Starting phenix.real_space_refine on Sun Jul 27 02:09:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vab_31836/07_2025/7vab_31836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vab_31836/07_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_31836/07_2025/7vab_31836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vab_31836/07_2025/7vab_31836.map" model { file = "/net/cci-nas-00/data/ceres_data/7vab_31836/07_2025/7vab_31836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vab_31836/07_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-5711/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: 5.52, per 1000 atoms: 0.63 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.08 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: 2.48 Time building geometry restraints manager: 2.63 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: 0.960 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.250 Find NCS groups from input model: 0.100 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.910 ------------------------------------------------------------------------------- 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 8968 Z= 0.189 Angle : 0.801 15.553 12176 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 Details of bonding type rmsd hydrogen bonds : bond 0.14833 ( 425) hydrogen bonds : angle 6.60614 ( 1242) SS BOND : bond 0.00190 ( 3) SS BOND : angle 1.98691 ( 6) covalent geometry : bond 0.00350 ( 8965) covalent geometry : angle 0.80018 (12170) *********************** 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 : 0.883 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: 0.2734 time to fit residues: 93.6837 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 : 0.872 ------------------------------------------------------------------------------- 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 8968 Z= 0.215 Angle : 0.604 14.598 12176 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 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 425) hydrogen bonds : angle 4.53495 ( 1242) SS BOND : bond 0.00505 ( 3) SS BOND : angle 0.96020 ( 6) covalent geometry : bond 0.00513 ( 8965) covalent geometry : angle 0.60394 (12170) *********************** 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 : 1.291 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: 0.2792 time to fit residues: 68.9105 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 : 0.990 ------------------------------------------------------------------------------- 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: 0.8980 chunk 89 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.210185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.166695 restraints weight = 9009.635| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.73 r_work: 0.3417 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8968 Z= 0.141 Angle : 0.522 12.541 12176 Z= 0.265 Chirality : 0.040 0.137 1369 Planarity : 0.003 0.039 1514 Dihedral : 6.107 46.627 1582 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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: 0.23 (0.26), residues: 1050 helix: 1.71 (0.25), residues: 433 sheet: -0.54 (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 0.002 TYR R 392 ARG 0.005 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 425) hydrogen bonds : angle 4.18114 ( 1242) SS BOND : bond 0.00188 ( 3) SS BOND : angle 0.72134 ( 6) covalent geometry : bond 0.00326 ( 8965) covalent geometry : angle 0.52204 (12170) *********************** 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 184 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.989 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: 0.8161 (mm-30) cc_final: 0.7928 (mm-30) REVERT: R 174 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7579 (mm) REVERT: R 181 MET cc_start: 0.8288 (ttm) cc_final: 0.7899 (mtp) REVERT: R 192 ARG cc_start: 0.7362 (mmt-90) cc_final: 0.6600 (mmp-170) REVERT: R 193 LEU cc_start: 0.7709 (mt) cc_final: 0.7360 (tt) REVERT: R 237 GLU cc_start: 0.7962 (tt0) cc_final: 0.7635 (tt0) REVERT: R 252 GLU cc_start: 0.5206 (mp0) cc_final: 0.4807 (mp0) REVERT: R 289 ARG cc_start: 0.7743 (mtp180) cc_final: 0.7270 (mtm180) REVERT: R 336 ARG cc_start: 0.6014 (mtt180) cc_final: 0.5325 (tpt170) REVERT: R 345 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7501 (t80) REVERT: A 15 ARG cc_start: 0.7285 (ttt90) cc_final: 0.6872 (ttt-90) REVERT: A 47 SER cc_start: 0.8536 (m) cc_final: 0.8238 (p) REVERT: A 182 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.8082 (p) REVERT: A 193 LYS cc_start: 0.8157 (mtpt) cc_final: 0.7949 (mtmm) REVERT: A 310 ASP cc_start: 0.8104 (t70) cc_final: 0.7849 (t0) REVERT: A 323 ARG cc_start: 0.7541 (mtm-85) cc_final: 0.7185 (mtm110) REVERT: B 262 MET cc_start: 0.7315 (tpt) cc_final: 0.7086 (tpt) REVERT: N 90 ASP cc_start: 0.8469 (t0) cc_final: 0.8250 (t0) REVERT: N 114 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7726 (t) outliers start: 22 outliers final: 13 residues processed: 177 average time/residue: 0.2938 time to fit residues: 66.9171 Evaluate side-chains 164 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 B residue 334 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: 0.8980 chunk 28 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 259 ASN B 259 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.209509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.162233 restraints weight = 8893.620| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.14 r_work: 0.3431 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8968 Z= 0.140 Angle : 0.513 11.126 12176 Z= 0.261 Chirality : 0.040 0.183 1369 Planarity : 0.003 0.040 1514 Dihedral : 5.772 44.203 1582 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.03 % Allowed : 11.58 % 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: 0.44 (0.26), residues: 1050 helix: 2.00 (0.25), residues: 436 sheet: -0.59 (0.33), residues: 231 loop : -1.11 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.005 0.001 HIS B 266 PHE 0.016 0.001 PHE R 386 TYR 0.017 0.001 TYR R 392 ARG 0.004 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 425) hydrogen bonds : angle 4.04155 ( 1242) SS BOND : bond 0.00175 ( 3) SS BOND : angle 0.59507 ( 6) covalent geometry : bond 0.00322 ( 8965) covalent geometry : angle 0.51317 (12170) *********************** 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: 28 poor density : 154 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8077 (mm-30) REVERT: R 174 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7450 (mm) REVERT: R 181 MET cc_start: 0.8175 (ttm) cc_final: 0.7615 (mtp) REVERT: R 192 ARG cc_start: 0.7335 (mmt-90) cc_final: 0.6547 (mmp-170) REVERT: R 193 LEU cc_start: 0.7503 (mt) cc_final: 0.7278 (tt) REVERT: R 237 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: R 289 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7225 (mtm180) REVERT: R 336 ARG cc_start: 0.6034 (mtt180) cc_final: 0.5332 (tpt170) REVERT: R 345 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7463 (t80) REVERT: A 15 ARG cc_start: 0.7198 (ttt90) cc_final: 0.6884 (ttt-90) REVERT: A 31 ARG cc_start: 0.8389 (mtm110) cc_final: 0.8058 (mtt-85) REVERT: A 47 SER cc_start: 0.8540 (m) cc_final: 0.8180 (p) REVERT: A 187 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8743 (p) REVERT: A 193 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7974 (mtmm) REVERT: A 310 ASP cc_start: 0.8085 (t70) cc_final: 0.7811 (t0) REVERT: A 323 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.7261 (mtm110) REVERT: B 262 MET cc_start: 0.7339 (tpt) cc_final: 0.7130 (tpt) REVERT: N 90 ASP cc_start: 0.8528 (t0) cc_final: 0.8274 (t0) REVERT: N 114 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7736 (t) outliers start: 28 outliers final: 14 residues processed: 172 average time/residue: 0.2969 time to fit residues: 65.4150 Evaluate side-chains 165 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 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 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 118 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 16 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 54 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.209614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.155579 restraints weight = 8842.729| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.44 r_work: 0.3468 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8968 Z= 0.125 Angle : 0.496 9.909 12176 Z= 0.253 Chirality : 0.039 0.136 1369 Planarity : 0.003 0.037 1514 Dihedral : 5.522 42.332 1582 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.49 % Allowed : 12.88 % Favored : 84.63 % 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: 2.21 (0.25), residues: 436 sheet: -0.46 (0.33), residues: 228 loop : -1.07 (0.31), residues: 386 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 0.019 0.001 PHE R 379 TYR 0.017 0.001 TYR R 141 ARG 0.005 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.03257 ( 425) hydrogen bonds : angle 3.91663 ( 1242) SS BOND : bond 0.00215 ( 3) SS BOND : angle 0.58963 ( 6) covalent geometry : bond 0.00286 ( 8965) covalent geometry : angle 0.49621 (12170) *********************** 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 180 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8419 (tmm) cc_final: 0.7057 (mmm) REVERT: R 174 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7367 (mm) REVERT: R 181 MET cc_start: 0.8143 (ttm) cc_final: 0.7621 (mtp) REVERT: R 183 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6489 (ttm-80) REVERT: R 192 ARG cc_start: 0.7475 (mmt-90) cc_final: 0.6728 (mmp-170) REVERT: R 237 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: R 289 ARG cc_start: 0.7678 (mtp180) cc_final: 0.7175 (mtm180) REVERT: R 336 ARG cc_start: 0.6142 (mtt180) cc_final: 0.5418 (tpt170) REVERT: R 345 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7525 (t80) REVERT: A 15 ARG cc_start: 0.7209 (ttt90) cc_final: 0.6954 (ttt-90) REVERT: A 31 ARG cc_start: 0.8358 (mtm110) cc_final: 0.8103 (mtt-85) REVERT: A 47 SER cc_start: 0.8563 (m) cc_final: 0.8198 (p) REVERT: A 187 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8746 (p) REVERT: A 274 LYS cc_start: 0.8134 (ptpt) cc_final: 0.7664 (ptpp) REVERT: A 310 ASP cc_start: 0.8020 (t70) cc_final: 0.7755 (t0) REVERT: A 323 ARG cc_start: 0.7648 (mtm-85) cc_final: 0.7270 (mtm110) REVERT: B 262 MET cc_start: 0.7300 (tpt) cc_final: 0.6965 (tpt) REVERT: N 90 ASP cc_start: 0.8285 (t0) cc_final: 0.7673 (t0) REVERT: N 114 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7710 (t) REVERT: N 117 TYR cc_start: 0.8519 (m-10) cc_final: 0.7880 (m-80) outliers start: 23 outliers final: 13 residues processed: 172 average time/residue: 0.3325 time to fit residues: 73.7507 Evaluate side-chains 163 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 395 ILE 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 118 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 56 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.208895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.154851 restraints weight = 8821.532| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.78 r_work: 0.3537 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8968 Z= 0.129 Angle : 0.502 10.744 12176 Z= 0.253 Chirality : 0.040 0.153 1369 Planarity : 0.003 0.036 1514 Dihedral : 5.314 40.398 1582 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.81 % Allowed : 12.66 % 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: 0.76 (0.27), residues: 1050 helix: 2.30 (0.25), residues: 437 sheet: -0.50 (0.33), residues: 231 loop : -0.95 (0.31), residues: 382 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 0.007 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 425) hydrogen bonds : angle 3.85342 ( 1242) SS BOND : bond 0.00207 ( 3) SS BOND : angle 0.58855 ( 6) covalent geometry : bond 0.00298 ( 8965) covalent geometry : angle 0.50227 (12170) *********************** 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 183 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7976 (mm-30) REVERT: R 174 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7692 (mm) REVERT: R 181 MET cc_start: 0.8391 (ttm) cc_final: 0.7917 (mtp) REVERT: R 183 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6791 (ttm-80) REVERT: R 192 ARG cc_start: 0.7545 (mmt-90) cc_final: 0.6810 (mmp-170) REVERT: R 194 LEU cc_start: 0.7296 (pt) cc_final: 0.7015 (tp) REVERT: R 289 ARG cc_start: 0.7556 (mtp180) cc_final: 0.7209 (mtm180) REVERT: R 336 ARG cc_start: 0.6167 (mtt180) cc_final: 0.5492 (tpt170) REVERT: R 345 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7726 (t80) REVERT: A 15 ARG cc_start: 0.7367 (ttt90) cc_final: 0.7077 (ttt-90) REVERT: A 31 ARG cc_start: 0.8533 (mtm110) cc_final: 0.8220 (mtt-85) REVERT: A 47 SER cc_start: 0.8600 (m) cc_final: 0.8182 (p) REVERT: A 187 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8786 (p) REVERT: A 274 LYS cc_start: 0.8129 (ptpt) cc_final: 0.7648 (ptpp) REVERT: A 310 ASP cc_start: 0.8387 (t70) cc_final: 0.8168 (t0) REVERT: A 323 ARG cc_start: 0.7702 (mtm-85) cc_final: 0.7367 (mtm110) REVERT: B 262 MET cc_start: 0.7575 (tpt) cc_final: 0.7312 (tpt) REVERT: G 47 GLU cc_start: 0.7591 (mp0) cc_final: 0.7184 (mp0) REVERT: N 90 ASP cc_start: 0.8484 (t0) cc_final: 0.7902 (t0) REVERT: N 117 TYR cc_start: 0.8562 (m-10) cc_final: 0.7970 (m-80) outliers start: 26 outliers final: 16 residues processed: 175 average time/residue: 0.3070 time to fit residues: 69.4528 Evaluate side-chains 166 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 218 CYS Chi-restraints excluded: chain B residue 245 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: 2.9990 chunk 16 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 0.0270 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.209388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163027 restraints weight = 8943.844| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 3.24 r_work: 0.3431 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8968 Z= 0.111 Angle : 0.487 9.042 12176 Z= 0.246 Chirality : 0.039 0.133 1369 Planarity : 0.003 0.032 1514 Dihedral : 5.112 37.769 1582 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.92 % Allowed : 13.42 % Favored : 83.66 % 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: 0.87 (0.27), residues: 1050 helix: 2.41 (0.25), residues: 439 sheet: -0.46 (0.33), residues: 230 loop : -0.94 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.004 0.001 HIS B 142 PHE 0.021 0.001 PHE R 379 TYR 0.017 0.001 TYR R 141 ARG 0.007 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 425) hydrogen bonds : angle 3.74478 ( 1242) SS BOND : bond 0.00285 ( 3) SS BOND : angle 0.96373 ( 6) covalent geometry : bond 0.00249 ( 8965) covalent geometry : angle 0.48684 (12170) *********************** 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 177 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8057 (mm-30) REVERT: R 140 MET cc_start: 0.8415 (tmm) cc_final: 0.7106 (mmm) REVERT: R 174 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7351 (mm) REVERT: R 181 MET cc_start: 0.8191 (ttm) cc_final: 0.7669 (mtp) REVERT: R 183 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6513 (ttm-80) REVERT: R 192 ARG cc_start: 0.7490 (mmt-90) cc_final: 0.6708 (mmp-170) REVERT: R 194 LEU cc_start: 0.7404 (pt) cc_final: 0.7088 (tp) REVERT: R 237 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: R 289 ARG cc_start: 0.7631 (mtp180) cc_final: 0.7193 (mtm180) REVERT: R 336 ARG cc_start: 0.6176 (mtt180) cc_final: 0.5480 (tpt170) REVERT: R 345 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7652 (t80) REVERT: A 15 ARG cc_start: 0.7236 (ttt90) cc_final: 0.6945 (ttt-90) REVERT: A 31 ARG cc_start: 0.8417 (mtm110) cc_final: 0.8089 (mtt-85) REVERT: A 47 SER cc_start: 0.8563 (m) cc_final: 0.8186 (p) REVERT: A 187 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8725 (p) REVERT: A 274 LYS cc_start: 0.8098 (ptpt) cc_final: 0.7734 (ptpp) REVERT: A 310 ASP cc_start: 0.8135 (t70) cc_final: 0.7881 (t0) REVERT: A 323 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7210 (mtm110) REVERT: A 353 MET cc_start: 0.8228 (tmm) cc_final: 0.7757 (tmm) REVERT: B 262 MET cc_start: 0.7419 (tpt) cc_final: 0.7131 (tpt) REVERT: G 17 GLU cc_start: 0.8297 (tp30) cc_final: 0.7926 (tt0) REVERT: G 47 GLU cc_start: 0.7521 (mp0) cc_final: 0.7116 (mp0) REVERT: N 90 ASP cc_start: 0.8351 (t0) cc_final: 0.7797 (t0) REVERT: N 117 TYR cc_start: 0.8501 (m-10) cc_final: 0.7889 (m-80) outliers start: 27 outliers final: 19 residues processed: 169 average time/residue: 0.4128 time to fit residues: 87.9293 Evaluate side-chains 169 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 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 192 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 12 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.205998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3686 r_free = 0.3686 target = 0.147327 restraints weight = 8912.099| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.38 r_work: 0.3485 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8968 Z= 0.186 Angle : 0.541 9.404 12176 Z= 0.276 Chirality : 0.041 0.137 1369 Planarity : 0.004 0.040 1514 Dihedral : 5.141 38.402 1582 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.60 % Allowed : 13.74 % Favored : 83.66 % 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: 0.83 (0.27), residues: 1050 helix: 2.36 (0.25), residues: 437 sheet: -0.56 (0.34), residues: 214 loop : -0.84 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 47 HIS 0.005 0.001 HIS A 354 PHE 0.014 0.002 PHE A 189 TYR 0.016 0.002 TYR R 141 ARG 0.009 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 425) hydrogen bonds : angle 3.94868 ( 1242) SS BOND : bond 0.00190 ( 3) SS BOND : angle 1.15060 ( 6) covalent geometry : bond 0.00441 ( 8965) covalent geometry : angle 0.54066 (12170) *********************** 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: 24 poor density : 148 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8118 (mm-30) REVERT: R 140 MET cc_start: 0.8474 (tmm) cc_final: 0.7079 (mmm) REVERT: R 174 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7193 (mm) REVERT: R 181 MET cc_start: 0.8301 (ttm) cc_final: 0.7697 (mtp) REVERT: R 183 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6515 (ttm-80) REVERT: R 192 ARG cc_start: 0.7457 (mmt-90) cc_final: 0.6685 (mmp-170) REVERT: R 194 LEU cc_start: 0.7417 (pt) cc_final: 0.7124 (tp) REVERT: R 237 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: R 289 ARG cc_start: 0.7626 (mtp180) cc_final: 0.7167 (mtm180) REVERT: R 336 ARG cc_start: 0.6244 (mtt180) cc_final: 0.5433 (tpt170) REVERT: R 345 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7689 (t80) REVERT: A 31 ARG cc_start: 0.8526 (mtm110) cc_final: 0.8112 (mtt-85) REVERT: A 274 LYS cc_start: 0.8075 (ptpt) cc_final: 0.7691 (ptpp) REVERT: A 310 ASP cc_start: 0.8219 (t70) cc_final: 0.7949 (t0) REVERT: B 258 ASP cc_start: 0.8129 (t70) cc_final: 0.7241 (t0) REVERT: B 262 MET cc_start: 0.7738 (tpt) cc_final: 0.7455 (tpt) REVERT: G 17 GLU cc_start: 0.8296 (tp30) cc_final: 0.7895 (tt0) REVERT: N 82 GLN cc_start: 0.7922 (tp-100) cc_final: 0.7403 (tp-100) REVERT: N 90 ASP cc_start: 0.8447 (t0) cc_final: 0.7870 (t0) outliers start: 24 outliers final: 17 residues processed: 164 average time/residue: 0.2858 time to fit residues: 59.8537 Evaluate side-chains 164 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 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 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 52 SER Chi-restraints excluded: chain N residue 83 MET 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: 0.0040 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.206904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.149845 restraints weight = 8938.427| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.12 r_work: 0.3478 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8968 Z= 0.155 Angle : 0.561 11.567 12176 Z= 0.283 Chirality : 0.041 0.271 1369 Planarity : 0.004 0.037 1514 Dihedral : 5.120 37.099 1582 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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: 0.86 (0.27), residues: 1050 helix: 2.45 (0.25), residues: 436 sheet: -0.60 (0.33), residues: 230 loop : -0.88 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.004 0.001 HIS A 354 PHE 0.026 0.001 PHE R 379 TYR 0.017 0.001 TYR R 141 ARG 0.009 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 425) hydrogen bonds : angle 3.86753 ( 1242) SS BOND : bond 0.00238 ( 3) SS BOND : angle 4.90220 ( 6) covalent geometry : bond 0.00368 ( 8965) covalent geometry : angle 0.55061 (12170) *********************** 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: 22 poor density : 143 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8020 (mm-30) REVERT: R 140 MET cc_start: 0.8438 (tmm) cc_final: 0.7131 (mmm) REVERT: R 174 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7494 (mm) REVERT: R 181 MET cc_start: 0.8424 (ttm) cc_final: 0.7882 (mtp) REVERT: R 183 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6770 (ttm-80) REVERT: R 192 ARG cc_start: 0.7536 (mmt-90) cc_final: 0.6794 (mmp-170) REVERT: R 194 LEU cc_start: 0.7420 (pt) cc_final: 0.7081 (tp) REVERT: R 237 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: R 253 GLU cc_start: 0.4846 (pm20) cc_final: 0.4039 (tp30) REVERT: R 289 ARG cc_start: 0.7460 (mtp180) cc_final: 0.7176 (mtm180) REVERT: R 336 ARG cc_start: 0.6316 (mtt180) cc_final: 0.5409 (tpt170) REVERT: R 345 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7895 (t80) REVERT: A 31 ARG cc_start: 0.8600 (mtm110) cc_final: 0.8226 (mtt-85) REVERT: A 274 LYS cc_start: 0.8104 (ptpt) cc_final: 0.7711 (ptpp) REVERT: A 310 ASP cc_start: 0.8390 (t70) cc_final: 0.8151 (t0) REVERT: A 323 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7347 (mmm160) REVERT: A 353 MET cc_start: 0.8394 (tmm) cc_final: 0.7978 (tmm) REVERT: B 258 ASP cc_start: 0.8126 (t70) cc_final: 0.7194 (t0) REVERT: G 17 GLU cc_start: 0.8301 (tp30) cc_final: 0.7923 (tt0) REVERT: N 82 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7549 (tp-100) REVERT: N 90 ASP cc_start: 0.8472 (t0) cc_final: 0.7922 (t0) outliers start: 22 outliers final: 17 residues processed: 157 average time/residue: 0.2855 time to fit residues: 58.0034 Evaluate side-chains 163 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 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 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: 7.9990 chunk 58 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 33 optimal weight: 0.4980 chunk 17 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.209046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.157316 restraints weight = 8922.981| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.01 r_work: 0.3515 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8968 Z= 0.113 Angle : 0.509 8.097 12176 Z= 0.258 Chirality : 0.039 0.146 1369 Planarity : 0.003 0.037 1514 Dihedral : 4.938 36.994 1582 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.16 % Allowed : 14.72 % Favored : 83.12 % 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: 0.97 (0.27), residues: 1050 helix: 2.56 (0.25), residues: 437 sheet: -0.53 (0.33), residues: 229 loop : -0.86 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.002 0.001 HIS A 354 PHE 0.026 0.001 PHE R 379 TYR 0.018 0.001 TYR R 141 ARG 0.009 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.03040 ( 425) hydrogen bonds : angle 3.71757 ( 1242) SS BOND : bond 0.00200 ( 3) SS BOND : angle 3.27649 ( 6) covalent geometry : bond 0.00256 ( 8965) covalent geometry : angle 0.50393 (12170) ********************** 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 168 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8031 (mm-30) REVERT: R 140 MET cc_start: 0.8425 (tmm) cc_final: 0.7120 (mmm) REVERT: R 174 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7421 (mm) REVERT: R 181 MET cc_start: 0.8309 (ttm) cc_final: 0.7785 (mtp) REVERT: R 183 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6622 (ttm-80) REVERT: R 192 ARG cc_start: 0.7387 (mmt-90) cc_final: 0.6727 (mmp-170) REVERT: R 253 GLU cc_start: 0.4860 (pm20) cc_final: 0.4088 (tp30) REVERT: R 289 ARG cc_start: 0.7432 (mtp180) cc_final: 0.7129 (mtm180) REVERT: R 336 ARG cc_start: 0.6297 (mtt180) cc_final: 0.5377 (tpt170) REVERT: R 345 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7800 (t80) REVERT: A 31 ARG cc_start: 0.8551 (mtm110) cc_final: 0.8180 (mtt-85) REVERT: A 47 SER cc_start: 0.8604 (m) cc_final: 0.8170 (p) REVERT: A 310 ASP cc_start: 0.8290 (t70) cc_final: 0.8045 (t0) REVERT: A 323 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7333 (mmm160) REVERT: A 353 MET cc_start: 0.8392 (tmm) cc_final: 0.7945 (tmm) REVERT: B 258 ASP cc_start: 0.7940 (t70) cc_final: 0.7058 (t0) REVERT: B 262 MET cc_start: 0.7516 (tpt) cc_final: 0.7305 (tpt) REVERT: G 17 GLU cc_start: 0.8270 (tp30) cc_final: 0.7901 (tt0) REVERT: N 82 GLN cc_start: 0.8009 (tp-100) cc_final: 0.7550 (tp-100) REVERT: N 90 ASP cc_start: 0.8405 (t0) cc_final: 0.7877 (t0) REVERT: N 117 TYR cc_start: 0.8536 (m-10) cc_final: 0.7949 (m-80) outliers start: 20 outliers final: 15 residues processed: 160 average time/residue: 0.2871 time to fit residues: 58.8580 Evaluate side-chains 161 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 318 LEU Chi-restraints excluded: chain R residue 345 PHE 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 118 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 B residue 275 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: 8.9990 chunk 69 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 18 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4274 r_free = 0.4274 target = 0.207076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.155292 restraints weight = 8986.896| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.80 r_work: 0.3484 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8968 Z= 0.162 Angle : 0.541 7.717 12176 Z= 0.276 Chirality : 0.041 0.147 1369 Planarity : 0.004 0.038 1514 Dihedral : 5.003 35.921 1582 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.84 % Allowed : 15.15 % Favored : 83.01 % 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: 0.89 (0.27), residues: 1050 helix: 2.48 (0.25), residues: 437 sheet: -0.62 (0.33), residues: 230 loop : -0.85 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.004 0.001 HIS A 354 PHE 0.022 0.002 PHE R 379 TYR 0.017 0.001 TYR R 141 ARG 0.009 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 425) hydrogen bonds : angle 3.85864 ( 1242) SS BOND : bond 0.00246 ( 3) SS BOND : angle 3.35858 ( 6) covalent geometry : bond 0.00384 ( 8965) covalent geometry : angle 0.53555 (12170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6267.83 seconds wall clock time: 112 minutes 34.53 seconds (6754.53 seconds total)