Starting phenix.real_space_refine on Wed Jan 15 15:01:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvi_38705/01_2025/8xvi_38705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvi_38705/01_2025/8xvi_38705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xvi_38705/01_2025/8xvi_38705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvi_38705/01_2025/8xvi_38705.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvi_38705/01_2025/8xvi_38705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvi_38705/01_2025/8xvi_38705.cif" } resolution = 3.32 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= 0.028 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 67 5.16 5 C 5449 2.51 5 N 1484 2.21 5 O 1587 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8587 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1943 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} 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: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2476 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 11, 'TRANS': 296} Chain breaks: 1 Chain: "T" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 171 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Time building chain proxies: 5.41, per 1000 atoms: 0.63 Number of scatterers: 8587 At special positions: 0 Unit cell: (85.44, 103.68, 144.96, 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 67 16.00 O 1587 8.00 N 1484 7.00 C 5449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 69 " - pdb=" SG CYS R 341 " distance=2.03 Simple disulfide: pdb=" SG CYS R 158 " - pdb=" SG CYS R 239 " distance=2.03 Simple disulfide: pdb=" SG CYS T 1 " - pdb=" SG CYS T 15 " distance=2.03 Simple disulfide: pdb=" SG CYS T 3 " - pdb=" SG CYS T 11 " 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: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2044 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 40.5% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 3.577A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.622A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 321 through 342 removed outlier: 3.793A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 379 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.950A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.722A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.701A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 61 through 65 removed outlier: 3.676A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 108 removed outlier: 4.045A pdb=" N ILE R 92 " --> pdb=" O CYS R 88 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN R 98 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR R 106 " --> pdb=" O LEU R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 143 removed outlier: 3.627A pdb=" N LEU R 118 " --> pdb=" O GLY R 114 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU R 134 " --> pdb=" O VAL R 130 " (cutoff:3.500A) Proline residue: R 135 - end of helix Processing helix chain 'R' and resid 151 through 188 removed outlier: 3.809A pdb=" N VAL R 155 " --> pdb=" O ASN R 151 " (cutoff:3.500A) Proline residue: R 162 - end of helix removed outlier: 3.627A pdb=" N TYR R 184 " --> pdb=" O SER R 180 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG R 185 " --> pdb=" O VAL R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 216 Processing helix chain 'R' and resid 217 through 222 Processing helix chain 'R' and resid 245 through 254 Processing helix chain 'R' and resid 255 through 284 removed outlier: 3.977A pdb=" N TYR R 263 " --> pdb=" O LEU R 259 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET R 266 " --> pdb=" O PHE R 262 " (cutoff:3.500A) Proline residue: R 267 - end of helix removed outlier: 3.854A pdb=" N TYR R 275 " --> pdb=" O THR R 271 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU R 281 " --> pdb=" O LEU R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 332 removed outlier: 4.101A pdb=" N LYS R 299 " --> pdb=" O SER R 295 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLN R 300 " --> pdb=" O GLU R 296 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU R 311 " --> pdb=" O THR R 307 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL R 312 " --> pdb=" O VAL R 308 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 339 through 360 removed outlier: 3.696A pdb=" N LEU R 343 " --> pdb=" O ASN R 339 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU R 349 " --> pdb=" O SER R 345 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N MET R 350 " --> pdb=" O PHE R 346 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP R 351 " --> pdb=" O LEU R 347 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET R 360 " --> pdb=" O ASN R 356 " (cutoff:3.500A) Processing helix chain 'R' and resid 363 through 371 removed outlier: 3.840A pdb=" N LEU R 369 " --> pdb=" O ASN R 365 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR R 370 " --> pdb=" O PRO R 366 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE R 371 " --> pdb=" O ILE R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 382 removed outlier: 3.636A pdb=" N CYS R 379 " --> pdb=" O LYS R 375 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 17 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 5.939A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.985A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.595A pdb=" N TYR B 59 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.870A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.051A 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: 6.573A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.894A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.745A 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 232 removed outlier: 6.978A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 277 removed outlier: 3.948A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.606A 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 58 through 59 removed outlier: 3.666A pdb=" N VAL N 48 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 225 through 227 removed outlier: 4.132A pdb=" N THR R 238 " --> pdb=" O VAL R 227 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 230 through 231 386 hydrogen bonds defined for protein. 1125 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: 2.42 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2808 1.34 - 1.47: 2110 1.47 - 1.59: 3750 1.59 - 1.71: 0 1.71 - 1.83: 93 Bond restraints: 8761 Sorted by residual: bond pdb=" C ARG N 98 " pdb=" N CYS N 99 " ideal model delta sigma weight residual 1.331 1.294 0.037 2.07e-02 2.33e+03 3.17e+00 bond pdb=" CB LYS A 216 " pdb=" CG LYS A 216 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" CG LYS A 216 " pdb=" CD LYS A 216 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CA ASP A 313 " pdb=" CB ASP A 313 " ideal model delta sigma weight residual 1.536 1.563 -0.028 2.53e-02 1.56e+03 1.19e+00 bond pdb=" CB ASP B 298 " pdb=" CG ASP B 298 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.11e+00 ... (remaining 8756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 11682 2.15 - 4.30: 147 4.30 - 6.44: 19 6.44 - 8.59: 3 8.59 - 10.74: 3 Bond angle restraints: 11854 Sorted by residual: angle pdb=" CB MET R 266 " pdb=" CG MET R 266 " pdb=" SD MET R 266 " ideal model delta sigma weight residual 112.70 123.44 -10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" CB LYS A 216 " pdb=" CG LYS A 216 " pdb=" CD LYS A 216 " ideal model delta sigma weight residual 111.30 119.37 -8.07 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CA GLN R 72 " pdb=" CB GLN R 72 " pdb=" CG GLN R 72 " ideal model delta sigma weight residual 114.10 119.44 -5.34 2.00e+00 2.50e-01 7.12e+00 angle pdb=" CA LEU T 17 " pdb=" CB LEU T 17 " pdb=" CG LEU T 17 " ideal model delta sigma weight residual 116.30 125.43 -9.13 3.50e+00 8.16e-02 6.81e+00 angle pdb=" CA LEU B 198 " pdb=" CB LEU B 198 " pdb=" CG LEU B 198 " ideal model delta sigma weight residual 116.30 125.34 -9.04 3.50e+00 8.16e-02 6.68e+00 ... (remaining 11849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 4449 17.48 - 34.97: 588 34.97 - 52.45: 188 52.45 - 69.93: 17 69.93 - 87.42: 9 Dihedral angle restraints: 5251 sinusoidal: 2094 harmonic: 3157 Sorted by residual: 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 93.00 7.74 85.26 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CB CYS R 69 " pdb=" SG CYS R 69 " pdb=" SG CYS R 341 " pdb=" CB CYS R 341 " ideal model delta sinusoidal sigma weight residual 93.00 157.92 -64.92 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 44.89 48.11 1 1.00e+01 1.00e-02 3.19e+01 ... (remaining 5248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 872 0.035 - 0.070: 311 0.070 - 0.105: 112 0.105 - 0.140: 33 0.140 - 0.175: 1 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CB ILE B 43 " pdb=" CA ILE B 43 " pdb=" CG1 ILE B 43 " pdb=" CG2 ILE B 43 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CG LEU R 349 " pdb=" CB LEU R 349 " pdb=" CD1 LEU R 349 " pdb=" CD2 LEU R 349 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE R 75 " pdb=" N ILE R 75 " pdb=" C ILE R 75 " pdb=" CB ILE R 75 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 1326 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 227 " -0.051 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO R 228 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO R 228 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 228 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO B 236 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 304 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C GLU A 304 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU A 304 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A 305 " 0.010 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 823 2.74 - 3.28: 8290 3.28 - 3.82: 13814 3.82 - 4.36: 15342 4.36 - 4.90: 27009 Nonbonded interactions: 65278 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.200 3.040 nonbonded pdb=" O MET R 111 " pdb=" ND2 ASN R 116 " model vdw 2.219 3.120 nonbonded pdb=" NH1 ARG B 49 " pdb=" O TYR B 85 " model vdw 2.234 3.120 nonbonded pdb=" OD1 ASP T 18 " pdb=" N ILE T 19 " model vdw 2.238 3.120 ... (remaining 65273 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 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 0.037 8761 Z= 0.234 Angle : 0.621 10.740 11854 Z= 0.328 Chirality : 0.043 0.175 1329 Planarity : 0.004 0.078 1513 Dihedral : 16.873 87.416 3189 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.43 % Allowed : 33.33 % Favored : 66.24 % 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: -0.52 (0.26), residues: 1068 helix: 1.23 (0.27), residues: 408 sheet: -0.28 (0.39), residues: 197 loop : -1.87 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 352 PHE 0.022 0.002 PHE B 151 TYR 0.019 0.002 TYR A 253 ARG 0.010 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 213 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7595 (mtpt) cc_final: 0.7307 (mtmm) REVERT: R 137 ASN cc_start: 0.7780 (m-40) cc_final: 0.7374 (m110) outliers start: 4 outliers final: 3 residues processed: 215 average time/residue: 0.2733 time to fit residues: 74.9229 Evaluate side-chains 214 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 211 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 LYS Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 367 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.0770 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.167875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140078 restraints weight = 12753.218| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.73 r_work: 0.3637 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8761 Z= 0.198 Angle : 0.556 11.023 11854 Z= 0.293 Chirality : 0.041 0.158 1329 Planarity : 0.004 0.055 1513 Dihedral : 4.990 44.971 1185 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.26 % Allowed : 28.97 % Favored : 66.77 % 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: -0.15 (0.26), residues: 1068 helix: 1.60 (0.26), residues: 421 sheet: -0.17 (0.38), residues: 206 loop : -1.81 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.005 0.001 HIS A 352 PHE 0.020 0.001 PHE N 108 TYR 0.016 0.001 TYR A 253 ARG 0.007 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: B 228 ASP cc_start: 0.7397 (m-30) cc_final: 0.7118 (m-30) REVERT: N 36 TRP cc_start: 0.7975 (m100) cc_final: 0.7352 (m100) REVERT: R 79 PHE cc_start: 0.7459 (t80) cc_final: 0.7218 (t80) REVERT: R 83 ASN cc_start: 0.6265 (OUTLIER) cc_final: 0.6005 (m-40) REVERT: R 196 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6841 (tt) outliers start: 40 outliers final: 21 residues processed: 234 average time/residue: 0.2436 time to fit residues: 74.5792 Evaluate side-chains 229 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 83 ASN Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 355 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 43 optimal weight: 0.0060 chunk 75 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 ASN R 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.166708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138457 restraints weight = 12903.131| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.81 r_work: 0.3624 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8761 Z= 0.227 Angle : 0.553 8.506 11854 Z= 0.292 Chirality : 0.042 0.190 1329 Planarity : 0.004 0.047 1513 Dihedral : 4.434 20.750 1177 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.90 % Allowed : 27.80 % Favored : 67.31 % 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: -0.14 (0.26), residues: 1068 helix: 1.66 (0.26), residues: 421 sheet: -0.23 (0.38), residues: 206 loop : -1.81 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 352 PHE 0.021 0.001 PHE N 108 TYR 0.013 0.002 TYR A 253 ARG 0.007 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 0.936 Fit side-chains REVERT: A 255 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7710 (ptm160) REVERT: A 350 TYR cc_start: 0.8496 (m-80) cc_final: 0.8294 (m-10) REVERT: A 371 ASP cc_start: 0.7712 (t0) cc_final: 0.7492 (t0) REVERT: N 36 TRP cc_start: 0.8053 (m100) cc_final: 0.7377 (m100) REVERT: R 91 PHE cc_start: 0.7830 (t80) cc_final: 0.7589 (t80) REVERT: R 111 MET cc_start: 0.5888 (tpt) cc_final: 0.5576 (tpt) REVERT: R 113 ASN cc_start: 0.6206 (p0) cc_final: 0.5893 (p0) REVERT: R 196 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6852 (tt) REVERT: T 7 MET cc_start: 0.7830 (pmm) cc_final: 0.7434 (pmm) outliers start: 46 outliers final: 33 residues processed: 237 average time/residue: 0.2397 time to fit residues: 74.3767 Evaluate side-chains 239 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 367 ILE Chi-restraints excluded: chain T residue 17 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 8 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.166987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138976 restraints weight = 12726.064| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.76 r_work: 0.3630 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8761 Z= 0.209 Angle : 0.547 8.353 11854 Z= 0.286 Chirality : 0.042 0.197 1329 Planarity : 0.003 0.049 1513 Dihedral : 4.348 20.196 1177 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.54 % Allowed : 27.37 % Favored : 67.09 % 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: -0.10 (0.26), residues: 1068 helix: 1.70 (0.26), residues: 421 sheet: -0.23 (0.38), residues: 206 loop : -1.80 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS A 352 PHE 0.021 0.001 PHE N 108 TYR 0.010 0.001 TYR A 253 ARG 0.003 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.893 Fit side-chains REVERT: A 255 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7680 (ptm160) REVERT: A 371 ASP cc_start: 0.7726 (t0) cc_final: 0.7513 (t0) REVERT: B 228 ASP cc_start: 0.7273 (m-30) cc_final: 0.6918 (m-30) REVERT: N 36 TRP cc_start: 0.8045 (m100) cc_final: 0.7374 (m100) REVERT: R 72 GLN cc_start: 0.7222 (pp30) cc_final: 0.6990 (pp30) REVERT: R 91 PHE cc_start: 0.7804 (t80) cc_final: 0.7592 (t80) REVERT: R 111 MET cc_start: 0.5817 (tpt) cc_final: 0.5514 (tpt) REVERT: R 113 ASN cc_start: 0.6160 (p0) cc_final: 0.5787 (p0) REVERT: R 133 ASP cc_start: 0.5853 (OUTLIER) cc_final: 0.5430 (m-30) REVERT: R 196 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6839 (tt) REVERT: T 7 MET cc_start: 0.7834 (pmm) cc_final: 0.7519 (pmm) outliers start: 52 outliers final: 35 residues processed: 239 average time/residue: 0.2505 time to fit residues: 78.2123 Evaluate side-chains 242 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 367 ILE Chi-restraints excluded: chain T residue 17 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 86 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.167453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.139298 restraints weight = 12753.218| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.77 r_work: 0.3637 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8761 Z= 0.183 Angle : 0.543 8.444 11854 Z= 0.281 Chirality : 0.042 0.214 1329 Planarity : 0.003 0.050 1513 Dihedral : 4.246 19.714 1177 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.01 % Allowed : 28.01 % Favored : 66.99 % 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: -0.06 (0.26), residues: 1068 helix: 1.76 (0.26), residues: 421 sheet: -0.19 (0.38), residues: 204 loop : -1.81 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 352 PHE 0.019 0.001 PHE N 108 TYR 0.009 0.001 TYR A 329 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.912 Fit side-chains REVERT: A 255 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7691 (ptm160) REVERT: B 321 THR cc_start: 0.6141 (t) cc_final: 0.4948 (p) REVERT: B 322 ASP cc_start: 0.7108 (m-30) cc_final: 0.6843 (m-30) REVERT: N 36 TRP cc_start: 0.8015 (m100) cc_final: 0.7361 (m100) REVERT: N 60 TYR cc_start: 0.7883 (m-80) cc_final: 0.7127 (m-80) REVERT: R 72 GLN cc_start: 0.7223 (pp30) cc_final: 0.6972 (pp30) REVERT: R 91 PHE cc_start: 0.7812 (t80) cc_final: 0.7585 (t80) REVERT: R 133 ASP cc_start: 0.5776 (OUTLIER) cc_final: 0.5333 (m-30) REVERT: R 196 ILE cc_start: 0.7019 (tt) cc_final: 0.6806 (tt) REVERT: R 215 ILE cc_start: 0.7636 (tt) cc_final: 0.7374 (tt) outliers start: 47 outliers final: 39 residues processed: 242 average time/residue: 0.2588 time to fit residues: 81.5611 Evaluate side-chains 243 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 172 THR Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 270 CYS Chi-restraints excluded: chain R residue 309 PHE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 367 ILE Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 20 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.167854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.139712 restraints weight = 12689.428| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.77 r_work: 0.3632 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8761 Z= 0.213 Angle : 0.566 8.778 11854 Z= 0.292 Chirality : 0.042 0.208 1329 Planarity : 0.003 0.051 1513 Dihedral : 4.261 19.702 1177 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 6.39 % Allowed : 26.84 % Favored : 66.77 % 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: -0.07 (0.26), residues: 1068 helix: 1.75 (0.26), residues: 419 sheet: -0.18 (0.38), residues: 209 loop : -1.83 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 352 PHE 0.020 0.001 PHE N 108 TYR 0.010 0.001 TYR A 329 ARG 0.008 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 214 time to evaluate : 0.991 Fit side-chains REVERT: A 255 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7676 (ptm160) REVERT: A 333 ASP cc_start: 0.7046 (m-30) cc_final: 0.6789 (m-30) REVERT: B 59 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7651 (m-80) REVERT: B 321 THR cc_start: 0.6061 (t) cc_final: 0.4881 (p) REVERT: N 36 TRP cc_start: 0.8074 (m100) cc_final: 0.7409 (m100) REVERT: N 60 TYR cc_start: 0.7917 (m-80) cc_final: 0.7181 (m-80) REVERT: R 95 MET cc_start: 0.7027 (mmm) cc_final: 0.6785 (mmm) REVERT: R 111 MET cc_start: 0.5996 (tpt) cc_final: 0.5612 (tpt) REVERT: R 113 ASN cc_start: 0.6305 (p0) cc_final: 0.5918 (p0) REVERT: R 133 ASP cc_start: 0.5841 (OUTLIER) cc_final: 0.5435 (m-30) REVERT: R 174 LEU cc_start: 0.8114 (mt) cc_final: 0.7912 (mm) REVERT: R 215 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7407 (tt) REVERT: T 18 ASP cc_start: 0.8025 (t0) cc_final: 0.7778 (t0) outliers start: 60 outliers final: 46 residues processed: 251 average time/residue: 0.2476 time to fit residues: 82.1683 Evaluate side-chains 260 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 172 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 215 ILE Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 270 CYS Chi-restraints excluded: chain R residue 309 PHE Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 367 ILE Chi-restraints excluded: chain T residue 17 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 0.0970 chunk 71 optimal weight: 0.0470 chunk 102 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN R 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.169563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.141381 restraints weight = 12858.678| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.79 r_work: 0.3672 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8761 Z= 0.142 Angle : 0.536 9.244 11854 Z= 0.274 Chirality : 0.041 0.178 1329 Planarity : 0.003 0.051 1513 Dihedral : 4.026 18.419 1177 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.11 % Allowed : 28.75 % Favored : 66.13 % 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: 0.06 (0.27), residues: 1068 helix: 1.83 (0.26), residues: 421 sheet: -0.15 (0.39), residues: 207 loop : -1.70 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS A 352 PHE 0.012 0.001 PHE R 315 TYR 0.008 0.001 TYR A 253 ARG 0.008 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 0.779 Fit side-chains REVERT: A 53 LYS cc_start: 0.7277 (mtpt) cc_final: 0.7003 (mtmm) REVERT: A 255 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7665 (ptm160) REVERT: A 350 TYR cc_start: 0.8488 (m-80) cc_final: 0.8232 (m-10) REVERT: B 47 THR cc_start: 0.8568 (t) cc_final: 0.7761 (p) REVERT: B 59 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: B 126 LEU cc_start: 0.8301 (mm) cc_final: 0.8013 (mm) REVERT: B 228 ASP cc_start: 0.7010 (m-30) cc_final: 0.6777 (m-30) REVERT: N 36 TRP cc_start: 0.7940 (m100) cc_final: 0.7301 (m100) REVERT: R 98 ASN cc_start: 0.7272 (m-40) cc_final: 0.6913 (t0) REVERT: R 133 ASP cc_start: 0.5732 (OUTLIER) cc_final: 0.5511 (m-30) REVERT: R 137 ASN cc_start: 0.7697 (m-40) cc_final: 0.7246 (m110) REVERT: R 309 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.6713 (t80) REVERT: R 360 MET cc_start: 0.7949 (tpp) cc_final: 0.7684 (mmm) REVERT: T 7 MET cc_start: 0.7763 (pmm) cc_final: 0.7537 (pmm) outliers start: 48 outliers final: 35 residues processed: 239 average time/residue: 0.2559 time to fit residues: 79.3051 Evaluate side-chains 241 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 270 CYS Chi-restraints excluded: chain R residue 309 PHE Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 367 ILE Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 20 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 83 optimal weight: 0.1980 chunk 99 optimal weight: 0.0030 chunk 101 optimal weight: 3.9990 chunk 33 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 overall best weight: 0.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.170028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.141496 restraints weight = 12976.443| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.83 r_work: 0.3654 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8761 Z= 0.164 Angle : 0.555 9.101 11854 Z= 0.284 Chirality : 0.042 0.224 1329 Planarity : 0.003 0.051 1513 Dihedral : 4.023 18.759 1177 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.37 % Allowed : 29.61 % Favored : 66.03 % 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: 0.06 (0.26), residues: 1068 helix: 1.80 (0.26), residues: 421 sheet: -0.06 (0.39), residues: 202 loop : -1.70 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 352 PHE 0.015 0.001 PHE N 108 TYR 0.008 0.001 TYR A 329 ARG 0.008 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7296 (mtpt) cc_final: 0.7021 (mtmm) REVERT: B 47 THR cc_start: 0.8592 (t) cc_final: 0.7820 (p) REVERT: B 59 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: B 126 LEU cc_start: 0.8306 (mm) cc_final: 0.8026 (mm) REVERT: B 214 ARG cc_start: 0.7395 (mtp85) cc_final: 0.7182 (mtp85) REVERT: B 228 ASP cc_start: 0.7102 (m-30) cc_final: 0.6840 (m-30) REVERT: B 321 THR cc_start: 0.6094 (t) cc_final: 0.4922 (p) REVERT: G 38 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6633 (mtt) REVERT: N 36 TRP cc_start: 0.7981 (m100) cc_final: 0.7353 (m100) REVERT: R 98 ASN cc_start: 0.7237 (m-40) cc_final: 0.6855 (t0) REVERT: R 111 MET cc_start: 0.5881 (tpt) cc_final: 0.5426 (tpt) REVERT: R 137 ASN cc_start: 0.7719 (m-40) cc_final: 0.7266 (m110) REVERT: R 360 MET cc_start: 0.7996 (tpp) cc_final: 0.7782 (mmm) REVERT: T 7 MET cc_start: 0.7765 (pmm) cc_final: 0.7557 (pmm) outliers start: 41 outliers final: 36 residues processed: 237 average time/residue: 0.2652 time to fit residues: 81.1873 Evaluate side-chains 247 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 270 CYS Chi-restraints excluded: chain R residue 309 PHE Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 367 ILE Chi-restraints excluded: chain T residue 17 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.169503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.140955 restraints weight = 12838.241| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.81 r_work: 0.3641 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8761 Z= 0.196 Angle : 0.575 9.622 11854 Z= 0.293 Chirality : 0.042 0.225 1329 Planarity : 0.003 0.051 1513 Dihedral : 4.103 19.105 1177 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.69 % Allowed : 29.50 % Favored : 65.81 % 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: 0.05 (0.27), residues: 1068 helix: 1.80 (0.26), residues: 421 sheet: -0.11 (0.39), residues: 204 loop : -1.71 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 352 PHE 0.020 0.001 PHE N 108 TYR 0.010 0.001 TYR A 329 ARG 0.008 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 1.010 Fit side-chains REVERT: B 47 THR cc_start: 0.8599 (t) cc_final: 0.7837 (p) REVERT: B 59 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: B 126 LEU cc_start: 0.8311 (mm) cc_final: 0.8042 (mm) REVERT: B 214 ARG cc_start: 0.7386 (mtp85) cc_final: 0.7169 (mtp85) REVERT: B 228 ASP cc_start: 0.7124 (m-30) cc_final: 0.6891 (m-30) REVERT: B 321 THR cc_start: 0.6054 (t) cc_final: 0.4835 (p) REVERT: N 36 TRP cc_start: 0.8040 (m100) cc_final: 0.7412 (m100) REVERT: R 98 ASN cc_start: 0.7278 (m-40) cc_final: 0.6894 (t0) REVERT: R 137 ASN cc_start: 0.7723 (m-40) cc_final: 0.7255 (m110) REVERT: R 360 MET cc_start: 0.8011 (tpp) cc_final: 0.7804 (mmm) outliers start: 44 outliers final: 37 residues processed: 238 average time/residue: 0.2684 time to fit residues: 83.2822 Evaluate side-chains 244 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 270 CYS Chi-restraints excluded: chain R residue 309 PHE Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 367 ILE Chi-restraints excluded: chain T residue 17 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 16 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 91 optimal weight: 0.0870 chunk 60 optimal weight: 4.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.169850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141465 restraints weight = 12893.079| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.80 r_work: 0.3652 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8761 Z= 0.175 Angle : 0.570 10.592 11854 Z= 0.290 Chirality : 0.042 0.201 1329 Planarity : 0.003 0.051 1513 Dihedral : 4.085 18.651 1177 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.15 % Allowed : 30.46 % Favored : 65.39 % 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: 0.09 (0.27), residues: 1068 helix: 1.82 (0.26), residues: 421 sheet: -0.03 (0.39), residues: 202 loop : -1.69 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS A 352 PHE 0.017 0.001 PHE N 108 TYR 0.009 0.001 TYR A 329 ARG 0.009 0.000 ARG N 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.924 Fit side-chains REVERT: A 53 LYS cc_start: 0.7292 (mtpt) cc_final: 0.7011 (mtmm) REVERT: B 47 THR cc_start: 0.8597 (t) cc_final: 0.7828 (p) REVERT: B 59 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: B 126 LEU cc_start: 0.8312 (mm) cc_final: 0.8027 (mm) REVERT: B 214 ARG cc_start: 0.7368 (mtp85) cc_final: 0.7157 (mtp85) REVERT: B 228 ASP cc_start: 0.7128 (m-30) cc_final: 0.6886 (m-30) REVERT: B 321 THR cc_start: 0.6041 (t) cc_final: 0.4823 (p) REVERT: G 38 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6668 (mtt) REVERT: N 36 TRP cc_start: 0.8010 (m100) cc_final: 0.7371 (m100) REVERT: R 137 ASN cc_start: 0.7728 (m-40) cc_final: 0.7259 (m110) REVERT: R 174 LEU cc_start: 0.8039 (mm) cc_final: 0.7779 (mp) REVERT: R 360 MET cc_start: 0.8027 (tpp) cc_final: 0.7824 (mmm) outliers start: 39 outliers final: 37 residues processed: 238 average time/residue: 0.2655 time to fit residues: 81.6164 Evaluate side-chains 249 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 270 CYS Chi-restraints excluded: chain R residue 309 PHE Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 367 ILE Chi-restraints excluded: chain T residue 17 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 98 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 239 ASN R 83 ASN ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.165879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.137676 restraints weight = 12788.967| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.73 r_work: 0.3598 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8761 Z= 0.353 Angle : 0.673 11.740 11854 Z= 0.347 Chirality : 0.046 0.218 1329 Planarity : 0.004 0.051 1513 Dihedral : 4.585 20.413 1177 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.05 % Allowed : 30.35 % Favored : 65.60 % 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: -0.17 (0.26), residues: 1068 helix: 1.61 (0.26), residues: 421 sheet: -0.16 (0.38), residues: 205 loop : -1.86 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 319 HIS 0.006 0.001 HIS A 220 PHE 0.033 0.002 PHE N 108 TYR 0.016 0.002 TYR A 350 ARG 0.009 0.000 ARG N 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4315.98 seconds wall clock time: 77 minutes 22.74 seconds (4642.74 seconds total)