Starting phenix.real_space_refine on Tue Apr 29 08:44:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvi_38705/04_2025/8xvi_38705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvi_38705/04_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_38705/04_2025/8xvi_38705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvi_38705/04_2025/8xvi_38705.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvi_38705/04_2025/8xvi_38705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvi_38705/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 4.98, per 1000 atoms: 0.58 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: 2.01 Conformation dependent library (CDL) restraints added in 933.7 milliseconds 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: 0.95 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: 2.09 Time building geometry restraints manager: 2.40 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: 1.030 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.910 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.110 ------------------------------------------------------------------------------- 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 8767 Z= 0.164 Angle : 0.623 10.740 11866 Z= 0.329 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 Details of bonding type rmsd hydrogen bonds : bond 0.13380 ( 386) hydrogen bonds : angle 5.50626 ( 1125) SS BOND : bond 0.00276 ( 6) SS BOND : angle 1.29777 ( 12) covalent geometry : bond 0.00364 ( 8761) covalent geometry : angle 0.62144 (11854) *********************** 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 : 0.889 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: 0.2721 time to fit residues: 74.9409 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 : 1.040 ------------------------------------------------------------------------------- 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: 0.0000 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: 0.6386 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.167923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140126 restraints weight = 12767.728| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.73 r_work: 0.3636 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8767 Z= 0.139 Angle : 0.557 10.923 11866 Z= 0.294 Chirality : 0.042 0.177 1329 Planarity : 0.004 0.056 1513 Dihedral : 4.986 45.053 1185 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.05 % Allowed : 29.18 % 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: -0.13 (0.26), residues: 1068 helix: 1.61 (0.26), residues: 422 sheet: -0.17 (0.38), residues: 206 loop : -1.79 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.005 0.001 HIS A 352 PHE 0.020 0.001 PHE N 108 TYR 0.017 0.001 TYR A 253 ARG 0.007 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.05300 ( 386) hydrogen bonds : angle 4.51471 ( 1125) SS BOND : bond 0.00275 ( 6) SS BOND : angle 1.13783 ( 12) covalent geometry : bond 0.00302 ( 8761) covalent geometry : angle 0.55582 (11854) *********************** 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 249 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: B 228 ASP cc_start: 0.7388 (m-30) cc_final: 0.7114 (m-30) REVERT: N 36 TRP cc_start: 0.7975 (m100) cc_final: 0.7355 (m100) REVERT: N 60 TYR cc_start: 0.7795 (m-80) cc_final: 0.7390 (m-80) REVERT: R 79 PHE cc_start: 0.7459 (t80) cc_final: 0.7219 (t80) REVERT: R 83 ASN cc_start: 0.6269 (OUTLIER) cc_final: 0.6011 (m-40) REVERT: R 196 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6843 (tt) outliers start: 38 outliers final: 21 residues processed: 233 average time/residue: 0.2486 time to fit residues: 75.8316 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 : 0.971 ------------------------------------------------------------------------------- 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: 0.9990 chunk 75 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.166830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.138418 restraints weight = 12862.564| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.81 r_work: 0.3607 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8767 Z= 0.189 Angle : 0.585 8.524 11866 Z= 0.309 Chirality : 0.043 0.185 1329 Planarity : 0.004 0.047 1513 Dihedral : 4.590 21.466 1177 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.01 % Allowed : 27.48 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.26), residues: 1068 helix: 1.60 (0.26), residues: 420 sheet: -0.17 (0.39), residues: 199 loop : -1.91 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.005 0.001 HIS A 352 PHE 0.025 0.002 PHE N 108 TYR 0.014 0.002 TYR A 253 ARG 0.007 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.05916 ( 386) hydrogen bonds : angle 4.56672 ( 1125) SS BOND : bond 0.00319 ( 6) SS BOND : angle 1.23696 ( 12) covalent geometry : bond 0.00430 ( 8761) covalent geometry : angle 0.58385 (11854) *********************** 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 261 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 0.884 Fit side-chains REVERT: A 255 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7641 (ptm160) REVERT: A 333 ASP cc_start: 0.7112 (m-30) cc_final: 0.6812 (m-30) REVERT: B 246 ASP cc_start: 0.7416 (t70) cc_final: 0.7171 (t0) REVERT: N 36 TRP cc_start: 0.8130 (m100) cc_final: 0.7422 (m100) REVERT: R 91 PHE cc_start: 0.7787 (t80) cc_final: 0.7549 (t80) REVERT: R 111 MET cc_start: 0.5864 (tpt) cc_final: 0.5513 (tpt) REVERT: R 113 ASN cc_start: 0.6304 (p0) cc_final: 0.5980 (p0) REVERT: R 174 LEU cc_start: 0.8146 (mt) cc_final: 0.7841 (mp) REVERT: R 196 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6855 (tt) REVERT: T 7 MET cc_start: 0.7820 (pmm) cc_final: 0.7419 (pmm) outliers start: 47 outliers final: 33 residues processed: 243 average time/residue: 0.2443 time to fit residues: 77.7016 Evaluate side-chains 245 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU 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 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 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 318 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR 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: 0.8980 chunk 93 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 ASN R 323 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.168283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.140037 restraints weight = 12708.018| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.80 r_work: 0.3631 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8767 Z= 0.134 Angle : 0.547 8.522 11866 Z= 0.287 Chirality : 0.042 0.192 1329 Planarity : 0.004 0.049 1513 Dihedral : 4.364 20.538 1177 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 5.43 % Allowed : 27.80 % 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: -0.09 (0.26), residues: 1068 helix: 1.68 (0.26), residues: 421 sheet: -0.23 (0.38), residues: 206 loop : -1.76 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS A 352 PHE 0.019 0.001 PHE N 108 TYR 0.010 0.001 TYR A 253 ARG 0.003 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.04946 ( 386) hydrogen bonds : angle 4.36276 ( 1125) SS BOND : bond 0.00254 ( 6) SS BOND : angle 1.07082 ( 12) covalent geometry : bond 0.00295 ( 8761) covalent geometry : angle 0.54605 (11854) *********************** 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 258 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 0.961 Fit side-chains REVERT: A 255 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7669 (ptm160) REVERT: B 228 ASP cc_start: 0.7507 (m-30) cc_final: 0.7185 (m-30) REVERT: B 246 ASP cc_start: 0.7454 (t70) cc_final: 0.7099 (t70) REVERT: B 322 ASP cc_start: 0.7117 (m-30) cc_final: 0.6904 (m-30) REVERT: N 36 TRP cc_start: 0.8034 (m100) cc_final: 0.7352 (m100) REVERT: N 60 TYR cc_start: 0.7879 (m-80) cc_final: 0.7204 (m-80) REVERT: R 72 GLN cc_start: 0.7216 (pp30) cc_final: 0.6981 (pp30) REVERT: R 95 MET cc_start: 0.7083 (mmm) cc_final: 0.6871 (mmm) REVERT: R 111 MET cc_start: 0.5843 (tpt) cc_final: 0.5534 (tpt) REVERT: R 113 ASN cc_start: 0.6113 (p0) cc_final: 0.5690 (p0) REVERT: R 133 ASP cc_start: 0.5844 (OUTLIER) cc_final: 0.5418 (m-30) REVERT: R 196 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6842 (tt) REVERT: T 7 MET cc_start: 0.7837 (pmm) cc_final: 0.7518 (pmm) outliers start: 51 outliers final: 37 residues processed: 238 average time/residue: 0.2470 time to fit residues: 77.5925 Evaluate side-chains 247 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 357 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 75 GLN 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 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 321 THR 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 50 ASP 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 196 ILE Chi-restraints excluded: chain R residue 198 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 86 optimal weight: 0.0040 chunk 11 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 49 optimal weight: 0.0870 chunk 14 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 chunk 16 optimal weight: 8.9990 overall best weight: 0.3370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 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 = 0.170420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.142057 restraints weight = 12726.776| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.80 r_work: 0.3660 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8767 Z= 0.107 Angle : 0.529 8.509 11866 Z= 0.273 Chirality : 0.041 0.214 1329 Planarity : 0.003 0.050 1513 Dihedral : 4.148 19.263 1177 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.01 % Allowed : 27.90 % 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: 0.03 (0.27), residues: 1068 helix: 1.77 (0.26), residues: 421 sheet: -0.09 (0.39), residues: 202 loop : -1.71 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.006 0.001 HIS A 352 PHE 0.013 0.001 PHE N 108 TYR 0.009 0.001 TYR A 253 ARG 0.005 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 386) hydrogen bonds : angle 4.18721 ( 1125) SS BOND : bond 0.00216 ( 6) SS BOND : angle 0.93279 ( 12) covalent geometry : bond 0.00226 ( 8761) covalent geometry : angle 0.52835 (11854) *********************** 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 260 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 213 time to evaluate : 0.918 Fit side-chains REVERT: A 255 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7648 (ptm160) REVERT: A 377 ASN cc_start: 0.7724 (m-40) cc_final: 0.7486 (m-40) REVERT: B 47 THR cc_start: 0.8593 (t) cc_final: 0.7837 (p) REVERT: B 59 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7692 (m-80) REVERT: B 228 ASP cc_start: 0.7500 (m-30) cc_final: 0.7157 (m-30) REVERT: B 246 ASP cc_start: 0.7494 (t70) cc_final: 0.7229 (t0) REVERT: N 36 TRP cc_start: 0.7981 (m100) cc_final: 0.7306 (m100) REVERT: N 60 TYR cc_start: 0.7858 (m-80) cc_final: 0.7181 (m-80) REVERT: R 72 GLN cc_start: 0.7221 (pp30) cc_final: 0.6980 (pp30) REVERT: R 133 ASP cc_start: 0.5801 (OUTLIER) cc_final: 0.5565 (m-30) REVERT: R 137 ASN cc_start: 0.7757 (m-40) cc_final: 0.7275 (m110) REVERT: R 196 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6800 (tt) REVERT: R 309 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6698 (t80) outliers start: 47 outliers final: 32 residues processed: 240 average time/residue: 0.2667 time to fit residues: 83.6738 Evaluate side-chains 245 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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 75 GLN 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 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 321 THR 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 196 ILE Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 259 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** 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 = 0.4139 r_free = 0.4139 target = 0.169222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.140907 restraints weight = 12665.885| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.78 r_work: 0.3645 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8767 Z= 0.132 Angle : 0.552 8.731 11866 Z= 0.284 Chirality : 0.041 0.209 1329 Planarity : 0.003 0.051 1513 Dihedral : 4.188 19.560 1177 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.32 % Allowed : 27.90 % 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: 0.03 (0.26), residues: 1068 helix: 1.81 (0.26), residues: 419 sheet: -0.12 (0.39), residues: 204 loop : -1.73 (0.28), residues: 445 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 0.019 0.001 PHE N 108 TYR 0.010 0.001 TYR A 329 ARG 0.005 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 386) hydrogen bonds : angle 4.23780 ( 1125) SS BOND : bond 0.00247 ( 6) SS BOND : angle 1.01753 ( 12) covalent geometry : bond 0.00296 ( 8761) covalent geometry : angle 0.55149 (11854) *********************** 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 259 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 0.925 Fit side-chains REVERT: A 255 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7685 (ptm160) REVERT: B 47 THR cc_start: 0.8623 (t) cc_final: 0.7869 (p) REVERT: B 59 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7633 (m-80) REVERT: B 228 ASP cc_start: 0.7426 (m-30) cc_final: 0.7081 (m-30) REVERT: B 246 ASP cc_start: 0.7523 (t70) cc_final: 0.7014 (t70) REVERT: N 36 TRP cc_start: 0.8048 (m100) cc_final: 0.7343 (m100) REVERT: N 60 TYR cc_start: 0.7907 (m-80) cc_final: 0.7251 (m-80) REVERT: R 137 ASN cc_start: 0.7773 (m-40) cc_final: 0.7301 (m110) REVERT: R 196 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6731 (tt) outliers start: 50 outliers final: 40 residues processed: 240 average time/residue: 0.2521 time to fit residues: 80.4407 Evaluate side-chains 251 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 276 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN 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 321 THR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 49 optimal weight: 0.2980 chunk 44 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.168832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.140544 restraints weight = 12773.623| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.80 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: 0.6885 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8767 Z= 0.135 Angle : 0.568 8.886 11866 Z= 0.290 Chirality : 0.042 0.214 1329 Planarity : 0.003 0.051 1513 Dihedral : 4.191 19.398 1177 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 5.54 % Allowed : 28.54 % Favored : 65.92 % 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: 0.01 (0.27), residues: 1068 helix: 1.77 (0.26), residues: 421 sheet: -0.15 (0.39), residues: 204 loop : -1.72 (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 0.019 0.001 PHE N 108 TYR 0.010 0.001 TYR A 329 ARG 0.005 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 386) hydrogen bonds : angle 4.23891 ( 1125) SS BOND : bond 0.00289 ( 6) SS BOND : angle 1.01157 ( 12) covalent geometry : bond 0.00303 ( 8761) covalent geometry : angle 0.56749 (11854) *********************** 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 264 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 212 time to evaluate : 0.957 Fit side-chains REVERT: A 255 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7700 (ptm160) REVERT: B 47 THR cc_start: 0.8620 (t) cc_final: 0.7874 (p) REVERT: B 59 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: B 126 LEU cc_start: 0.8342 (mm) cc_final: 0.8063 (mm) REVERT: B 228 ASP cc_start: 0.7566 (m-30) cc_final: 0.7186 (m-30) REVERT: B 246 ASP cc_start: 0.7502 (t70) cc_final: 0.7001 (t70) REVERT: N 36 TRP cc_start: 0.8047 (m100) cc_final: 0.7352 (m100) REVERT: N 60 TYR cc_start: 0.7903 (m-80) cc_final: 0.7252 (m-80) REVERT: R 137 ASN cc_start: 0.7747 (m-40) cc_final: 0.7300 (m110) REVERT: R 196 ILE cc_start: 0.6943 (tt) cc_final: 0.6714 (tt) REVERT: T 18 ASP cc_start: 0.7991 (t0) cc_final: 0.7736 (t0) outliers start: 52 outliers final: 42 residues processed: 245 average time/residue: 0.2805 time to fit residues: 91.0114 Evaluate side-chains 253 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 383 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN 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 321 THR 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 176 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 33 optimal weight: 0.0670 chunk 63 optimal weight: 0.8980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** 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 = 0.169789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.141739 restraints weight = 12933.585| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.76 r_work: 0.3655 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8767 Z= 0.120 Angle : 0.561 9.324 11866 Z= 0.286 Chirality : 0.041 0.236 1329 Planarity : 0.003 0.051 1513 Dihedral : 4.131 19.033 1177 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.43 % Allowed : 28.54 % 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 (0.27), residues: 1068 helix: 1.78 (0.26), residues: 421 sheet: -0.06 (0.39), residues: 202 loop : -1.68 (0.28), residues: 445 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 0.015 0.001 PHE N 108 TYR 0.016 0.001 TYR A 253 ARG 0.008 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 386) hydrogen bonds : angle 4.18928 ( 1125) SS BOND : bond 0.00264 ( 6) SS BOND : angle 0.94945 ( 12) covalent geometry : bond 0.00265 ( 8761) covalent geometry : angle 0.56039 (11854) *********************** 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 257 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 206 time to evaluate : 0.837 Fit side-chains REVERT: A 255 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7674 (ptm160) REVERT: B 47 THR cc_start: 0.8620 (t) cc_final: 0.7849 (p) REVERT: B 59 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: B 126 LEU cc_start: 0.8340 (mm) cc_final: 0.8074 (mm) REVERT: B 228 ASP cc_start: 0.7498 (m-30) cc_final: 0.7058 (m-30) REVERT: B 246 ASP cc_start: 0.7480 (t70) cc_final: 0.7000 (t70) REVERT: N 36 TRP cc_start: 0.7995 (m100) cc_final: 0.7329 (m100) REVERT: R 137 ASN cc_start: 0.7732 (m-40) cc_final: 0.7254 (m110) REVERT: R 196 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6711 (tt) outliers start: 51 outliers final: 42 residues processed: 233 average time/residue: 0.2525 time to fit residues: 77.2263 Evaluate side-chains 249 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 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 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 383 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN 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 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 33 LYS 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 175 ASN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.0050 chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** 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 = 0.4149 r_free = 0.4149 target = 0.170269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142107 restraints weight = 12816.477| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.75 r_work: 0.3658 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8767 Z= 0.121 Angle : 0.572 9.606 11866 Z= 0.289 Chirality : 0.042 0.227 1329 Planarity : 0.003 0.051 1513 Dihedral : 4.106 18.928 1177 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.43 % Allowed : 28.22 % Favored : 66.35 % 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 (0.26), residues: 1068 helix: 1.75 (0.26), residues: 421 sheet: -0.03 (0.39), residues: 202 loop : -1.67 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 352 PHE 0.016 0.001 PHE N 108 TYR 0.015 0.001 TYR A 253 ARG 0.008 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 386) hydrogen bonds : angle 4.20717 ( 1125) SS BOND : bond 0.00281 ( 6) SS BOND : angle 0.96557 ( 12) covalent geometry : bond 0.00270 ( 8761) covalent geometry : angle 0.57182 (11854) *********************** 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 256 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 0.936 Fit side-chains REVERT: A 53 LYS cc_start: 0.7326 (mtpt) cc_final: 0.7059 (mtmm) REVERT: A 255 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7670 (ptm160) REVERT: B 47 THR cc_start: 0.8612 (t) cc_final: 0.7834 (p) REVERT: B 59 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: B 126 LEU cc_start: 0.8336 (mm) cc_final: 0.8072 (mm) REVERT: B 228 ASP cc_start: 0.7397 (m-30) cc_final: 0.6969 (m-30) REVERT: B 246 ASP cc_start: 0.7487 (t70) cc_final: 0.7005 (t70) REVERT: N 36 TRP cc_start: 0.7990 (m100) cc_final: 0.7327 (m100) REVERT: R 98 ASN cc_start: 0.7332 (m-40) cc_final: 0.6939 (t0) REVERT: R 137 ASN cc_start: 0.7723 (m-40) cc_final: 0.7268 (m110) REVERT: R 196 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6723 (tt) outliers start: 51 outliers final: 45 residues processed: 236 average time/residue: 0.2413 time to fit residues: 74.6639 Evaluate side-chains 252 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 204 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 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 286 LEU 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 75 GLN 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 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 33 LYS 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 172 THR Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 196 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 16 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** 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 = 0.4148 r_free = 0.4148 target = 0.170085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142050 restraints weight = 12849.371| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.74 r_work: 0.3663 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8767 Z= 0.121 Angle : 0.578 10.875 11866 Z= 0.291 Chirality : 0.041 0.217 1329 Planarity : 0.003 0.051 1513 Dihedral : 4.089 18.909 1177 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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: 1.75 (0.26), residues: 421 sheet: -0.05 (0.39), residues: 202 loop : -1.65 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 352 PHE 0.016 0.001 PHE N 108 TYR 0.014 0.001 TYR A 253 ARG 0.009 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 386) hydrogen bonds : angle 4.20067 ( 1125) SS BOND : bond 0.00269 ( 6) SS BOND : angle 0.95779 ( 12) covalent geometry : bond 0.00271 ( 8761) covalent geometry : angle 0.57770 (11854) ********************** 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 255 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.911 Fit side-chains REVERT: A 53 LYS cc_start: 0.7321 (mtpt) cc_final: 0.7052 (mtmm) REVERT: A 255 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7698 (ptm160) REVERT: B 47 THR cc_start: 0.8613 (t) cc_final: 0.7830 (p) REVERT: B 59 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7489 (m-80) REVERT: B 126 LEU cc_start: 0.8326 (mm) cc_final: 0.8060 (mm) REVERT: B 228 ASP cc_start: 0.7389 (m-30) cc_final: 0.6958 (m-30) REVERT: B 246 ASP cc_start: 0.7484 (t70) cc_final: 0.7004 (t70) REVERT: N 36 TRP cc_start: 0.8015 (m100) cc_final: 0.7373 (m100) REVERT: R 111 MET cc_start: 0.5535 (tpt) cc_final: 0.5229 (tpt) REVERT: R 137 ASN cc_start: 0.7717 (m-40) cc_final: 0.7256 (m110) REVERT: R 196 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6725 (tt) outliers start: 48 outliers final: 44 residues processed: 236 average time/residue: 0.2478 time to fit residues: 76.0248 Evaluate side-chains 255 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 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 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 75 GLN 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 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 33 LYS 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 175 ASN Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 196 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 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: 2.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.165345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.137354 restraints weight = 12841.933| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.72 r_work: 0.3596 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 8767 Z= 0.257 Angle : 0.695 11.956 11866 Z= 0.357 Chirality : 0.046 0.220 1329 Planarity : 0.004 0.052 1513 Dihedral : 4.701 20.792 1177 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.47 % Allowed : 28.86 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1068 helix: 1.48 (0.26), residues: 419 sheet: -0.15 (0.39), residues: 202 loop : -1.82 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 319 HIS 0.007 0.002 HIS A 220 PHE 0.035 0.002 PHE N 108 TYR 0.018 0.002 TYR N 60 ARG 0.009 0.001 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.06464 ( 386) hydrogen bonds : angle 4.62370 ( 1125) SS BOND : bond 0.00409 ( 6) SS BOND : angle 1.32402 ( 12) covalent geometry : bond 0.00596 ( 8761) covalent geometry : angle 0.69413 (11854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4994.04 seconds wall clock time: 87 minutes 38.96 seconds (5258.96 seconds total)