Starting phenix.real_space_refine on Thu Mar 13 15:23:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vab_31836/03_2025/7vab_31836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vab_31836/03_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_31836/03_2025/7vab_31836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vab_31836/03_2025/7vab_31836.map" model { file = "/net/cci-nas-00/data/ceres_data/7vab_31836/03_2025/7vab_31836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vab_31836/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.30, per 1000 atoms: 0.60 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: 2.12 Conformation dependent library (CDL) restraints added in 951.9 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: 0.89 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: 2.40 Time building geometry restraints manager: 2.52 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.880 Find NCS groups from input model: 0.090 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.580 ------------------------------------------------------------------------------- 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 : 0.925 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: 0.2895 time to fit residues: 99.9178 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 : 0.951 ------------------------------------------------------------------------------- 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 = 0.153405 restraints weight = 8916.423| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.17 r_work: 0.3527 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- 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 : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7963 (mm-30) REVERT: R 181 MET cc_start: 0.8310 (ttm) cc_final: 0.7996 (mtt) REVERT: R 192 ARG cc_start: 0.7294 (mmt-90) cc_final: 0.6588 (mmp-170) REVERT: R 193 LEU cc_start: 0.7674 (mt) cc_final: 0.7347 (tt) REVERT: R 252 GLU cc_start: 0.5303 (mp0) cc_final: 0.4672 (pm20) REVERT: R 253 GLU cc_start: 0.4792 (pm20) cc_final: 0.3894 (mm-30) REVERT: R 289 ARG cc_start: 0.7913 (mtp180) cc_final: 0.7308 (mtm180) REVERT: R 336 ARG cc_start: 0.6071 (mtt180) cc_final: 0.5361 (tpt170) REVERT: R 345 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7243 (t80) REVERT: A 31 ARG cc_start: 0.8355 (mtm110) cc_final: 0.7928 (mtt-85) REVERT: A 47 SER cc_start: 0.8543 (m) cc_final: 0.8244 (p) REVERT: A 53 MET cc_start: 0.8026 (mmt) cc_final: 0.7819 (mmt) REVERT: A 193 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7936 (mtmm) REVERT: A 274 LYS cc_start: 0.8219 (ptmt) cc_final: 0.8014 (ptpp) REVERT: A 310 ASP cc_start: 0.8127 (t70) cc_final: 0.7792 (t0) REVERT: A 323 ARG cc_start: 0.7651 (mtm-85) cc_final: 0.7186 (mtm110) REVERT: B 13 GLN cc_start: 0.8791 (pt0) cc_final: 0.8548 (pt0) REVERT: B 44 GLN cc_start: 0.8439 (mt0) cc_final: 0.8052 (mm-40) REVERT: B 215 GLU cc_start: 0.7955 (mp0) cc_final: 0.7627 (mp0) REVERT: N 67 ARG cc_start: 0.6720 (mtp85) cc_final: 0.6515 (mtm180) REVERT: N 87 LYS cc_start: 0.7995 (mttt) cc_final: 0.7628 (ttmt) REVERT: N 90 ASP cc_start: 0.8543 (t0) cc_final: 0.8277 (t0) outliers start: 14 outliers final: 6 residues processed: 191 average time/residue: 0.2786 time to fit residues: 68.4209 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 : 1.032 ------------------------------------------------------------------------------- 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: 0.6980 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 B 239 ASN B 259 GLN N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.210230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.162251 restraints weight = 9006.209| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.58 r_work: 0.3432 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8965 Z= 0.212 Angle : 0.521 12.395 12170 Z= 0.265 Chirality : 0.040 0.138 1369 Planarity : 0.003 0.034 1514 Dihedral : 6.061 45.583 1582 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.71 % Allowed : 10.82 % Favored : 86.47 % 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: 0.24 (0.26), residues: 1050 helix: 1.71 (0.25), residues: 433 sheet: -0.54 (0.33), residues: 228 loop : -1.15 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 47 HIS 0.004 0.001 HIS B 142 PHE 0.019 0.002 PHE R 386 TYR 0.022 0.002 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 188 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.000 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: 0.8277 (mm-30) cc_final: 0.8006 (mm-30) REVERT: R 174 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7404 (mm) REVERT: R 181 MET cc_start: 0.8224 (ttm) cc_final: 0.7791 (mtp) REVERT: R 192 ARG cc_start: 0.7293 (mmt-90) cc_final: 0.6580 (mmp-170) REVERT: R 193 LEU cc_start: 0.7571 (mt) cc_final: 0.7243 (tt) REVERT: R 237 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: R 252 GLU cc_start: 0.5230 (mp0) cc_final: 0.4816 (mp0) REVERT: R 289 ARG cc_start: 0.7812 (mtp180) cc_final: 0.7258 (mtm180) REVERT: R 336 ARG cc_start: 0.5991 (mtt180) cc_final: 0.5255 (tpt170) REVERT: R 345 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7386 (t80) REVERT: A 15 ARG cc_start: 0.7229 (ttt90) cc_final: 0.6797 (ttt-90) REVERT: A 31 ARG cc_start: 0.8416 (mtm110) cc_final: 0.8091 (mtt-85) REVERT: A 47 SER cc_start: 0.8499 (m) cc_final: 0.8158 (p) REVERT: A 182 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.8040 (p) REVERT: A 193 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7973 (mtmm) REVERT: A 310 ASP cc_start: 0.8047 (t70) cc_final: 0.7763 (t0) REVERT: A 323 ARG cc_start: 0.7546 (mtm-85) cc_final: 0.7143 (mtm110) REVERT: B 262 MET cc_start: 0.7291 (tpt) cc_final: 0.7054 (tpt) REVERT: N 90 ASP cc_start: 0.8477 (t0) cc_final: 0.8269 (t0) REVERT: N 114 THR cc_start: 0.7957 (OUTLIER) cc_final: 0.7707 (t) outliers start: 25 outliers final: 14 residues processed: 180 average time/residue: 0.3245 time to fit residues: 76.3115 Evaluate side-chains 164 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 237 GLU 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 374 LEU Chi-restraints excluded: chain R residue 378 ILE 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: 0.5980 chunk 28 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 259 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.209448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.151314 restraints weight = 8896.611| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.94 r_work: 0.3435 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8965 Z= 0.196 Angle : 0.510 10.974 12170 Z= 0.259 Chirality : 0.040 0.141 1369 Planarity : 0.003 0.038 1514 Dihedral : 5.729 43.841 1582 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.60 % Allowed : 12.01 % Favored : 85.39 % 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: 0.46 (0.26), residues: 1050 helix: 2.01 (0.25), residues: 437 sheet: -0.58 (0.33), residues: 231 loop : -1.12 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 47 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.001 PHE R 386 TYR 0.017 0.001 TYR R 392 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 181 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8064 (mm-30) REVERT: R 174 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7551 (mm) REVERT: R 181 MET cc_start: 0.8274 (ttm) cc_final: 0.7720 (mtp) REVERT: R 192 ARG cc_start: 0.7357 (mmt-90) cc_final: 0.6582 (mmp-170) REVERT: R 193 LEU cc_start: 0.7544 (mt) cc_final: 0.7310 (tt) REVERT: R 237 GLU cc_start: 0.8118 (tt0) cc_final: 0.7877 (tt0) REVERT: R 289 ARG cc_start: 0.7655 (mtp180) cc_final: 0.7176 (mtm180) REVERT: R 336 ARG cc_start: 0.6014 (mtt180) cc_final: 0.5322 (tpt170) REVERT: R 345 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7436 (t80) REVERT: A 15 ARG cc_start: 0.7219 (ttt90) cc_final: 0.6889 (ttt-90) REVERT: A 31 ARG cc_start: 0.8460 (mtm110) cc_final: 0.8073 (mtt-85) REVERT: A 47 SER cc_start: 0.8535 (m) cc_final: 0.8166 (p) REVERT: A 187 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8772 (p) REVERT: A 193 LYS cc_start: 0.8219 (mtpt) cc_final: 0.7976 (mtmm) REVERT: A 310 ASP cc_start: 0.8185 (t70) cc_final: 0.7913 (t0) REVERT: A 323 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7254 (mtm110) REVERT: B 262 MET cc_start: 0.7527 (tpt) cc_final: 0.7316 (tpt) REVERT: N 90 ASP cc_start: 0.8576 (t0) cc_final: 0.8317 (t0) REVERT: N 114 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7809 (t) outliers start: 24 outliers final: 12 residues processed: 172 average time/residue: 0.2919 time to fit residues: 64.6328 Evaluate side-chains 164 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 271 VAL 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 187 THR Chi-restraints excluded: chain A residue 191 VAL 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 118 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: 7.9990 chunk 102 optimal weight: 0.0670 chunk 21 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.209533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.156519 restraints weight = 8870.636| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.91 r_work: 0.3515 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3556 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= 0.175 Angle : 0.493 9.831 12170 Z= 0.252 Chirality : 0.039 0.135 1369 Planarity : 0.003 0.036 1514 Dihedral : 5.495 41.946 1582 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.49 % Allowed : 12.99 % 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: 0.66 (0.26), residues: 1050 helix: 2.20 (0.25), residues: 437 sheet: -0.46 (0.33), residues: 228 loop : -1.05 (0.31), residues: 385 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 0.022 0.001 PHE R 379 TYR 0.017 0.001 TYR R 141 ARG 0.006 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 174 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 174 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7785 (mm) REVERT: R 181 MET cc_start: 0.8441 (ttm) cc_final: 0.7965 (mtp) REVERT: R 183 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6838 (ttm-80) REVERT: R 192 ARG cc_start: 0.7537 (mmt-90) cc_final: 0.6817 (mmp-170) REVERT: R 237 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: R 289 ARG cc_start: 0.7585 (mtp180) cc_final: 0.7216 (mtm180) REVERT: R 336 ARG cc_start: 0.6219 (mtt180) cc_final: 0.5519 (tpt170) REVERT: R 345 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7680 (t80) REVERT: A 15 ARG cc_start: 0.7362 (ttt90) cc_final: 0.7100 (ttt-90) REVERT: A 31 ARG cc_start: 0.8512 (mtm110) cc_final: 0.8247 (mtt-85) REVERT: A 47 SER cc_start: 0.8573 (m) cc_final: 0.8243 (p) REVERT: A 187 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8833 (p) REVERT: A 274 LYS cc_start: 0.8175 (ptpt) cc_final: 0.7687 (ptpp) REVERT: A 310 ASP cc_start: 0.8389 (t70) cc_final: 0.8178 (t0) REVERT: A 323 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7373 (mtm110) REVERT: B 262 MET cc_start: 0.7521 (tpt) cc_final: 0.7235 (tpt) REVERT: N 90 ASP cc_start: 0.8396 (t0) cc_final: 0.7726 (t0) REVERT: N 117 TYR cc_start: 0.8572 (m-10) cc_final: 0.7972 (m-80) outliers start: 23 outliers final: 14 residues processed: 167 average time/residue: 0.3283 time to fit residues: 69.9555 Evaluate side-chains 159 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 174 ILE 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 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 35 ASN Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 51 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 56 optimal weight: 0.0050 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.4305 r_free = 0.4305 target = 0.210521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.154190 restraints weight = 8852.787| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.92 r_work: 0.3525 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8965 Z= 0.138 Angle : 0.476 10.846 12170 Z= 0.241 Chirality : 0.039 0.133 1369 Planarity : 0.003 0.030 1514 Dihedral : 5.194 38.742 1582 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.38 % Allowed : 13.20 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.27), residues: 1050 helix: 2.40 (0.25), residues: 438 sheet: -0.36 (0.33), residues: 228 loop : -0.96 (0.31), residues: 384 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 0.013 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 184 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8363 (tmm) cc_final: 0.7058 (mmm) REVERT: R 174 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7522 (mm) REVERT: R 181 MET cc_start: 0.8256 (ttm) cc_final: 0.7757 (mtp) REVERT: R 183 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6636 (ttm-80) REVERT: R 192 ARG cc_start: 0.7506 (mmt-90) cc_final: 0.6813 (mmp-170) REVERT: R 289 ARG cc_start: 0.7561 (mtp180) cc_final: 0.7195 (mtm180) REVERT: R 336 ARG cc_start: 0.6106 (mtt180) cc_final: 0.5500 (tpt170) REVERT: R 345 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7596 (t80) REVERT: A 15 ARG cc_start: 0.7268 (ttt90) cc_final: 0.6939 (ttt-90) REVERT: A 31 ARG cc_start: 0.8444 (mtm110) cc_final: 0.8125 (mtt-85) REVERT: A 47 SER cc_start: 0.8550 (m) cc_final: 0.8181 (p) REVERT: A 187 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8763 (p) REVERT: A 274 LYS cc_start: 0.8082 (ptpt) cc_final: 0.7586 (ptpp) REVERT: A 310 ASP cc_start: 0.8262 (t70) cc_final: 0.8025 (t0) REVERT: A 323 ARG cc_start: 0.7614 (mtm-85) cc_final: 0.7261 (mtm110) REVERT: B 226 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8090 (mt-10) REVERT: B 246 ASP cc_start: 0.8192 (m-30) cc_final: 0.7988 (m-30) REVERT: B 262 MET cc_start: 0.7552 (tpt) cc_final: 0.7255 (tpt) REVERT: N 90 ASP cc_start: 0.8457 (t0) cc_final: 0.7857 (t0) REVERT: N 117 TYR cc_start: 0.8525 (m-10) cc_final: 0.7927 (m-80) outliers start: 22 outliers final: 15 residues processed: 177 average time/residue: 0.3184 time to fit residues: 72.5959 Evaluate side-chains 169 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 174 ILE 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 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 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 35 ASN Chi-restraints excluded: chain N residue 91 THR 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: 0.9990 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 0.0270 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 230 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.208281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.161878 restraints weight = 8956.881| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.31 r_work: 0.3386 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8965 Z= 0.193 Angle : 0.502 9.285 12170 Z= 0.253 Chirality : 0.039 0.153 1369 Planarity : 0.003 0.034 1514 Dihedral : 5.106 37.693 1582 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.14 % Allowed : 12.99 % Favored : 83.87 % 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: 2.40 (0.25), residues: 438 sheet: -0.34 (0.34), residues: 212 loop : -0.93 (0.30), residues: 400 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 0.023 0.001 PHE R 379 TYR 0.017 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 175 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8136 (mm-30) REVERT: R 140 MET cc_start: 0.8447 (tmm) cc_final: 0.7040 (mmm) REVERT: R 174 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7316 (mm) REVERT: R 181 MET cc_start: 0.8198 (ttm) cc_final: 0.7650 (mtp) REVERT: R 183 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6463 (ttm-80) REVERT: R 192 ARG cc_start: 0.7424 (mmt-90) cc_final: 0.6650 (mmp-170) REVERT: R 194 LEU cc_start: 0.7246 (pt) cc_final: 0.7028 (tp) REVERT: R 289 ARG cc_start: 0.7555 (mtp180) cc_final: 0.7050 (mtm180) REVERT: R 336 ARG cc_start: 0.6165 (mtt180) cc_final: 0.5458 (tpt170) REVERT: R 345 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7660 (t80) REVERT: A 31 ARG cc_start: 0.8399 (mtm110) cc_final: 0.8063 (mtt-85) REVERT: A 274 LYS cc_start: 0.8098 (ptpt) cc_final: 0.7720 (ptpp) REVERT: A 310 ASP cc_start: 0.8134 (t70) cc_final: 0.7871 (t0) REVERT: A 323 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7255 (mtm110) REVERT: B 262 MET cc_start: 0.7433 (tpt) cc_final: 0.7140 (tpt) REVERT: G 17 GLU cc_start: 0.8223 (tp30) cc_final: 0.7868 (tt0) REVERT: N 90 ASP cc_start: 0.8398 (t0) cc_final: 0.7830 (t0) REVERT: N 117 TYR cc_start: 0.8540 (m-10) cc_final: 0.7901 (m-80) outliers start: 29 outliers final: 21 residues processed: 167 average time/residue: 0.3201 time to fit residues: 68.2841 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 : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 174 ILE 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 A residue 206 ASP Chi-restraints excluded: chain B residue 118 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 87 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4279 r_free = 0.4279 target = 0.207601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.155534 restraints weight = 8918.457| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.79 r_work: 0.3510 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8965 Z= 0.228 Angle : 0.539 10.757 12170 Z= 0.270 Chirality : 0.040 0.241 1369 Planarity : 0.003 0.036 1514 Dihedral : 5.136 36.773 1582 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.92 % Allowed : 13.10 % Favored : 83.98 % 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: 0.93 (0.27), residues: 1050 helix: 2.43 (0.25), residues: 438 sheet: -0.37 (0.35), residues: 212 loop : -0.90 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 47 HIS 0.004 0.001 HIS A 354 PHE 0.024 0.001 PHE R 379 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 174 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8312 (tmm) cc_final: 0.7002 (mmm) REVERT: R 174 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7634 (mm) REVERT: R 181 MET cc_start: 0.8385 (ttm) cc_final: 0.7893 (mtp) REVERT: R 183 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6854 (ttm-80) REVERT: R 192 ARG cc_start: 0.7551 (mmt-90) cc_final: 0.6831 (mmp-170) REVERT: R 194 LEU cc_start: 0.7251 (pt) cc_final: 0.6988 (tp) REVERT: R 237 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: R 289 ARG cc_start: 0.7464 (mtp180) cc_final: 0.7106 (mtm180) REVERT: R 336 ARG cc_start: 0.6242 (mtt180) cc_final: 0.5574 (tpt170) REVERT: R 345 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7830 (t80) REVERT: A 31 ARG cc_start: 0.8524 (mtm110) cc_final: 0.8209 (mtt-85) REVERT: A 187 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8759 (p) REVERT: A 274 LYS cc_start: 0.8113 (ptpt) cc_final: 0.7717 (ptpp) REVERT: A 310 ASP cc_start: 0.8418 (t70) cc_final: 0.8196 (t0) REVERT: A 323 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7357 (mtm110) REVERT: A 353 MET cc_start: 0.8415 (tmm) cc_final: 0.8036 (tmm) REVERT: B 262 MET cc_start: 0.7685 (tpt) cc_final: 0.7445 (tpt) REVERT: G 17 GLU cc_start: 0.8270 (tp30) cc_final: 0.7917 (tt0) REVERT: N 82 GLN cc_start: 0.8073 (tp-100) cc_final: 0.7525 (tp-100) REVERT: N 90 ASP cc_start: 0.8438 (t0) cc_final: 0.7867 (t0) outliers start: 27 outliers final: 18 residues processed: 166 average time/residue: 0.2903 time to fit residues: 62.6069 Evaluate side-chains 166 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 174 ILE 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 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 206 ASP Chi-restraints excluded: chain B residue 118 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 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 102 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 76 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.208417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156693 restraints weight = 8912.252| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.19 r_work: 0.3450 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4063 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= 0.198 Angle : 0.515 8.767 12170 Z= 0.261 Chirality : 0.040 0.154 1369 Planarity : 0.003 0.034 1514 Dihedral : 5.028 36.410 1582 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.71 % Allowed : 13.53 % Favored : 83.77 % 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: 0.99 (0.27), residues: 1050 helix: 2.51 (0.25), residues: 437 sheet: -0.38 (0.34), residues: 212 loop : -0.84 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.003 0.001 HIS A 354 PHE 0.024 0.001 PHE R 379 TYR 0.017 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 170 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8502 (tmm) cc_final: 0.7123 (mmm) REVERT: R 174 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7338 (mm) REVERT: R 181 MET cc_start: 0.8317 (ttm) cc_final: 0.7738 (mtp) REVERT: R 183 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6632 (ttm-80) REVERT: R 192 ARG cc_start: 0.7468 (mmt-90) cc_final: 0.6707 (mmp-170) REVERT: R 194 LEU cc_start: 0.7342 (pt) cc_final: 0.7035 (tp) REVERT: R 237 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: R 253 GLU cc_start: 0.4681 (pm20) cc_final: 0.3912 (tp30) REVERT: R 289 ARG cc_start: 0.7489 (mtp180) cc_final: 0.7035 (mtm180) REVERT: R 336 ARG cc_start: 0.6264 (mtt180) cc_final: 0.5326 (tpt170) REVERT: R 345 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7679 (t80) REVERT: R 400 GLN cc_start: 0.6236 (mt0) cc_final: 0.5955 (mt0) REVERT: A 31 ARG cc_start: 0.8527 (mtm110) cc_final: 0.8113 (mtt-85) REVERT: A 54 ARG cc_start: 0.6601 (mtt180) cc_final: 0.6101 (ttp80) REVERT: A 310 ASP cc_start: 0.8338 (t70) cc_final: 0.8068 (t0) REVERT: A 353 MET cc_start: 0.8390 (tmm) cc_final: 0.7897 (tmm) REVERT: B 226 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8175 (mt-10) REVERT: B 258 ASP cc_start: 0.7958 (t70) cc_final: 0.7093 (t0) REVERT: B 262 MET cc_start: 0.7717 (tpt) cc_final: 0.7443 (tpt) REVERT: G 17 GLU cc_start: 0.8275 (tp30) cc_final: 0.7881 (tt0) REVERT: N 82 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7424 (tp-100) REVERT: N 90 ASP cc_start: 0.8465 (t0) cc_final: 0.7910 (t0) REVERT: N 117 TYR cc_start: 0.8581 (m-10) cc_final: 0.7943 (m-80) outliers start: 25 outliers final: 20 residues processed: 163 average time/residue: 0.2852 time to fit residues: 59.4980 Evaluate side-chains 166 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 174 ILE 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 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 206 ASP Chi-restraints excluded: chain B residue 118 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 Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 96 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.207641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.155328 restraints weight = 8928.255| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.80 r_work: 0.3487 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4161 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= 0.208 Angle : 0.518 8.227 12170 Z= 0.264 Chirality : 0.040 0.142 1369 Planarity : 0.003 0.036 1514 Dihedral : 4.971 36.255 1582 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.60 % Allowed : 13.96 % Favored : 83.44 % 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: 1.00 (0.27), residues: 1050 helix: 2.53 (0.25), residues: 437 sheet: -0.38 (0.34), residues: 212 loop : -0.85 (0.31), residues: 401 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 0.022 0.001 PHE R 379 TYR 0.017 0.001 TYR R 141 ARG 0.009 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 164 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8387 (tmm) cc_final: 0.7102 (mmm) REVERT: R 181 MET cc_start: 0.8418 (ttm) cc_final: 0.7905 (mtp) REVERT: R 183 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6813 (ttm-80) REVERT: R 192 ARG cc_start: 0.7508 (mmt-90) cc_final: 0.6785 (mmp-170) REVERT: R 194 LEU cc_start: 0.7304 (pt) cc_final: 0.6982 (tp) REVERT: R 253 GLU cc_start: 0.4935 (pm20) cc_final: 0.4182 (tp30) REVERT: R 336 ARG cc_start: 0.6382 (mtt180) cc_final: 0.5488 (tpt170) REVERT: R 345 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7901 (t80) REVERT: R 400 GLN cc_start: 0.6318 (mt0) cc_final: 0.6022 (mt0) REVERT: A 31 ARG cc_start: 0.8529 (mtm110) cc_final: 0.8218 (mtt-85) REVERT: A 310 ASP cc_start: 0.8373 (t70) cc_final: 0.8164 (t0) REVERT: A 323 ARG cc_start: 0.7739 (mtm110) cc_final: 0.7407 (mmm160) REVERT: A 353 MET cc_start: 0.8377 (tmm) cc_final: 0.8008 (tmm) REVERT: B 226 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 258 ASP cc_start: 0.7961 (t70) cc_final: 0.7120 (t0) REVERT: B 262 MET cc_start: 0.7694 (tpt) cc_final: 0.7457 (tpt) REVERT: G 17 GLU cc_start: 0.8293 (tp30) cc_final: 0.7927 (tt0) REVERT: N 82 GLN cc_start: 0.8040 (tp-100) cc_final: 0.7557 (tp-100) REVERT: N 90 ASP cc_start: 0.8448 (t0) cc_final: 0.7905 (t0) REVERT: N 117 TYR cc_start: 0.8557 (m-10) cc_final: 0.7978 (m-80) outliers start: 24 outliers final: 20 residues processed: 157 average time/residue: 0.3611 time to fit residues: 73.3449 Evaluate side-chains 162 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 271 VAL 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 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 118 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 Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 27 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 18 optimal weight: 0.3980 chunk 2 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4286 r_free = 0.4286 target = 0.208281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147225 restraints weight = 8956.973| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.93 r_work: 0.3421 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8965 Z= 0.198 Angle : 0.510 7.741 12170 Z= 0.260 Chirality : 0.040 0.134 1369 Planarity : 0.003 0.037 1514 Dihedral : 4.894 36.534 1582 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.38 % Allowed : 14.39 % Favored : 83.23 % 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: 1.03 (0.27), residues: 1050 helix: 2.59 (0.25), residues: 437 sheet: -0.46 (0.33), residues: 229 loop : -0.84 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.003 0.001 HIS A 354 PHE 0.023 0.001 PHE R 379 TYR 0.017 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: 5983.63 seconds wall clock time: 105 minutes 27.53 seconds (6327.53 seconds total)