0.9075 (m-80) cc_final: 0.8872 (m-80) REVERT: G 47 GLU cc_start: 0.7600 (mp0) cc_final: 0.7302 (mp0) REVERT: N 87 LYS cc_start: 0.8101 (tttt) cc_final: 0.7847 (tttp) REVERT: N 90 ASP cc_start: 0.8524 (t0) cc_final: 0.7861 (t0) REVERT: N 117 TYR cc_start: 0.8553 (m-10) cc_final: 0.7971 (m-80) outliers start: 21 outliers final: 14 residues processed: 167 average time/residue: 0.2910 time to fit residues: 62.2523 Evaluate side-chains 167 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 374 LEU Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 0.0270 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 0.0020 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 overall best weight: 0.4246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.211401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.151183 restraints weight = 8951.590| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.92 r_work: 0.3536 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8965 Z= 0.136 Angle : 0.473 9.553 12170 Z= 0.239 Chirality : 0.039 0.134 1369 Planarity : 0.003 0.031 1514 Dihedral : 5.096 37.719 1582 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.38 % Allowed : 13.10 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.27), residues: 1050 helix: 2.45 (0.25), residues: 439 sheet: -0.27 (0.33), residues: 223 loop : -1.00 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.003 0.001 HIS A 354 PHE 0.021 0.001 PHE R 379 TYR 0.018 0.001 TYR R 141 ARG 0.008 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8513 (tmm) cc_final: 0.7177 (mmm) REVERT: R 181 MET cc_start: 0.8264 (ttm) cc_final: 0.7766 (mtp) REVERT: R 183 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6690 (ttm-80) REVERT: R 192 ARG cc_start: 0.7517 (mmt-90) cc_final: 0.6688 (mmp-170) REVERT: R 194 LEU cc_start: 0.7173 (pt) cc_final: 0.6967 (tp) REVERT: R 289 ARG cc_start: 0.7578 (mtp180) cc_final: 0.7124 (mtm180) REVERT: R 336 ARG cc_start: 0.6090 (mtt180) cc_final: 0.5434 (tpt170) REVERT: R 345 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7618 (t80) REVERT: A 20 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7511 (mm-30) REVERT: A 47 SER cc_start: 0.8519 (m) cc_final: 0.8142 (p) REVERT: A 187 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8758 (p) REVERT: A 274 LYS cc_start: 0.8089 (ptpt) cc_final: 0.7590 (ptpp) REVERT: A 310 ASP cc_start: 0.8312 (t70) cc_final: 0.8076 (t0) REVERT: A 323 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7235 (mtm110) REVERT: A 353 MET cc_start: 0.8387 (tmm) cc_final: 0.7913 (tmm) REVERT: B 226 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8132 (mt-10) REVERT: B 264 TYR cc_start: 0.9143 (m-80) cc_final: 0.8866 (m-80) REVERT: G 47 GLU cc_start: 0.7592 (mp0) cc_final: 0.7158 (mp0) REVERT: N 87 LYS cc_start: 0.8076 (tttt) cc_final: 0.7733 (mtpt) REVERT: N 90 ASP cc_start: 0.8531 (t0) cc_final: 0.8064 (m-30) REVERT: N 117 TYR cc_start: 0.8523 (m-10) cc_final: 0.7927 (m-80) outliers start: 22 outliers final: 13 residues processed: 170 average time/residue: 0.2870 time to fit residues: 62.7249 Evaluate side-chains 163 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 374 LEU Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.0770 chunk 1 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.208304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.156001 restraints weight = 8889.603| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.73 r_work: 0.3525 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 0.004 0.032 8965 Z= 0.230 Angle : 0.514 8.449 12170 Z= 0.263 Chirality : 0.040 0.133 1369 Planarity : 0.003 0.038 1514 Dihedral : 5.066 36.850 1582 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.49 % Allowed : 13.31 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 1050 helix: 2.43 (0.25), residues: 438 sheet: -0.37 (0.35), residues: 208 loop : -0.96 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.004 0.001 HIS A 354 PHE 0.014 0.001 PHE A 189 TYR 0.017 0.001 TYR R 141 ARG 0.009 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8407 (tmm) cc_final: 0.7138 (mmm) REVERT: R 181 MET cc_start: 0.8424 (ttm) cc_final: 0.7922 (mtp) REVERT: R 183 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6832 (ttm-80) REVERT: R 192 ARG cc_start: 0.7572 (mmt-90) cc_final: 0.6813 (mmp-170) REVERT: R 194 LEU cc_start: 0.7210 (pt) cc_final: 0.6939 (tp) REVERT: R 237 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: R 289 ARG cc_start: 0.7438 (mtp180) cc_final: 0.7086 (mtm180) REVERT: R 336 ARG cc_start: 0.6275 (mtt180) cc_final: 0.5622 (tpt170) REVERT: R 345 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7905 (t80) REVERT: A 31 ARG cc_start: 0.8486 (mtm110) cc_final: 0.8200 (mtt-85) REVERT: A 187 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8734 (p) REVERT: A 274 LYS cc_start: 0.8111 (ptpt) cc_final: 0.7705 (ptpp) REVERT: A 323 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7344 (mtm110) REVERT: A 353 MET cc_start: 0.8356 (tmm) cc_final: 0.7974 (tmm) REVERT: B 264 TYR cc_start: 0.9090 (m-80) cc_final: 0.8807 (m-80) REVERT: G 17 GLU cc_start: 0.8287 (tp30) cc_final: 0.7935 (tt0) REVERT: N 82 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7587 (tp-100) REVERT: N 90 ASP cc_start: 0.8505 (t0) cc_final: 0.8058 (m-30) outliers start: 23 outliers final: 15 residues processed: 163 average time/residue: 0.2891 time to fit residues: 60.6138 Evaluate side-chains 160 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 102 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.209954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.162749 restraints weight = 8919.988| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.23 r_work: 0.3421 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8965 Z= 0.176 Angle : 0.523 10.617 12170 Z= 0.264 Chirality : 0.040 0.258 1369 Planarity : 0.003 0.036 1514 Dihedral : 5.019 36.867 1582 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.60 % Allowed : 13.20 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.27), residues: 1050 helix: 2.54 (0.25), residues: 438 sheet: -0.26 (0.35), residues: 207 loop : -0.92 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.004 0.001 HIS A 354 PHE 0.022 0.001 PHE R 379 TYR 0.018 0.001 TYR R 141 ARG 0.009 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8587 (tmm) cc_final: 0.7218 (mmm) REVERT: R 181 MET cc_start: 0.8185 (ttm) cc_final: 0.7624 (mtp) REVERT: R 183 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6522 (ttm-80) REVERT: R 192 ARG cc_start: 0.7410 (mmt-90) cc_final: 0.6629 (mmp-170) REVERT: R 194 LEU cc_start: 0.7232 (pt) cc_final: 0.6994 (tp) REVERT: R 237 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7626 (tt0) REVERT: R 289 ARG cc_start: 0.7521 (mtp180) cc_final: 0.7058 (mtm180) REVERT: R 336 ARG cc_start: 0.6202 (mtt180) cc_final: 0.5481 (tpt170) REVERT: R 345 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7739 (t80) REVERT: A 31 ARG cc_start: 0.8394 (mtm110) cc_final: 0.8073 (mtt-85) REVERT: A 187 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8717 (p) REVERT: A 323 ARG cc_start: 0.7599 (mtm-85) cc_final: 0.7220 (mtm110) REVERT: A 353 MET cc_start: 0.8192 (tmm) cc_final: 0.7722 (tmm) REVERT: B 264 TYR cc_start: 0.9126 (m-80) cc_final: 0.8792 (m-80) REVERT: G 17 GLU cc_start: 0.8252 (tp30) cc_final: 0.7869 (tt0) REVERT: N 82 GLN cc_start: 0.7945 (tp-100) cc_final: 0.7447 (tp-100) REVERT: N 117 TYR cc_start: 0.8469 (m-10) cc_final: 0.7836 (m-80) outliers start: 24 outliers final: 18 residues processed: 156 average time/residue: 0.2881 time to fit residues: 57.7668 Evaluate side-chains 156 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 39 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 13 optimal weight: 6.9990 chunk 23 optimal weight: 0.0570 chunk 75 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.210437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.157609 restraints weight = 8911.818| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.98 r_work: 0.3437 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8965 Z= 0.159 Angle : 0.495 7.847 12170 Z= 0.251 Chirality : 0.039 0.150 1369 Planarity : 0.003 0.036 1514 Dihedral : 4.898 37.137 1582 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.06 % Allowed : 14.39 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1050 helix: 2.67 (0.25), residues: 438 sheet: -0.26 (0.35), residues: 207 loop : -0.90 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.003 0.001 HIS A 354 PHE 0.012 0.001 PHE A 189 TYR 0.018 0.001 TYR R 141 ARG 0.008 0.000 ARG A 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8375 (tmm) cc_final: 0.7155 (mmm) REVERT: R 181 MET cc_start: 0.8344 (ttm) cc_final: 0.7862 (mtp) REVERT: R 183 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6824 (ttm-80) REVERT: R 192 ARG cc_start: 0.7455 (mmt-90) cc_final: 0.6779 (mmp-170) REVERT: R 194 LEU cc_start: 0.7174 (pt) cc_final: 0.6899 (tp) REVERT: R 237 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: R 289 ARG cc_start: 0.7341 (mtp180) cc_final: 0.7068 (mtm180) REVERT: R 336 ARG cc_start: 0.6242 (mtt180) cc_final: 0.5441 (tpt170) REVERT: R 345 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7890 (t80) REVERT: A 31 ARG cc_start: 0.8480 (mtm110) cc_final: 0.8218 (mtt-85) REVERT: A 54 ARG cc_start: 0.6585 (mtt180) cc_final: 0.6166 (ttp80) REVERT: A 187 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8718 (p) REVERT: A 323 ARG cc_start: 0.7618 (mtm-85) cc_final: 0.7332 (mtm110) REVERT: A 353 MET cc_start: 0.8321 (tmm) cc_final: 0.8045 (tmm) REVERT: B 264 TYR cc_start: 0.9055 (m-80) cc_final: 0.8784 (m-80) REVERT: G 17 GLU cc_start: 0.8212 (tp30) cc_final: 0.7896 (tt0) REVERT: N 82 GLN cc_start: 0.8035 (tp-100) cc_final: 0.7570 (tp-100) REVERT: N 117 TYR cc_start: 0.8510 (m-10) cc_final: 0.7958 (m-80) outliers start: 19 outliers final: 14 residues processed: 151 average time/residue: 0.3130 time to fit residues: 60.2396 Evaluate side-chains 158 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 27 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.207380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.159251 restraints weight = 8952.566| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 3.29 r_work: 0.3378 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8965 Z= 0.261 Angle : 0.538 7.556 12170 Z= 0.276 Chirality : 0.041 0.158 1369 Planarity : 0.003 0.041 1514 Dihedral : 4.987 35.465 1582 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.38 % Allowed : 13.96 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.27), residues: 1050 helix: 2.59 (0.25), residues: 437 sheet: -0.43 (0.35), residues: 209 loop : -0.88 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 47 HIS 0.005 0.001 HIS A 354 PHE 0.022 0.002 PHE R 379 TYR 0.016 0.001 TYR R 141 ARG 0.009 0.000 ARG A 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5568.05 seconds wall clock time: 99 minutes 4.35 seconds (5944.35 seconds total)