Starting phenix.real_space_refine on Thu May 1 00:58:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgr_38330/05_2025/8xgr_38330.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgr_38330/05_2025/8xgr_38330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xgr_38330/05_2025/8xgr_38330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgr_38330/05_2025/8xgr_38330.map" model { file = "/net/cci-nas-00/data/ceres_data/8xgr_38330/05_2025/8xgr_38330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgr_38330/05_2025/8xgr_38330.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 1.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2378 atoms to isotropic. 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 5225 2.51 5 N 1394 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 8206 Number of models: 1 Model: "" Number of chains: 5 Chain: "G" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2062 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 251} Chain breaks: 3 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2415 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 171 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Time building chain proxies: 5.16, per 1000 atoms: 0.63 Number of scatterers: 8206 At special positions: 0 Unit cell: (95.865, 100.707, 137.503, 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 1520 8.00 N 1394 7.00 C 5225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.03 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " distance=2.03 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 15 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 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: 2.43 Conformation dependent library (CDL) restraints added in 1.0 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 15 sheets defined 41.3% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'G' and resid 12 through 22 removed outlier: 3.594A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 6.131A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 88 through 112 removed outlier: 3.918A pdb=" N ARG G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 132 removed outlier: 3.701A pdb=" N ILE G 129 " --> pdb=" O GLY G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 296 Processing helix chain 'G' and resid 323 through 335 Processing helix chain 'G' and resid 350 through 359 Processing helix chain 'G' and resid 362 through 366 removed outlier: 3.678A pdb=" N ASP G 365 " --> pdb=" O PRO G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 372 removed outlier: 4.106A pdb=" N ALA G 371 " --> pdb=" O PRO G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 390 removed outlier: 3.591A pdb=" N GLN G 386 " --> pdb=" O TYR G 382 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE G 387 " --> pdb=" O ILE G 383 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU G 390 " --> pdb=" O GLN G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 410 through 432 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.017A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 129 removed outlier: 3.700A pdb=" N VAL R 106 " --> pdb=" O TYR R 102 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU R 122 " --> pdb=" O GLY R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 133 Processing helix chain 'R' and resid 134 through 153 removed outlier: 3.867A pdb=" N LEU R 139 " --> pdb=" O GLY R 135 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU R 149 " --> pdb=" O LEU R 145 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS R 150 " --> pdb=" O GLY R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 164 removed outlier: 3.530A pdb=" N LYS R 161 " --> pdb=" O ILE R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 175 Processing helix chain 'R' and resid 176 through 205 removed outlier: 3.732A pdb=" N LYS R 182 " --> pdb=" O PRO R 178 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL R 203 " --> pdb=" O ARG R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 210 removed outlier: 3.950A pdb=" N LYS R 210 " --> pdb=" O TRP R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 233 removed outlier: 3.784A pdb=" N VAL R 223 " --> pdb=" O ALA R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 239 removed outlier: 3.922A pdb=" N ALA R 237 " --> pdb=" O ALA R 233 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 271 removed outlier: 3.622A pdb=" N THR R 271 " --> pdb=" O GLN R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 281 removed outlier: 4.178A pdb=" N PHE R 278 " --> pdb=" O ASP R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 301 removed outlier: 3.573A pdb=" N ALA R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 350 removed outlier: 3.939A pdb=" N GLU R 320 " --> pdb=" O LYS R 316 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA R 322 " --> pdb=" O ARG R 318 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS R 323 " --> pdb=" O ARG R 319 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL R 325 " --> pdb=" O VAL R 321 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU R 328 " --> pdb=" O THR R 324 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU R 330 " --> pdb=" O PHE R 326 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS R 335 " --> pdb=" O VAL R 331 " (cutoff:3.500A) Proline residue: R 338 - end of helix Processing helix chain 'R' and resid 357 through 380 removed outlier: 3.548A pdb=" N VAL R 366 " --> pdb=" O SER R 362 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE R 372 " --> pdb=" O ASP R 368 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN R 373 " --> pdb=" O TYR R 369 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER R 379 " --> pdb=" O ALA R 375 " (cutoff:3.500A) Processing helix chain 'R' and resid 381 through 388 Processing helix chain 'R' and resid 390 through 402 Processing helix chain 'L' and resid 8 through 18 removed outlier: 3.690A pdb=" N VAL L 12 " --> pdb=" O ASP L 8 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 265 through 266 removed outlier: 3.613A pdb=" N ASP G 280 " --> pdb=" O ILE G 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 265 through 266 removed outlier: 3.613A pdb=" N ASP G 280 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL G 114 " --> pdb=" O ARG G 277 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N PHE G 279 " --> pdb=" O VAL G 114 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU G 116 " --> pdb=" O PHE G 279 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N ALA G 300 " --> pdb=" O THR G 113 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LYS G 115 " --> pdb=" O ALA G 300 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ILE G 302 " --> pdb=" O LYS G 115 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU G 117 " --> pdb=" O ILE G 302 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.506A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.715A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.734A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 4.125A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 152 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.690A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 233 through 234 removed outlier: 3.574A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 277 removed outlier: 4.031A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.537A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'N' and resid 36 through 39 removed outlier: 6.348A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 240 through 242 Processing sheet with id=AB6, first strand: chain 'R' and resid 245 through 247 357 hydrogen bonds defined for protein. 984 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: 2.34 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2343 1.33 - 1.45: 1460 1.45 - 1.58: 4472 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 8367 Sorted by residual: bond pdb=" N GLU B 260 " pdb=" CA GLU B 260 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.24e-02 6.50e+03 7.90e+00 bond pdb=" N MET B 262 " pdb=" CA MET B 262 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.27e+00 bond pdb=" N LYS B 301 " pdb=" CA LYS B 301 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.42e-02 4.96e+03 6.51e+00 bond pdb=" N LEU B 261 " pdb=" CA LEU B 261 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.32e+00 bond pdb=" N GLN R 181 " pdb=" CA GLN R 181 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.69e+00 ... (remaining 8362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 10826 1.20 - 2.40: 394 2.40 - 3.60: 87 3.60 - 4.80: 18 4.80 - 6.00: 2 Bond angle restraints: 11327 Sorted by residual: angle pdb=" CA GLN R 181 " pdb=" C GLN R 181 " pdb=" O GLN R 181 " ideal model delta sigma weight residual 120.55 116.43 4.12 1.06e+00 8.90e-01 1.51e+01 angle pdb=" CA MET G 38 " pdb=" C MET G 38 " pdb=" O MET G 38 " ideal model delta sigma weight residual 120.55 116.49 4.06 1.06e+00 8.90e-01 1.47e+01 angle pdb=" CA ASP N 106 " pdb=" C ASP N 106 " pdb=" O ASP N 106 " ideal model delta sigma weight residual 121.66 117.52 4.14 1.17e+00 7.31e-01 1.25e+01 angle pdb=" CA MET B 262 " pdb=" C MET B 262 " pdb=" O MET B 262 " ideal model delta sigma weight residual 121.45 117.72 3.73 1.07e+00 8.73e-01 1.22e+01 angle pdb=" N THR R 294 " pdb=" CA THR R 294 " pdb=" C THR R 294 " ideal model delta sigma weight residual 111.36 107.80 3.56 1.09e+00 8.42e-01 1.07e+01 ... (remaining 11322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 4544 17.36 - 34.71: 388 34.71 - 52.07: 63 52.07 - 69.42: 18 69.42 - 86.78: 10 Dihedral angle restraints: 5023 sinusoidal: 1974 harmonic: 3049 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 160.83 -67.83 1 1.00e+01 1.00e-02 5.98e+01 dihedral pdb=" CB CYS L 3 " pdb=" SG CYS L 3 " pdb=" SG CYS L 11 " pdb=" CB CYS L 11 " ideal model delta sinusoidal sigma weight residual -86.00 -140.45 54.45 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CA SER G 31 " pdb=" C SER G 31 " pdb=" N LYS G 32 " pdb=" CA LYS G 32 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 5020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 833 0.030 - 0.061: 306 0.061 - 0.091: 86 0.091 - 0.122: 53 0.122 - 0.152: 15 Chirality restraints: 1293 Sorted by residual: chirality pdb=" CA ARG N 98 " pdb=" N ARG N 98 " pdb=" C ARG N 98 " pdb=" CB ARG N 98 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA ILE G 399 " pdb=" N ILE G 399 " pdb=" C ILE G 399 " pdb=" CB ILE G 399 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA LEU B 261 " pdb=" N LEU B 261 " pdb=" C LEU B 261 " pdb=" CB LEU B 261 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1290 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 337 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO R 338 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 338 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 338 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 98 " -0.192 9.50e-02 1.11e+02 8.59e-02 4.56e+00 pdb=" NE ARG N 98 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG N 98 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG N 98 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG N 98 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO B 236 " 0.074 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 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 183 2.68 - 3.24: 8478 3.24 - 3.79: 12195 3.79 - 4.35: 17377 4.35 - 4.90: 28156 Nonbonded interactions: 66389 Sorted by model distance: nonbonded pdb=" O ASP B 66 " pdb=" OG SER B 67 " model vdw 2.126 3.040 nonbonded pdb=" NZ LYS R 161 " pdb=" O ASP L 18 " model vdw 2.209 3.120 nonbonded pdb=" ND1 HIS B 311 " pdb=" OG SER B 331 " model vdw 2.223 3.120 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.276 3.040 nonbonded pdb=" O MET G 323 " pdb=" OG SER G 326 " model vdw 2.299 3.040 ... (remaining 66384 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.870 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 : 0.003 0.039 8374 Z= 0.169 Angle : 0.563 5.995 11341 Z= 0.333 Chirality : 0.040 0.152 1293 Planarity : 0.004 0.086 1431 Dihedral : 13.833 86.778 3028 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.22 % Allowed : 0.33 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.26), residues: 1031 helix: -0.52 (0.27), residues: 371 sheet: -2.41 (0.34), residues: 200 loop : -1.57 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 291 HIS 0.007 0.001 HIS B 142 PHE 0.013 0.001 PHE B 234 TYR 0.007 0.001 TYR R 387 ARG 0.004 0.000 ARG G 288 Details of bonding type rmsd hydrogen bonds : bond 0.27449 ( 356) hydrogen bonds : angle 9.77220 ( 984) SS BOND : bond 0.00354 ( 7) SS BOND : angle 1.15110 ( 14) covalent geometry : bond 0.00309 ( 8367) covalent geometry : angle 0.56201 (11327) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 311 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 265 PHE cc_start: 0.5559 (t80) cc_final: 0.5220 (t80) outliers start: 2 outliers final: 0 residues processed: 312 average time/residue: 0.2280 time to fit residues: 93.4382 Evaluate side-chains 186 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN N 3 GLN ** R 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.115033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.088115 restraints weight = 18111.567| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 4.13 r_work: 0.3343 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8374 Z= 0.199 Angle : 0.730 8.009 11341 Z= 0.376 Chirality : 0.045 0.197 1293 Planarity : 0.005 0.056 1431 Dihedral : 4.769 23.026 1128 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.23 % Allowed : 14.14 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.26), residues: 1031 helix: 0.30 (0.26), residues: 384 sheet: -2.22 (0.35), residues: 203 loop : -1.43 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 339 HIS 0.009 0.002 HIS G 402 PHE 0.028 0.002 PHE G 271 TYR 0.018 0.002 TYR B 145 ARG 0.007 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.05277 ( 356) hydrogen bonds : angle 5.47832 ( 984) SS BOND : bond 0.00457 ( 7) SS BOND : angle 1.71567 ( 14) covalent geometry : bond 0.00456 ( 8367) covalent geometry : angle 0.72793 (11327) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: G 271 PHE cc_start: 0.8674 (t80) cc_final: 0.8131 (t80) REVERT: G 345 ILE cc_start: 0.9259 (mt) cc_final: 0.9048 (tt) REVERT: G 388 LEU cc_start: 0.9131 (mt) cc_final: 0.8459 (pp) REVERT: G 402 HIS cc_start: 0.4869 (t-170) cc_final: 0.4664 (t-170) REVERT: B 19 ARG cc_start: 0.9430 (ttp80) cc_final: 0.9014 (tmm-80) REVERT: B 20 ASP cc_start: 0.9411 (m-30) cc_final: 0.9144 (m-30) REVERT: B 23 LYS cc_start: 0.8463 (ptpp) cc_final: 0.8117 (ptpp) REVERT: B 172 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8921 (mm-30) REVERT: B 301 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8813 (mmmm) REVERT: B 335 PHE cc_start: 0.8606 (m-80) cc_final: 0.8262 (m-80) REVERT: B 337 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8001 (mtpt) REVERT: N 38 ARG cc_start: 0.8450 (ptm-80) cc_final: 0.8128 (ptm-80) REVERT: N 58 ILE cc_start: 0.8763 (pt) cc_final: 0.8528 (mp) REVERT: N 82 GLN cc_start: 0.8312 (tp40) cc_final: 0.7846 (tp40) REVERT: N 83 MET cc_start: 0.8455 (mtp) cc_final: 0.7898 (ptp) REVERT: N 95 TYR cc_start: 0.8712 (m-80) cc_final: 0.8324 (m-80) REVERT: R 281 TYR cc_start: 0.8927 (m-80) cc_final: 0.8310 (m-80) REVERT: R 392 ARG cc_start: 0.7658 (ttp-170) cc_final: 0.6977 (ttp-170) REVERT: L 10 GLU cc_start: 0.8983 (mp0) cc_final: 0.8736 (mp0) outliers start: 29 outliers final: 17 residues processed: 225 average time/residue: 0.2216 time to fit residues: 66.0566 Evaluate side-chains 197 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 5.9990 chunk 82 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 328 ASN G 402 HIS B 75 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.115575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.089057 restraints weight = 18382.195| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 4.20 r_work: 0.3385 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8374 Z= 0.147 Angle : 0.653 8.360 11341 Z= 0.333 Chirality : 0.043 0.187 1293 Planarity : 0.005 0.054 1431 Dihedral : 4.592 18.606 1128 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.12 % Allowed : 16.93 % Favored : 79.96 % 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: -1.02 (0.26), residues: 1031 helix: 0.74 (0.26), residues: 391 sheet: -2.08 (0.36), residues: 193 loop : -1.23 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.004 0.001 HIS B 225 PHE 0.017 0.001 PHE R 265 TYR 0.018 0.002 TYR B 145 ARG 0.007 0.001 ARG G 277 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 356) hydrogen bonds : angle 5.03002 ( 984) SS BOND : bond 0.00279 ( 7) SS BOND : angle 1.08229 ( 14) covalent geometry : bond 0.00336 ( 8367) covalent geometry : angle 0.65225 (11327) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 ARG cc_start: 0.9225 (mtp85) cc_final: 0.8999 (ttm110) REVERT: G 271 PHE cc_start: 0.8710 (t80) cc_final: 0.8001 (t80) REVERT: G 273 ASP cc_start: 0.8118 (t0) cc_final: 0.7747 (t0) REVERT: G 323 MET cc_start: 0.7804 (pmm) cc_final: 0.7285 (pmm) REVERT: G 345 ILE cc_start: 0.9188 (mt) cc_final: 0.8917 (tt) REVERT: B 18 ILE cc_start: 0.9491 (mm) cc_final: 0.9239 (mm) REVERT: B 19 ARG cc_start: 0.9477 (ttp80) cc_final: 0.9050 (tmm-80) REVERT: B 20 ASP cc_start: 0.9440 (m-30) cc_final: 0.9106 (m-30) REVERT: B 23 LYS cc_start: 0.8540 (ptpp) cc_final: 0.8197 (ptpp) REVERT: B 172 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8898 (mm-30) REVERT: B 301 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8757 (mmmm) REVERT: B 335 PHE cc_start: 0.8625 (m-80) cc_final: 0.8317 (m-80) REVERT: B 336 LEU cc_start: 0.9264 (mt) cc_final: 0.8881 (mt) REVERT: N 20 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8985 (pt) REVERT: N 38 ARG cc_start: 0.8380 (ptm-80) cc_final: 0.8122 (ptm-80) REVERT: N 82 GLN cc_start: 0.8469 (tp40) cc_final: 0.7930 (tp40) REVERT: N 83 MET cc_start: 0.8481 (mtp) cc_final: 0.7922 (ptp) REVERT: N 95 TYR cc_start: 0.8719 (m-80) cc_final: 0.8313 (m-80) REVERT: R 267 GLN cc_start: 0.9089 (mm110) cc_final: 0.8602 (mm110) REVERT: R 281 TYR cc_start: 0.8836 (m-80) cc_final: 0.8155 (m-80) REVERT: R 299 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7778 (tt0) outliers start: 28 outliers final: 18 residues processed: 225 average time/residue: 0.2122 time to fit residues: 63.7784 Evaluate side-chains 195 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN G 24 ASN G 328 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 ASN ** R 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.111153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.084076 restraints weight = 18623.830| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 4.17 r_work: 0.3264 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8374 Z= 0.220 Angle : 0.693 8.410 11341 Z= 0.356 Chirality : 0.044 0.218 1293 Planarity : 0.005 0.058 1431 Dihedral : 4.661 19.893 1128 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.12 % Allowed : 17.59 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.26), residues: 1031 helix: 0.69 (0.26), residues: 391 sheet: -2.05 (0.36), residues: 195 loop : -1.15 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.010 0.002 HIS G 402 PHE 0.013 0.002 PHE R 282 TYR 0.022 0.002 TYR B 145 ARG 0.007 0.001 ARG G 277 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 356) hydrogen bonds : angle 5.06400 ( 984) SS BOND : bond 0.00424 ( 7) SS BOND : angle 1.75175 ( 14) covalent geometry : bond 0.00499 ( 8367) covalent geometry : angle 0.69064 (11327) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 273 ASP cc_start: 0.8318 (t0) cc_final: 0.7961 (t0) REVERT: G 323 MET cc_start: 0.7559 (pmm) cc_final: 0.7257 (pmm) REVERT: B 19 ARG cc_start: 0.9474 (ttp80) cc_final: 0.9098 (ttp80) REVERT: B 20 ASP cc_start: 0.9447 (m-30) cc_final: 0.9094 (m-30) REVERT: B 172 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8973 (mm-30) REVERT: B 301 LYS cc_start: 0.9128 (mmmm) cc_final: 0.8834 (mmmm) REVERT: B 335 PHE cc_start: 0.8715 (m-80) cc_final: 0.8479 (m-80) REVERT: N 71 SER cc_start: 0.8079 (t) cc_final: 0.7862 (p) REVERT: N 83 MET cc_start: 0.8530 (mtp) cc_final: 0.7949 (ptp) REVERT: N 95 TYR cc_start: 0.8787 (m-80) cc_final: 0.8551 (m-80) REVERT: N 123 GLN cc_start: 0.8988 (tp-100) cc_final: 0.8729 (tp-100) REVERT: R 245 MET cc_start: 0.7600 (tmm) cc_final: 0.7367 (tmm) REVERT: R 267 GLN cc_start: 0.9093 (mm110) cc_final: 0.8168 (mm110) REVERT: R 281 TYR cc_start: 0.8924 (m-80) cc_final: 0.8229 (m-80) REVERT: R 299 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7643 (tt0) REVERT: L 10 GLU cc_start: 0.9054 (mp0) cc_final: 0.8693 (mp0) outliers start: 46 outliers final: 30 residues processed: 215 average time/residue: 0.2046 time to fit residues: 59.5495 Evaluate side-chains 192 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 399 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 75 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN R 181 GLN ** R 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.115298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.088718 restraints weight = 17851.209| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 4.12 r_work: 0.3321 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8374 Z= 0.131 Angle : 0.640 9.187 11341 Z= 0.325 Chirality : 0.043 0.246 1293 Planarity : 0.005 0.055 1431 Dihedral : 4.529 19.239 1128 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.34 % Allowed : 19.38 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.26), residues: 1031 helix: 0.84 (0.26), residues: 390 sheet: -1.89 (0.36), residues: 193 loop : -1.18 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.008 0.001 HIS G 402 PHE 0.009 0.001 PHE B 241 TYR 0.019 0.001 TYR B 145 ARG 0.007 0.001 ARG G 277 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 356) hydrogen bonds : angle 4.84758 ( 984) SS BOND : bond 0.00358 ( 7) SS BOND : angle 0.99408 ( 14) covalent geometry : bond 0.00300 ( 8367) covalent geometry : angle 0.63946 (11327) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 273 ASP cc_start: 0.8631 (t0) cc_final: 0.7805 (t0) REVERT: G 345 ILE cc_start: 0.9023 (mp) cc_final: 0.8662 (tt) REVERT: B 19 ARG cc_start: 0.9475 (ttp80) cc_final: 0.9047 (tmm-80) REVERT: B 20 ASP cc_start: 0.9424 (m-30) cc_final: 0.9124 (m-30) REVERT: B 172 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8980 (mm-30) REVERT: B 301 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8758 (mmmm) REVERT: B 335 PHE cc_start: 0.8588 (m-80) cc_final: 0.8388 (m-80) REVERT: B 336 LEU cc_start: 0.9164 (mt) cc_final: 0.8885 (mt) REVERT: N 71 SER cc_start: 0.8022 (t) cc_final: 0.7795 (p) REVERT: N 82 GLN cc_start: 0.8614 (tp40) cc_final: 0.8387 (tp40) REVERT: N 83 MET cc_start: 0.8446 (mtp) cc_final: 0.7987 (ptp) REVERT: R 267 GLN cc_start: 0.8914 (mm110) cc_final: 0.7949 (tp40) REVERT: R 281 TYR cc_start: 0.8885 (m-80) cc_final: 0.8087 (m-80) REVERT: R 299 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7608 (tt0) REVERT: L 10 GLU cc_start: 0.9092 (mp0) cc_final: 0.8673 (mp0) outliers start: 39 outliers final: 30 residues processed: 213 average time/residue: 0.2103 time to fit residues: 60.1522 Evaluate side-chains 198 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain G residue 434 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 98 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 261 GLN ** 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 = 0.3928 r_free = 0.3928 target = 0.112786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.086347 restraints weight = 18187.296| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 4.08 r_work: 0.3339 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8374 Z= 0.195 Angle : 0.689 8.578 11341 Z= 0.352 Chirality : 0.044 0.208 1293 Planarity : 0.005 0.055 1431 Dihedral : 4.638 22.347 1128 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.90 % Allowed : 19.49 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.26), residues: 1031 helix: 0.71 (0.26), residues: 391 sheet: -1.90 (0.35), residues: 205 loop : -1.12 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.009 0.002 HIS G 402 PHE 0.012 0.002 PHE G 271 TYR 0.025 0.002 TYR B 145 ARG 0.006 0.001 ARG G 95 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 356) hydrogen bonds : angle 4.92618 ( 984) SS BOND : bond 0.00401 ( 7) SS BOND : angle 1.15164 ( 14) covalent geometry : bond 0.00449 ( 8367) covalent geometry : angle 0.68805 (11327) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 323 MET cc_start: 0.7729 (pmm) cc_final: 0.7503 (pmm) REVERT: B 19 ARG cc_start: 0.9506 (ttp80) cc_final: 0.9143 (tmm-80) REVERT: B 20 ASP cc_start: 0.9448 (m-30) cc_final: 0.9123 (m-30) REVERT: B 172 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8945 (mm-30) REVERT: B 301 LYS cc_start: 0.9092 (mmmm) cc_final: 0.8854 (mmmm) REVERT: B 335 PHE cc_start: 0.8684 (m-80) cc_final: 0.8478 (m-80) REVERT: N 82 GLN cc_start: 0.8769 (tp40) cc_final: 0.8528 (tp40) REVERT: N 83 MET cc_start: 0.8465 (mtp) cc_final: 0.8016 (ptp) REVERT: R 265 PHE cc_start: 0.6194 (t80) cc_final: 0.5934 (t80) REVERT: R 281 TYR cc_start: 0.8830 (m-80) cc_final: 0.8113 (m-80) REVERT: R 318 ARG cc_start: 0.9104 (ptp-170) cc_final: 0.8774 (mpp80) REVERT: L 10 GLU cc_start: 0.9098 (mp0) cc_final: 0.8699 (mp0) outliers start: 44 outliers final: 33 residues processed: 202 average time/residue: 0.2054 time to fit residues: 56.7365 Evaluate side-chains 193 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 51 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.115522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.088956 restraints weight = 18137.325| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 4.17 r_work: 0.3395 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8374 Z= 0.128 Angle : 0.656 9.108 11341 Z= 0.333 Chirality : 0.043 0.279 1293 Planarity : 0.004 0.053 1431 Dihedral : 4.502 22.853 1128 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.12 % Allowed : 21.16 % Favored : 74.72 % 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: -0.86 (0.26), residues: 1031 helix: 0.78 (0.26), residues: 391 sheet: -1.76 (0.36), residues: 199 loop : -1.13 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.008 0.001 HIS G 402 PHE 0.018 0.001 PHE G 271 TYR 0.023 0.001 TYR B 145 ARG 0.006 0.000 ARG G 277 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 356) hydrogen bonds : angle 4.76100 ( 984) SS BOND : bond 0.00256 ( 7) SS BOND : angle 0.89390 ( 14) covalent geometry : bond 0.00292 ( 8367) covalent geometry : angle 0.65530 (11327) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 273 ASP cc_start: 0.8488 (t0) cc_final: 0.8276 (t0) REVERT: G 323 MET cc_start: 0.7839 (pmm) cc_final: 0.7518 (pmm) REVERT: G 335 ASN cc_start: 0.8519 (m110) cc_final: 0.8173 (m-40) REVERT: G 343 SER cc_start: 0.9326 (m) cc_final: 0.8980 (t) REVERT: G 381 ASN cc_start: 0.9577 (m110) cc_final: 0.9355 (m110) REVERT: B 19 ARG cc_start: 0.9497 (ttp80) cc_final: 0.9138 (ttp80) REVERT: B 20 ASP cc_start: 0.9452 (m-30) cc_final: 0.9109 (m-30) REVERT: B 172 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8955 (mm-30) REVERT: B 301 LYS cc_start: 0.9035 (mmmm) cc_final: 0.8618 (mmmt) REVERT: B 336 LEU cc_start: 0.9196 (mt) cc_final: 0.8909 (mt) REVERT: N 19 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8570 (ptm-80) REVERT: N 82 GLN cc_start: 0.8759 (tp40) cc_final: 0.8385 (tp40) REVERT: N 83 MET cc_start: 0.8421 (mtp) cc_final: 0.8008 (ptp) REVERT: R 130 LYS cc_start: 0.9149 (tptt) cc_final: 0.8574 (tptp) REVERT: R 253 ARG cc_start: 0.8037 (mtm110) cc_final: 0.7519 (ptt90) REVERT: R 265 PHE cc_start: 0.6173 (t80) cc_final: 0.5867 (t80) REVERT: R 281 TYR cc_start: 0.8782 (m-80) cc_final: 0.8070 (m-80) REVERT: R 318 ARG cc_start: 0.9073 (ptp-170) cc_final: 0.8396 (mtm-85) outliers start: 37 outliers final: 27 residues processed: 203 average time/residue: 0.1950 time to fit residues: 54.1239 Evaluate side-chains 192 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 267 GLN Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN ** R 378 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 = 0.3981 r_free = 0.3981 target = 0.116339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.089865 restraints weight = 18190.670| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 4.16 r_work: 0.3396 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8374 Z= 0.127 Angle : 0.674 10.080 11341 Z= 0.339 Chirality : 0.044 0.323 1293 Planarity : 0.004 0.053 1431 Dihedral : 4.442 23.215 1128 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.56 % Allowed : 22.16 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.26), residues: 1031 helix: 0.89 (0.26), residues: 386 sheet: -1.71 (0.36), residues: 201 loop : -1.20 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.010 0.001 HIS G 402 PHE 0.009 0.001 PHE B 241 TYR 0.021 0.001 TYR B 145 ARG 0.006 0.000 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 356) hydrogen bonds : angle 4.72573 ( 984) SS BOND : bond 0.00397 ( 7) SS BOND : angle 1.12063 ( 14) covalent geometry : bond 0.00293 ( 8367) covalent geometry : angle 0.67309 (11327) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 323 MET cc_start: 0.7908 (pmm) cc_final: 0.7648 (pmm) REVERT: G 343 SER cc_start: 0.9255 (m) cc_final: 0.8934 (t) REVERT: B 19 ARG cc_start: 0.9493 (ttp80) cc_final: 0.9155 (ttp80) REVERT: B 20 ASP cc_start: 0.9447 (m-30) cc_final: 0.9196 (m-30) REVERT: B 57 LYS cc_start: 0.9123 (ptpp) cc_final: 0.8892 (ptpp) REVERT: B 172 GLU cc_start: 0.9356 (mm-30) cc_final: 0.8990 (mm-30) REVERT: B 301 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8668 (mmmt) REVERT: B 336 LEU cc_start: 0.9164 (mt) cc_final: 0.8810 (mt) REVERT: N 19 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8529 (ptm-80) REVERT: N 82 GLN cc_start: 0.8678 (tp40) cc_final: 0.8275 (tp40) REVERT: N 83 MET cc_start: 0.8410 (mtp) cc_final: 0.7971 (ptp) REVERT: N 125 THR cc_start: 0.8616 (m) cc_final: 0.8281 (p) REVERT: R 253 ARG cc_start: 0.8062 (mtm110) cc_final: 0.7551 (ptt90) REVERT: R 281 TYR cc_start: 0.8800 (m-80) cc_final: 0.8020 (m-80) outliers start: 32 outliers final: 28 residues processed: 200 average time/residue: 0.1990 time to fit residues: 54.2963 Evaluate side-chains 195 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain G residue 434 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 267 GLN Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 13 optimal weight: 0.0970 chunk 48 optimal weight: 0.0970 chunk 91 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 51 optimal weight: 0.0030 chunk 82 optimal weight: 10.0000 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.118394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092192 restraints weight = 18352.575| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 4.20 r_work: 0.3440 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8374 Z= 0.120 Angle : 0.690 10.864 11341 Z= 0.342 Chirality : 0.044 0.308 1293 Planarity : 0.004 0.052 1431 Dihedral : 4.343 23.219 1128 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.23 % Allowed : 23.72 % Favored : 73.05 % 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: -0.73 (0.26), residues: 1031 helix: 0.94 (0.27), residues: 386 sheet: -1.58 (0.35), residues: 205 loop : -1.15 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.010 0.001 HIS G 402 PHE 0.022 0.001 PHE G 271 TYR 0.019 0.001 TYR B 145 ARG 0.005 0.000 ARG G 277 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 356) hydrogen bonds : angle 4.65976 ( 984) SS BOND : bond 0.00298 ( 7) SS BOND : angle 0.87054 ( 14) covalent geometry : bond 0.00267 ( 8367) covalent geometry : angle 0.68926 (11327) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 36 ASP cc_start: 0.8950 (m-30) cc_final: 0.8550 (p0) REVERT: G 323 MET cc_start: 0.7923 (pmm) cc_final: 0.7698 (pmm) REVERT: G 324 GLN cc_start: 0.8484 (tp40) cc_final: 0.8014 (tp-100) REVERT: G 343 SER cc_start: 0.9247 (m) cc_final: 0.8930 (t) REVERT: B 19 ARG cc_start: 0.9499 (ttp80) cc_final: 0.9182 (ttp80) REVERT: B 20 ASP cc_start: 0.9462 (m-30) cc_final: 0.9195 (m-30) REVERT: B 45 MET cc_start: 0.8528 (ptp) cc_final: 0.8301 (ptp) REVERT: B 57 LYS cc_start: 0.9117 (ptpp) cc_final: 0.8786 (ptpp) REVERT: B 153 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8253 (t70) REVERT: B 172 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9006 (mm-30) REVERT: B 301 LYS cc_start: 0.9078 (mmmm) cc_final: 0.8679 (mmmt) REVERT: B 336 LEU cc_start: 0.9095 (mt) cc_final: 0.8729 (mt) REVERT: N 19 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8490 (ptm-80) REVERT: N 82 GLN cc_start: 0.8644 (tp40) cc_final: 0.8256 (tp40) REVERT: N 83 MET cc_start: 0.8357 (mtp) cc_final: 0.7966 (ptp) REVERT: N 125 THR cc_start: 0.8648 (m) cc_final: 0.8326 (p) REVERT: R 265 PHE cc_start: 0.6240 (t80) cc_final: 0.6007 (t80) REVERT: R 281 TYR cc_start: 0.8805 (m-80) cc_final: 0.8088 (m-80) outliers start: 29 outliers final: 23 residues processed: 201 average time/residue: 0.2232 time to fit residues: 61.2521 Evaluate side-chains 196 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 434 PHE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 267 GLN Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 0.0980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 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 = 0.4001 r_free = 0.4001 target = 0.117933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.091672 restraints weight = 18182.681| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 4.12 r_work: 0.3440 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8374 Z= 0.131 Angle : 0.719 10.654 11341 Z= 0.355 Chirality : 0.045 0.342 1293 Planarity : 0.004 0.052 1431 Dihedral : 4.350 23.147 1128 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.90 % Allowed : 24.72 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.26), residues: 1031 helix: 1.03 (0.27), residues: 377 sheet: -1.67 (0.35), residues: 209 loop : -1.05 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 36 HIS 0.011 0.001 HIS G 402 PHE 0.012 0.001 PHE R 265 TYR 0.020 0.002 TYR B 111 ARG 0.009 0.000 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 356) hydrogen bonds : angle 4.64865 ( 984) SS BOND : bond 0.00184 ( 7) SS BOND : angle 0.94819 ( 14) covalent geometry : bond 0.00305 ( 8367) covalent geometry : angle 0.71894 (11327) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 LYS cc_start: 0.7790 (pttm) cc_final: 0.7428 (mttm) REVERT: G 324 GLN cc_start: 0.8517 (tp40) cc_final: 0.8069 (tp-100) REVERT: G 343 SER cc_start: 0.9287 (m) cc_final: 0.8972 (t) REVERT: B 19 ARG cc_start: 0.9521 (ttp80) cc_final: 0.9116 (ttp80) REVERT: B 20 ASP cc_start: 0.9462 (m-30) cc_final: 0.9200 (m-30) REVERT: B 45 MET cc_start: 0.8402 (ptp) cc_final: 0.8164 (ptp) REVERT: B 57 LYS cc_start: 0.9146 (ptpp) cc_final: 0.8845 (ptpp) REVERT: B 153 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8285 (t70) REVERT: B 172 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8988 (mm-30) REVERT: B 226 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7708 (mt-10) REVERT: B 301 LYS cc_start: 0.9120 (mmmm) cc_final: 0.8775 (mmmt) REVERT: N 82 GLN cc_start: 0.8621 (tp40) cc_final: 0.8297 (tp40) REVERT: N 83 MET cc_start: 0.8408 (mtp) cc_final: 0.7920 (ptp) REVERT: N 125 THR cc_start: 0.8682 (m) cc_final: 0.8352 (p) REVERT: R 265 PHE cc_start: 0.6243 (t80) cc_final: 0.5985 (t80) REVERT: R 281 TYR cc_start: 0.8780 (m-80) cc_final: 0.8044 (m-80) REVERT: R 318 ARG cc_start: 0.9066 (ptp-170) cc_final: 0.8718 (mpp80) REVERT: R 359 GLU cc_start: 0.8489 (pt0) cc_final: 0.8067 (pm20) outliers start: 26 outliers final: 22 residues processed: 193 average time/residue: 0.1945 time to fit residues: 51.5707 Evaluate side-chains 193 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 434 PHE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 267 GLN Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 31 optimal weight: 0.4980 chunk 43 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 36 optimal weight: 0.0970 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.118535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.092082 restraints weight = 18353.562| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 4.20 r_work: 0.3443 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8374 Z= 0.127 Angle : 0.721 10.766 11341 Z= 0.355 Chirality : 0.045 0.325 1293 Planarity : 0.004 0.052 1431 Dihedral : 4.274 22.818 1128 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.67 % Allowed : 25.17 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.26), residues: 1031 helix: 1.00 (0.27), residues: 378 sheet: -1.62 (0.35), residues: 209 loop : -1.02 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.012 0.001 HIS G 402 PHE 0.016 0.001 PHE G 271 TYR 0.019 0.001 TYR B 111 ARG 0.007 0.000 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 356) hydrogen bonds : angle 4.64022 ( 984) SS BOND : bond 0.00194 ( 7) SS BOND : angle 1.01668 ( 14) covalent geometry : bond 0.00295 ( 8367) covalent geometry : angle 0.72059 (11327) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5418.77 seconds wall clock time: 94 minutes 21.82 seconds (5661.82 seconds total)