Starting phenix.real_space_refine on Wed Sep 17 17:29:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgr_38330/09_2025/8xgr_38330.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgr_38330/09_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_38330/09_2025/8xgr_38330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgr_38330/09_2025/8xgr_38330.map" model { file = "/net/cci-nas-00/data/ceres_data/8xgr_38330/09_2025/8xgr_38330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgr_38330/09_2025/8xgr_38330.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.06, per 1000 atoms: 0.25 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: 0.65 Conformation dependent library (CDL) restraints added in 290.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.21 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: 1.10 Time building geometry restraints manager: 0.80 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.320 ------------------------------------------------------------------------------- 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 : 7.39 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG G 288 TYR 0.007 0.001 TYR R 387 PHE 0.013 0.001 PHE B 234 TRP 0.007 0.001 TRP G 291 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8367) covalent geometry : angle 0.56201 (11327) SS BOND : bond 0.00354 ( 7) SS BOND : angle 1.15110 ( 14) hydrogen bonds : bond 0.27449 ( 356) hydrogen bonds : angle 9.77220 ( 984) *********************** 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 : 0.334 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: 0.1023 time to fit residues: 42.2573 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 : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.116958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.089846 restraints weight = 18204.145| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 4.19 r_work: 0.3361 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8374 Z= 0.165 Angle : 0.715 7.909 11341 Z= 0.367 Chirality : 0.045 0.200 1293 Planarity : 0.005 0.055 1431 Dihedral : 4.716 23.488 1128 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.23 % Allowed : 14.59 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.26), residues: 1031 helix: 0.35 (0.26), residues: 384 sheet: -2.13 (0.35), residues: 201 loop : -1.40 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 19 TYR 0.017 0.002 TYR B 145 PHE 0.025 0.002 PHE G 271 TRP 0.019 0.001 TRP B 339 HIS 0.009 0.002 HIS G 402 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8367) covalent geometry : angle 0.71253 (11327) SS BOND : bond 0.00354 ( 7) SS BOND : angle 1.73204 ( 14) hydrogen bonds : bond 0.05372 ( 356) hydrogen bonds : angle 5.45013 ( 984) *********************** 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 240 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 98 MET cc_start: 0.8835 (tmm) cc_final: 0.8625 (tmm) REVERT: G 271 PHE cc_start: 0.8637 (t80) cc_final: 0.8070 (t80) REVERT: G 388 LEU cc_start: 0.9144 (mt) cc_final: 0.8498 (pp) REVERT: B 19 ARG cc_start: 0.9434 (ttp80) cc_final: 0.9042 (ttp80) REVERT: B 20 ASP cc_start: 0.9407 (m-30) cc_final: 0.9147 (m-30) REVERT: B 23 LYS cc_start: 0.8504 (ptpp) cc_final: 0.8289 (pttm) REVERT: B 172 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8908 (mm-30) REVERT: B 335 PHE cc_start: 0.8588 (m-80) cc_final: 0.8249 (m-80) REVERT: B 337 LYS cc_start: 0.8695 (mmmt) cc_final: 0.7950 (mtpt) REVERT: N 5 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8557 (tm-30) REVERT: N 83 MET cc_start: 0.8428 (mtp) cc_final: 0.7821 (ptp) REVERT: N 95 TYR cc_start: 0.8599 (m-80) cc_final: 0.8297 (m-80) REVERT: R 266 MET cc_start: 0.8583 (mmm) cc_final: 0.8061 (ptm) REVERT: R 267 GLN cc_start: 0.8942 (mt0) cc_final: 0.8515 (mt0) REVERT: R 281 TYR cc_start: 0.8912 (m-80) cc_final: 0.8377 (m-80) REVERT: R 392 ARG cc_start: 0.7654 (ttp-170) cc_final: 0.7133 (ttp-170) REVERT: L 10 GLU cc_start: 0.8975 (mp0) cc_final: 0.8677 (mp0) outliers start: 20 outliers final: 10 residues processed: 232 average time/residue: 0.1030 time to fit residues: 31.9654 Evaluate side-chains 195 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 254 ASP 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 331 VAL Chi-restraints excluded: chain R residue 356 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 76 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN G 328 ASN ** G 402 HIS ** 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 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.114705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.087620 restraints weight = 18077.112| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 4.17 r_work: 0.3331 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3958 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= 0.180 Angle : 0.661 8.388 11341 Z= 0.340 Chirality : 0.044 0.176 1293 Planarity : 0.005 0.057 1431 Dihedral : 4.634 21.105 1128 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.90 % Allowed : 16.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.26), residues: 1031 helix: 0.70 (0.26), residues: 390 sheet: -2.06 (0.36), residues: 193 loop : -1.24 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 277 TYR 0.019 0.002 TYR B 145 PHE 0.015 0.002 PHE G 347 TRP 0.016 0.001 TRP B 339 HIS 0.008 0.002 HIS G 402 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8367) covalent geometry : angle 0.66073 (11327) SS BOND : bond 0.00462 ( 7) SS BOND : angle 1.11299 ( 14) hydrogen bonds : bond 0.04539 ( 356) hydrogen bonds : angle 5.10665 ( 984) *********************** 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 237 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 36 ASP cc_start: 0.8844 (m-30) cc_final: 0.8613 (m-30) REVERT: G 95 ARG cc_start: 0.9244 (mtp85) cc_final: 0.9001 (ttm110) REVERT: G 98 MET cc_start: 0.8925 (tmm) cc_final: 0.8663 (tmm) REVERT: G 271 PHE cc_start: 0.8706 (t80) cc_final: 0.8005 (t80) REVERT: G 273 ASP cc_start: 0.8140 (t0) cc_final: 0.7752 (t0) REVERT: G 323 MET cc_start: 0.7828 (pmm) cc_final: 0.7357 (pmm) REVERT: B 19 ARG cc_start: 0.9470 (ttp80) cc_final: 0.9030 (tmm-80) REVERT: B 20 ASP cc_start: 0.9438 (m-30) cc_final: 0.9105 (m-30) REVERT: B 23 LYS cc_start: 0.8510 (ptpp) cc_final: 0.8185 (ptpp) REVERT: B 172 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8925 (mm-30) REVERT: B 335 PHE cc_start: 0.8652 (m-80) cc_final: 0.8323 (m-80) REVERT: B 336 LEU cc_start: 0.9257 (mt) cc_final: 0.8855 (mt) REVERT: N 5 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8637 (tm-30) REVERT: N 19 ARG cc_start: 0.8826 (ptm160) cc_final: 0.8487 (ptm-80) REVERT: N 38 ARG cc_start: 0.8391 (ptm-80) cc_final: 0.8148 (ptm-80) REVERT: N 82 GLN cc_start: 0.8206 (tp40) cc_final: 0.7768 (tp40) REVERT: N 83 MET cc_start: 0.8490 (mtp) cc_final: 0.7918 (ptp) REVERT: N 95 TYR cc_start: 0.8710 (m-80) cc_final: 0.8351 (m-80) REVERT: R 208 ARG cc_start: 0.8545 (mmm160) cc_final: 0.8315 (mmm160) REVERT: R 265 PHE cc_start: 0.6596 (t80) cc_final: 0.6248 (t80) REVERT: R 266 MET cc_start: 0.8275 (mmm) cc_final: 0.7868 (mmm) REVERT: R 281 TYR cc_start: 0.8961 (m-80) cc_final: 0.8126 (m-80) REVERT: R 299 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7809 (tt0) REVERT: L 10 GLU cc_start: 0.9072 (mp0) cc_final: 0.8772 (mp0) outliers start: 35 outliers final: 24 residues processed: 220 average time/residue: 0.0974 time to fit residues: 28.8238 Evaluate side-chains 201 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 345 ILE 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 B residue 307 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 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 Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 59 optimal weight: 0.0370 chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN G 328 ASN B 75 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.114638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.087858 restraints weight = 18610.202| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 4.21 r_work: 0.3332 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8374 Z= 0.141 Angle : 0.637 8.815 11341 Z= 0.325 Chirality : 0.043 0.220 1293 Planarity : 0.004 0.054 1431 Dihedral : 4.482 18.445 1128 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.34 % Allowed : 17.71 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.26), residues: 1031 helix: 0.88 (0.26), residues: 391 sheet: -1.99 (0.35), residues: 201 loop : -1.21 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 277 TYR 0.017 0.001 TYR B 145 PHE 0.010 0.001 PHE B 241 TRP 0.015 0.001 TRP B 339 HIS 0.011 0.001 HIS G 402 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8367) covalent geometry : angle 0.63548 (11327) SS BOND : bond 0.00366 ( 7) SS BOND : angle 1.37992 ( 14) hydrogen bonds : bond 0.04033 ( 356) hydrogen bonds : angle 4.86459 ( 984) *********************** 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 242 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 36 ASP cc_start: 0.8888 (m-30) cc_final: 0.8654 (m-30) REVERT: G 271 PHE cc_start: 0.8665 (t80) cc_final: 0.7963 (t80) REVERT: G 273 ASP cc_start: 0.8314 (t0) cc_final: 0.7384 (t0) REVERT: G 323 MET cc_start: 0.7497 (pmm) cc_final: 0.7070 (pmm) REVERT: G 388 LEU cc_start: 0.9101 (mt) cc_final: 0.8422 (pp) REVERT: B 6 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8713 (mp10) REVERT: B 18 ILE cc_start: 0.9492 (mm) cc_final: 0.9234 (mm) REVERT: B 19 ARG cc_start: 0.9476 (ttp80) cc_final: 0.9069 (ttp80) REVERT: B 20 ASP cc_start: 0.9462 (m-30) cc_final: 0.9139 (m-30) REVERT: B 23 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8308 (pttm) REVERT: B 57 LYS cc_start: 0.9143 (ptpp) cc_final: 0.8918 (ptpp) REVERT: B 172 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8934 (mm-30) REVERT: B 335 PHE cc_start: 0.8672 (m-80) cc_final: 0.8452 (m-80) REVERT: B 336 LEU cc_start: 0.9206 (mt) cc_final: 0.8884 (mt) REVERT: N 83 MET cc_start: 0.8518 (mtp) cc_final: 0.7944 (ptp) REVERT: R 208 ARG cc_start: 0.8640 (mmm160) cc_final: 0.8371 (mmm160) REVERT: R 281 TYR cc_start: 0.8943 (m-80) cc_final: 0.8034 (m-80) REVERT: R 299 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7743 (tt0) REVERT: L 10 GLU cc_start: 0.8937 (mp0) cc_final: 0.8597 (mp0) outliers start: 39 outliers final: 18 residues processed: 222 average time/residue: 0.1001 time to fit residues: 30.0034 Evaluate side-chains 188 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain B residue 114 CYS 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 B residue 307 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 142 SER 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 356 ASN Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.112839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.085910 restraints weight = 18708.628| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 4.20 r_work: 0.3301 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8374 Z= 0.169 Angle : 0.646 8.127 11341 Z= 0.331 Chirality : 0.043 0.218 1293 Planarity : 0.005 0.055 1431 Dihedral : 4.507 21.928 1128 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.12 % Allowed : 18.49 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.26), residues: 1031 helix: 0.88 (0.26), residues: 390 sheet: -1.86 (0.35), residues: 206 loop : -1.17 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 277 TYR 0.018 0.001 TYR B 145 PHE 0.011 0.001 PHE B 241 TRP 0.013 0.001 TRP B 339 HIS 0.011 0.002 HIS G 402 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8367) covalent geometry : angle 0.64460 (11327) SS BOND : bond 0.00381 ( 7) SS BOND : angle 1.16556 ( 14) hydrogen bonds : bond 0.03913 ( 356) hydrogen bonds : angle 4.78489 ( 984) *********************** 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: 46 poor density : 184 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 36 ASP cc_start: 0.8937 (m-30) cc_final: 0.8690 (m-30) REVERT: G 271 PHE cc_start: 0.8756 (t80) cc_final: 0.8049 (t80) REVERT: G 273 ASP cc_start: 0.8537 (t0) cc_final: 0.7811 (t0) REVERT: G 323 MET cc_start: 0.7527 (pmm) cc_final: 0.7300 (pmm) REVERT: B 19 ARG cc_start: 0.9484 (ttp80) cc_final: 0.9050 (ttp80) REVERT: B 20 ASP cc_start: 0.9449 (m-30) cc_final: 0.9066 (m-30) REVERT: B 23 LYS cc_start: 0.8533 (ptpp) cc_final: 0.8287 (pttm) REVERT: B 172 GLU cc_start: 0.9311 (mm-30) cc_final: 0.8921 (mm-30) REVERT: B 335 PHE cc_start: 0.8664 (m-80) cc_final: 0.8433 (m-80) REVERT: N 83 MET cc_start: 0.8488 (mtp) cc_final: 0.8013 (ptp) REVERT: R 245 MET cc_start: 0.7601 (tmm) cc_final: 0.7335 (tmm) REVERT: R 281 TYR cc_start: 0.8944 (m-80) cc_final: 0.8087 (m-80) REVERT: R 299 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7713 (tt0) REVERT: R 318 ARG cc_start: 0.9105 (ptp-170) cc_final: 0.8716 (mpp80) REVERT: L 10 GLU cc_start: 0.9065 (mp0) cc_final: 0.8674 (mp0) REVERT: L 14 PHE cc_start: 0.9071 (t80) cc_final: 0.8851 (t80) outliers start: 46 outliers final: 33 residues processed: 212 average time/residue: 0.0955 time to fit residues: 27.5044 Evaluate side-chains 203 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 345 ILE 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 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 176 GLN 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN ** B 225 HIS ** 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 = 0.3975 r_free = 0.3975 target = 0.116096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.089897 restraints weight = 18102.876| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 4.14 r_work: 0.3399 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8374 Z= 0.125 Angle : 0.628 9.229 11341 Z= 0.319 Chirality : 0.042 0.241 1293 Planarity : 0.004 0.054 1431 Dihedral : 4.368 20.812 1128 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.90 % Allowed : 19.49 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.26), residues: 1031 helix: 1.02 (0.26), residues: 389 sheet: -1.73 (0.35), residues: 205 loop : -1.14 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 277 TYR 0.017 0.001 TYR B 145 PHE 0.011 0.001 PHE G 416 TRP 0.013 0.001 TRP B 339 HIS 0.012 0.001 HIS G 402 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8367) covalent geometry : angle 0.62746 (11327) SS BOND : bond 0.00274 ( 7) SS BOND : angle 0.97587 ( 14) hydrogen bonds : bond 0.03596 ( 356) hydrogen bonds : angle 4.60517 ( 984) *********************** 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 221 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 36 ASP cc_start: 0.8949 (m-30) cc_final: 0.8706 (m-30) REVERT: G 273 ASP cc_start: 0.8700 (t0) cc_final: 0.8290 (t0) REVERT: G 323 MET cc_start: 0.7497 (pmm) cc_final: 0.7159 (pmm) REVERT: G 338 TRP cc_start: 0.8936 (m-10) cc_final: 0.8725 (m-10) REVERT: G 388 LEU cc_start: 0.9120 (mt) cc_final: 0.8348 (pp) REVERT: G 403 MET cc_start: 0.6648 (pmm) cc_final: 0.6059 (pmm) REVERT: B 19 ARG cc_start: 0.9490 (ttp80) cc_final: 0.9153 (ttp80) REVERT: B 20 ASP cc_start: 0.9464 (m-30) cc_final: 0.9115 (m-30) REVERT: B 23 LYS cc_start: 0.8569 (ptpp) cc_final: 0.8369 (pttm) REVERT: B 57 LYS cc_start: 0.9162 (ptpp) cc_final: 0.8795 (ptpp) REVERT: B 172 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8951 (mm-30) REVERT: B 336 LEU cc_start: 0.9189 (mt) cc_final: 0.8908 (mt) REVERT: N 83 MET cc_start: 0.8447 (mtp) cc_final: 0.8024 (ptp) REVERT: R 208 ARG cc_start: 0.8165 (mmm160) cc_final: 0.7862 (mmm160) REVERT: R 281 TYR cc_start: 0.8862 (m-80) cc_final: 0.7968 (m-80) REVERT: R 299 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7538 (tt0) REVERT: R 318 ARG cc_start: 0.9154 (ptp-170) cc_final: 0.8847 (mpp80) outliers start: 35 outliers final: 27 residues processed: 207 average time/residue: 0.0896 time to fit residues: 25.6338 Evaluate side-chains 200 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 434 PHE 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 217 MET 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 69 THR Chi-restraints excluded: chain N residue 77 ASN 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 0.0070 overall best weight: 1.4002 ------------------------------------------------------------------------------- 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 349 ASN ** B 17 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.114708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.087850 restraints weight = 18328.657| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 4.18 r_work: 0.3356 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8374 Z= 0.153 Angle : 0.659 8.963 11341 Z= 0.337 Chirality : 0.043 0.216 1293 Planarity : 0.004 0.053 1431 Dihedral : 4.420 22.898 1128 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.68 % Allowed : 19.82 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.26), residues: 1031 helix: 1.00 (0.26), residues: 383 sheet: -1.69 (0.35), residues: 207 loop : -1.08 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 277 TYR 0.026 0.001 TYR B 145 PHE 0.014 0.001 PHE G 271 TRP 0.012 0.001 TRP B 339 HIS 0.010 0.001 HIS G 402 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8367) covalent geometry : angle 0.65763 (11327) SS BOND : bond 0.00493 ( 7) SS BOND : angle 1.21882 ( 14) hydrogen bonds : bond 0.03713 ( 356) hydrogen bonds : angle 4.70296 ( 984) *********************** 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 217 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.262 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 36 ASP cc_start: 0.8946 (m-30) cc_final: 0.8700 (m-30) REVERT: G 273 ASP cc_start: 0.8679 (t0) cc_final: 0.8311 (t0) REVERT: G 323 MET cc_start: 0.7567 (pmm) cc_final: 0.7223 (pmm) REVERT: G 338 TRP cc_start: 0.8987 (m-10) cc_final: 0.8762 (m-10) REVERT: G 349 ASN cc_start: 0.7131 (OUTLIER) cc_final: 0.6676 (m110) REVERT: G 392 MET cc_start: 0.3307 (mmp) cc_final: 0.3037 (mmp) REVERT: G 403 MET cc_start: 0.6520 (pmm) cc_final: 0.5855 (ptp) REVERT: B 19 ARG cc_start: 0.9477 (ttp80) cc_final: 0.9127 (ttp80) REVERT: B 20 ASP cc_start: 0.9485 (m-30) cc_final: 0.9143 (m-30) REVERT: B 57 LYS cc_start: 0.9173 (ptpp) cc_final: 0.8968 (ptpp) REVERT: B 172 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8958 (mm-30) REVERT: B 336 LEU cc_start: 0.9165 (mt) cc_final: 0.8807 (mt) REVERT: N 83 MET cc_start: 0.8482 (mtp) cc_final: 0.8046 (ptp) REVERT: R 173 MET cc_start: 0.8587 (ptt) cc_final: 0.7729 (tmm) REVERT: R 208 ARG cc_start: 0.8310 (mmm160) cc_final: 0.8080 (mmm160) REVERT: R 266 MET cc_start: 0.8492 (mmm) cc_final: 0.8174 (mmm) REVERT: R 281 TYR cc_start: 0.8906 (m-80) cc_final: 0.7995 (m-80) REVERT: R 299 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7532 (tt0) outliers start: 42 outliers final: 30 residues processed: 202 average time/residue: 0.0867 time to fit residues: 24.4045 Evaluate side-chains 191 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 349 ASN Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 415 VAL 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 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 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 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 224 LEU Chi-restraints excluded: chain R residue 288 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN G 349 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 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.112183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.085352 restraints weight = 18582.692| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 4.10 r_work: 0.3323 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8374 Z= 0.224 Angle : 0.698 8.897 11341 Z= 0.357 Chirality : 0.045 0.281 1293 Planarity : 0.005 0.054 1431 Dihedral : 4.570 22.335 1128 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.57 % Allowed : 20.60 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.26), residues: 1031 helix: 0.82 (0.26), residues: 385 sheet: -1.74 (0.35), residues: 203 loop : -1.11 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 277 TYR 0.027 0.002 TYR B 145 PHE 0.023 0.002 PHE G 271 TRP 0.014 0.002 TRP B 339 HIS 0.012 0.002 HIS G 402 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 8367) covalent geometry : angle 0.69630 (11327) SS BOND : bond 0.00598 ( 7) SS BOND : angle 1.44842 ( 14) hydrogen bonds : bond 0.04002 ( 356) hydrogen bonds : angle 4.86588 ( 984) *********************** 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 200 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 36 ASP cc_start: 0.8952 (m-30) cc_final: 0.8737 (m-30) REVERT: G 349 ASN cc_start: 0.7345 (OUTLIER) cc_final: 0.6869 (m110) REVERT: G 403 MET cc_start: 0.6516 (pmm) cc_final: 0.5901 (ptp) REVERT: B 19 ARG cc_start: 0.9492 (ttp80) cc_final: 0.9016 (tmm-80) REVERT: B 20 ASP cc_start: 0.9437 (m-30) cc_final: 0.9143 (m-30) REVERT: B 23 LYS cc_start: 0.8447 (pttm) cc_final: 0.8204 (pttm) REVERT: B 172 GLU cc_start: 0.9340 (mm-30) cc_final: 0.9136 (mm-30) REVERT: N 46 GLN cc_start: 0.8253 (tt0) cc_final: 0.7980 (tt0) REVERT: N 53 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6924 (tm-30) REVERT: N 83 MET cc_start: 0.8471 (mtp) cc_final: 0.8052 (ptp) REVERT: R 173 MET cc_start: 0.8545 (ptt) cc_final: 0.7822 (tmm) REVERT: R 266 MET cc_start: 0.8555 (mmm) cc_final: 0.8257 (mmm) REVERT: R 281 TYR cc_start: 0.8868 (m-80) cc_final: 0.8084 (m-80) REVERT: R 299 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7522 (tt0) outliers start: 41 outliers final: 33 residues processed: 186 average time/residue: 0.0872 time to fit residues: 22.7700 Evaluate side-chains 186 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 349 ASN Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 399 ILE Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL 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 53 GLN Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 108 PHE 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 140 ILE Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 209 ILE 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 356 ASN Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 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 82 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 = 0.3961 r_free = 0.3961 target = 0.114826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.088633 restraints weight = 18505.005| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 4.17 r_work: 0.3390 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8374 Z= 0.139 Angle : 0.697 12.315 11341 Z= 0.345 Chirality : 0.045 0.340 1293 Planarity : 0.004 0.053 1431 Dihedral : 4.442 22.496 1128 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.90 % Allowed : 20.94 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.26), residues: 1031 helix: 0.96 (0.26), residues: 383 sheet: -1.70 (0.35), residues: 203 loop : -1.06 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 277 TYR 0.020 0.001 TYR B 145 PHE 0.011 0.001 PHE B 335 TRP 0.013 0.001 TRP B 339 HIS 0.012 0.001 HIS G 402 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8367) covalent geometry : angle 0.69644 (11327) SS BOND : bond 0.00284 ( 7) SS BOND : angle 0.96070 ( 14) hydrogen bonds : bond 0.03690 ( 356) hydrogen bonds : angle 4.71557 ( 984) *********************** 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 205 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 36 ASP cc_start: 0.8985 (m-30) cc_final: 0.8767 (m-30) REVERT: G 343 SER cc_start: 0.9405 (m) cc_final: 0.9085 (t) REVERT: G 403 MET cc_start: 0.6409 (pmm) cc_final: 0.5829 (ptp) REVERT: B 19 ARG cc_start: 0.9498 (ttp80) cc_final: 0.9057 (tmm-80) REVERT: B 20 ASP cc_start: 0.9439 (m-30) cc_final: 0.9151 (m-30) REVERT: B 172 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8984 (mm-30) REVERT: B 336 LEU cc_start: 0.9177 (mt) cc_final: 0.8813 (mt) REVERT: N 46 GLN cc_start: 0.8202 (tt0) cc_final: 0.7940 (tt0) REVERT: N 83 MET cc_start: 0.8404 (mtp) cc_final: 0.8030 (ptp) REVERT: R 173 MET cc_start: 0.8491 (ptt) cc_final: 0.7713 (tmm) REVERT: R 266 MET cc_start: 0.8499 (mmm) cc_final: 0.8231 (mmm) REVERT: R 281 TYR cc_start: 0.8841 (m-80) cc_final: 0.8015 (m-80) REVERT: R 299 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7434 (tt0) REVERT: R 380 CYS cc_start: 0.7853 (t) cc_final: 0.7569 (t) REVERT: L 10 GLU cc_start: 0.9000 (mp0) cc_final: 0.8624 (mp0) outliers start: 35 outliers final: 28 residues processed: 195 average time/residue: 0.0872 time to fit residues: 23.5683 Evaluate side-chains 188 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 303 PHE Chi-restraints excluded: chain G residue 345 ILE 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 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL 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 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 79 LEU 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 224 LEU Chi-restraints excluded: chain R residue 227 VAL 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 35 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 0.0870 chunk 55 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 chunk 89 optimal weight: 0.0670 chunk 53 optimal weight: 0.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.117564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.091321 restraints weight = 18333.821| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 4.21 r_work: 0.3432 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5414 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= 0.126 Angle : 0.690 12.855 11341 Z= 0.344 Chirality : 0.045 0.359 1293 Planarity : 0.004 0.052 1431 Dihedral : 4.403 23.617 1128 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.78 % Allowed : 21.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.26), residues: 1031 helix: 0.98 (0.26), residues: 387 sheet: -1.64 (0.34), residues: 201 loop : -1.00 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 208 TYR 0.021 0.001 TYR B 145 PHE 0.025 0.001 PHE G 271 TRP 0.018 0.001 TRP G 291 HIS 0.013 0.001 HIS G 402 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8367) covalent geometry : angle 0.68967 (11327) SS BOND : bond 0.00548 ( 7) SS BOND : angle 1.04962 ( 14) hydrogen bonds : bond 0.03550 ( 356) hydrogen bonds : angle 4.65406 ( 984) ********************** 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 201 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 36 ASP cc_start: 0.8963 (m-30) cc_final: 0.8738 (m-30) REVERT: G 343 SER cc_start: 0.9347 (m) cc_final: 0.9047 (t) REVERT: G 403 MET cc_start: 0.6248 (pmm) cc_final: 0.5696 (ptp) REVERT: B 19 ARG cc_start: 0.9515 (ttp80) cc_final: 0.9195 (tmm-80) REVERT: B 20 ASP cc_start: 0.9432 (m-30) cc_final: 0.9229 (m-30) REVERT: B 57 LYS cc_start: 0.9142 (ptpp) cc_final: 0.8820 (ptpp) REVERT: B 172 GLU cc_start: 0.9347 (mm-30) cc_final: 0.9014 (mm-30) REVERT: N 19 ARG cc_start: 0.8840 (ptm160) cc_final: 0.8404 (ptm-80) REVERT: N 46 GLN cc_start: 0.8150 (tt0) cc_final: 0.7891 (tt0) REVERT: N 82 GLN cc_start: 0.8158 (tp40) cc_final: 0.7631 (tp-100) REVERT: N 83 MET cc_start: 0.8406 (mtp) cc_final: 0.7993 (ptp) REVERT: N 87 LYS cc_start: 0.8190 (mppt) cc_final: 0.7856 (mmtm) REVERT: N 125 THR cc_start: 0.8665 (m) cc_final: 0.8376 (p) REVERT: R 130 LYS cc_start: 0.9193 (tptt) cc_final: 0.8451 (tptp) REVERT: R 147 ASP cc_start: 0.8534 (t70) cc_final: 0.8283 (t0) REVERT: R 173 MET cc_start: 0.8560 (ptt) cc_final: 0.7848 (tmm) REVERT: R 266 MET cc_start: 0.8523 (mmm) cc_final: 0.8207 (mmm) REVERT: R 281 TYR cc_start: 0.8849 (m-80) cc_final: 0.7995 (m-80) REVERT: R 299 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7423 (tt0) REVERT: R 318 ARG cc_start: 0.9210 (ptp-170) cc_final: 0.8873 (mpp80) REVERT: R 359 GLU cc_start: 0.8435 (pt0) cc_final: 0.7944 (pm20) REVERT: R 380 CYS cc_start: 0.7857 (t) cc_final: 0.7654 (t) outliers start: 25 outliers final: 22 residues processed: 193 average time/residue: 0.0929 time to fit residues: 24.5776 Evaluate side-chains 189 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 303 PHE Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 390 LEU 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 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 77 ASN Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 149 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 76 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 84 optimal weight: 0.0770 chunk 66 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.0940 ------------------------------------------------------------------------------- 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** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.116247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.090431 restraints weight = 18314.441| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 4.14 r_work: 0.3417 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8374 Z= 0.144 Angle : 0.723 12.557 11341 Z= 0.358 Chirality : 0.045 0.345 1293 Planarity : 0.004 0.052 1431 Dihedral : 4.369 22.476 1128 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.45 % Allowed : 22.49 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.26), residues: 1031 helix: 0.82 (0.26), residues: 395 sheet: -1.64 (0.34), residues: 205 loop : -1.07 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 133 TYR 0.021 0.001 TYR B 111 PHE 0.050 0.001 PHE G 434 TRP 0.012 0.001 TRP B 339 HIS 0.014 0.001 HIS G 402 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8367) covalent geometry : angle 0.72185 (11327) SS BOND : bond 0.00230 ( 7) SS BOND : angle 1.15576 ( 14) hydrogen bonds : bond 0.03662 ( 356) hydrogen bonds : angle 4.69590 ( 984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2542.01 seconds wall clock time: 44 minutes 12.57 seconds (2652.57 seconds total)