Starting phenix.real_space_refine on Sat Oct 11 13:35:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rbf_19030/10_2025/8rbf_19030.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rbf_19030/10_2025/8rbf_19030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rbf_19030/10_2025/8rbf_19030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rbf_19030/10_2025/8rbf_19030.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rbf_19030/10_2025/8rbf_19030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rbf_19030/10_2025/8rbf_19030.map" } resolution = 4.2 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 97 5.16 5 C 9372 2.51 5 N 2504 2.21 5 O 2805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14790 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5944 Classifications: {'peptide': 731} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 704} Chain breaks: 1 Chain: "B" Number of atoms: 2936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2936 Unusual residues: {'ACE': 1} Classifications: {'peptide': 375, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 355} Chain: "C" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "D" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.03, per 1000 atoms: 0.20 Number of scatterers: 14790 At special positions: 0 Unit cell: (107, 160.5, 141.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 97 16.00 P 8 15.00 Mg 4 11.99 O 2805 8.00 N 2504 7.00 C 9372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.18 Conformation dependent library (CDL) restraints added in 651.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3454 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 25 sheets defined 49.7% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 154 Processing helix chain 'A' and resid 168 through 183 Processing helix chain 'A' and resid 191 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.086A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.503A pdb=" N MET A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.940A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 316 Processing helix chain 'A' and resid 318 through 338 Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.718A pdb=" N ILE A 499 " --> pdb=" O CYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.550A pdb=" N LEU A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.580A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.819A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 627 through 631 Processing helix chain 'A' and resid 634 through 653 removed outlier: 3.525A pdb=" N THR A 653 " --> pdb=" O THR A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 684 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.590A pdb=" N THR A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 711 Processing helix chain 'A' and resid 722 through 735 removed outlier: 3.578A pdb=" N GLU A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 753 through 767 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 79 through 94 removed outlier: 3.860A pdb=" N GLU B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 127 removed outlier: 3.606A pdb=" N ARG B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.720A pdb=" N GLU B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 218 removed outlier: 3.654A pdb=" N ILE B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 234 Processing helix chain 'B' and resid 253 through 261 Proline residue: B 259 - end of helix Processing helix chain 'B' and resid 262 through 263 No H-bonds generated for 'chain 'B' and resid 262 through 263' Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 274 through 286 removed outlier: 3.521A pdb=" N CYS B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.518A pdb=" N LEU B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 360 through 367 Processing helix chain 'B' and resid 369 through 376 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.752A pdb=" N GLU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.580A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.555A pdb=" N LEU C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.720A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 338 through 349 Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 368 through 375 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.537A pdb=" N PHE D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.508A pdb=" N LEU D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.782A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.623A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 375 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 51 removed outlier: 4.690A pdb=" N LYS A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU A 42 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 48 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS A 61 " --> pdb=" O TRP A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.578A pdb=" N VAL A 106 " --> pdb=" O CYS A 103 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU A 107 " --> pdb=" O ARG A 659 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE A 661 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA A 109 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER A 158 " --> pdb=" O HIS A 656 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL A 658 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A 160 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N CYS A 660 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER A 162 " --> pdb=" O CYS A 660 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 211 removed outlier: 6.444A pdb=" N ALA A 209 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN A 216 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA6, first strand: chain 'A' and resid 547 through 551 Processing sheet with id=AA7, first strand: chain 'A' and resid 700 through 702 Processing sheet with id=AA8, first strand: chain 'B' and resid 30 through 32 removed outlier: 3.530A pdb=" N LYS B 19 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 9 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N THR B 107 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N CYS B 11 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.735A pdb=" N VAL B 36 " --> pdb=" O LYS B 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AB2, first strand: chain 'B' and resid 177 through 179 removed outlier: 6.559A pdb=" N ASN B 298 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 177 through 179 removed outlier: 4.176A pdb=" N GLN D 41 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 239 through 242 Processing sheet with id=AB5, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.586A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.209A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 165 through 166 Processing sheet with id=AC1, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC2, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.671A pdb=" N LYS D 18 " --> pdb=" O ASP D 11 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.714A pdb=" N VAL D 35 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC6, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC7, first strand: chain 'D' and resid 238 through 241 735 hydrogen bonds defined for protein. 2013 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: 3.05 Time building geometry restraints manager: 1.61 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: 2961 1.33 - 1.45: 3506 1.45 - 1.58: 8475 1.58 - 1.70: 11 1.70 - 1.82: 164 Bond restraints: 15117 Sorted by residual: bond pdb=" C4 ADP A1902 " pdb=" C5 ADP A1902 " ideal model delta sigma weight residual 1.490 1.377 0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" CA PRO A 351 " pdb=" C PRO A 351 " ideal model delta sigma weight residual 1.514 1.542 -0.028 5.50e-03 3.31e+04 2.54e+01 ... (remaining 15112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 16732 2.24 - 4.49: 3498 4.49 - 6.73: 198 6.73 - 8.97: 20 8.97 - 11.22: 18 Bond angle restraints: 20466 Sorted by residual: angle pdb=" N HIS A 430 " pdb=" CA HIS A 430 " pdb=" C HIS A 430 " ideal model delta sigma weight residual 113.50 104.69 8.81 1.23e+00 6.61e-01 5.13e+01 angle pdb=" CA GLY C 251 " pdb=" C GLY C 251 " pdb=" O GLY C 251 " ideal model delta sigma weight residual 121.06 116.13 4.93 9.00e-01 1.23e+00 3.00e+01 angle pdb=" CA ASN D 111 " pdb=" C ASN D 111 " pdb=" O ASN D 111 " ideal model delta sigma weight residual 120.19 115.65 4.54 8.40e-01 1.42e+00 2.93e+01 angle pdb=" CA ASN B 112 " pdb=" C ASN B 112 " pdb=" O ASN B 112 " ideal model delta sigma weight residual 120.19 115.71 4.48 8.40e-01 1.42e+00 2.85e+01 angle pdb=" N THR D 66 " pdb=" CA THR D 66 " pdb=" C THR D 66 " ideal model delta sigma weight residual 110.17 101.62 8.55 1.61e+00 3.86e-01 2.82e+01 ... (remaining 20461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 8866 35.15 - 70.31: 216 70.31 - 105.46: 20 105.46 - 140.61: 1 140.61 - 175.76: 9 Dihedral angle restraints: 9112 sinusoidal: 3734 harmonic: 5378 Sorted by residual: dihedral pdb=" C5' ADP A1902 " pdb=" O5' ADP A1902 " pdb=" PA ADP A1902 " pdb=" O2A ADP A1902 " ideal model delta sinusoidal sigma weight residual 300.00 124.24 175.76 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 90.76 -150.76 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.63 -149.63 1 2.00e+01 2.50e-03 4.47e+01 ... (remaining 9109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1267 0.078 - 0.156: 738 0.156 - 0.235: 203 0.235 - 0.313: 29 0.313 - 0.391: 4 Chirality restraints: 2241 Sorted by residual: chirality pdb=" CA PHE A 444 " pdb=" N PHE A 444 " pdb=" C PHE A 444 " pdb=" CB PHE A 444 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CA ASP B 2 " pdb=" N ASP B 2 " pdb=" C ASP B 2 " pdb=" CB ASP B 2 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA SER C 234 " pdb=" N SER C 234 " pdb=" C SER C 234 " pdb=" CB SER C 234 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 2238 not shown) Planarity restraints: 2622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 65 " 0.025 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C LEU D 65 " -0.088 2.00e-02 2.50e+03 pdb=" O LEU D 65 " 0.034 2.00e-02 2.50e+03 pdb=" N THR D 66 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 304 " 0.017 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" C THR D 304 " -0.061 2.00e-02 2.50e+03 pdb=" O THR D 304 " 0.023 2.00e-02 2.50e+03 pdb=" N MET D 305 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 169 " -0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C LYS A 169 " 0.061 2.00e-02 2.50e+03 pdb=" O LYS A 169 " -0.023 2.00e-02 2.50e+03 pdb=" N THR A 170 " -0.021 2.00e-02 2.50e+03 ... (remaining 2619 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 11 2.05 - 2.77: 973 2.77 - 3.48: 21208 3.48 - 4.19: 36458 4.19 - 4.90: 62119 Nonbonded interactions: 120769 Sorted by model distance: nonbonded pdb=" CG GLN A 474 " pdb=" OH TYR A 477 " model vdw 1.342 3.440 nonbonded pdb=" NE ARG A 90 " pdb=" OE2 GLU A 674 " model vdw 1.366 3.120 nonbonded pdb=" CA GLN A 474 " pdb=" CE2 TYR A 477 " model vdw 1.398 3.770 nonbonded pdb=" C GLN A 474 " pdb=" CE2 TYR A 477 " model vdw 1.677 3.570 nonbonded pdb=" CZ ARG A 90 " pdb=" OE2 GLU A 674 " model vdw 1.699 3.270 ... (remaining 120764 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 6 through 402) selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 4.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.180 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 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 : 0.013 0.113 15117 Z= 0.884 Angle : 1.689 11.216 20466 Z= 1.153 Chirality : 0.097 0.391 2241 Planarity : 0.008 0.069 2622 Dihedral : 15.606 175.763 5658 Min Nonbonded Distance : 1.342 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.54 % Favored : 96.41 % Rotamer: Outliers : 0.19 % Allowed : 4.60 % Favored : 95.21 % Cbeta Deviations : 0.06 % 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: -1.94 (0.17), residues: 1838 helix: -1.49 (0.14), residues: 825 sheet: -0.90 (0.30), residues: 210 loop : -0.96 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 291 TYR 0.025 0.002 TYR A 100 PHE 0.034 0.003 PHE B 22 TRP 0.019 0.003 TRP C 356 HIS 0.008 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.01307 (15117) covalent geometry : angle 1.68930 (20466) hydrogen bonds : bond 0.18392 ( 729) hydrogen bonds : angle 7.28833 ( 2013) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 803 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7541 (mtpt) REVERT: A 29 LYS cc_start: 0.7739 (ptmt) cc_final: 0.7395 (ttpp) REVERT: A 32 LYS cc_start: 0.8644 (mttp) cc_final: 0.8324 (mttp) REVERT: A 110 ILE cc_start: 0.7444 (mp) cc_final: 0.7209 (mp) REVERT: A 132 MET cc_start: 0.3384 (ppp) cc_final: 0.3168 (ppp) REVERT: A 140 PHE cc_start: 0.8328 (m-10) cc_final: 0.7778 (m-10) REVERT: A 148 LYS cc_start: 0.8965 (tttt) cc_final: 0.8644 (tttt) REVERT: A 149 GLN cc_start: 0.8344 (mt0) cc_final: 0.7978 (mm-40) REVERT: A 150 MET cc_start: 0.7645 (ttp) cc_final: 0.7301 (ttp) REVERT: A 194 GLU cc_start: 0.7724 (tt0) cc_final: 0.7434 (tt0) REVERT: A 210 LYS cc_start: 0.7163 (tmtt) cc_final: 0.6432 (tptp) REVERT: A 222 LYS cc_start: 0.7607 (ttpt) cc_final: 0.7120 (ttpt) REVERT: A 223 TYR cc_start: 0.7894 (t80) cc_final: 0.6602 (t80) REVERT: A 228 PHE cc_start: 0.7537 (m-80) cc_final: 0.7157 (m-80) REVERT: A 230 LYS cc_start: 0.8875 (mttt) cc_final: 0.8556 (mmtm) REVERT: A 246 LYS cc_start: 0.8345 (mmtt) cc_final: 0.8106 (mmtt) REVERT: A 249 VAL cc_start: 0.8559 (t) cc_final: 0.8271 (t) REVERT: A 259 TYR cc_start: 0.7097 (m-80) cc_final: 0.6153 (m-10) REVERT: A 262 PHE cc_start: 0.7984 (m-80) cc_final: 0.7357 (m-80) REVERT: A 277 LEU cc_start: 0.8717 (mp) cc_final: 0.8282 (tp) REVERT: A 310 GLN cc_start: 0.8986 (mt0) cc_final: 0.8449 (mt0) REVERT: A 315 LEU cc_start: 0.7602 (mt) cc_final: 0.7304 (mt) REVERT: A 328 ILE cc_start: 0.8374 (mt) cc_final: 0.8144 (mm) REVERT: A 354 HIS cc_start: 0.7441 (t70) cc_final: 0.6730 (t70) REVERT: A 356 PRO cc_start: 0.8579 (Cg_exo) cc_final: 0.8336 (Cg_endo) REVERT: A 364 MET cc_start: 0.6997 (mmt) cc_final: 0.5999 (mmt) REVERT: A 370 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7890 (mm-30) REVERT: A 385 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6789 (mt-10) REVERT: A 387 TYR cc_start: 0.7251 (m-80) cc_final: 0.6815 (m-80) REVERT: A 389 LYS cc_start: 0.8690 (mmtp) cc_final: 0.7987 (mmtp) REVERT: A 408 TYR cc_start: 0.8255 (t80) cc_final: 0.7807 (t80) REVERT: A 413 ASN cc_start: 0.8659 (m-40) cc_final: 0.8177 (m-40) REVERT: A 414 TRP cc_start: 0.7682 (t60) cc_final: 0.7444 (t60) REVERT: A 416 VAL cc_start: 0.8508 (t) cc_final: 0.8174 (p) REVERT: A 427 VAL cc_start: 0.8163 (t) cc_final: 0.7941 (p) REVERT: A 438 ILE cc_start: 0.7423 (tt) cc_final: 0.6745 (pt) REVERT: A 451 GLN cc_start: 0.8319 (mp10) cc_final: 0.7473 (mp-120) REVERT: A 452 PHE cc_start: 0.8374 (t80) cc_final: 0.7728 (t80) REVERT: A 453 CYS cc_start: 0.8684 (m) cc_final: 0.8375 (m) REVERT: A 454 ILE cc_start: 0.8741 (mm) cc_final: 0.8407 (tt) REVERT: A 455 ASN cc_start: 0.8912 (m-40) cc_final: 0.7651 (m110) REVERT: A 462 GLN cc_start: 0.7624 (tp-100) cc_final: 0.6880 (tp40) REVERT: A 464 GLN cc_start: 0.8594 (tt0) cc_final: 0.8311 (tt0) REVERT: A 472 LEU cc_start: 0.8518 (tp) cc_final: 0.8291 (pp) REVERT: A 475 GLU cc_start: 0.8766 (tp30) cc_final: 0.8524 (tp30) REVERT: A 480 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6895 (mm-30) REVERT: A 496 ILE cc_start: 0.8085 (mt) cc_final: 0.7767 (mm) REVERT: A 499 ILE cc_start: 0.8410 (mt) cc_final: 0.8078 (tt) REVERT: A 508 LEU cc_start: 0.8307 (mt) cc_final: 0.8064 (mt) REVERT: A 509 LEU cc_start: 0.7863 (tp) cc_final: 0.7442 (tp) REVERT: A 520 ASP cc_start: 0.6441 (m-30) cc_final: 0.6071 (m-30) REVERT: A 522 THR cc_start: 0.7529 (m) cc_final: 0.7304 (p) REVERT: A 525 GLN cc_start: 0.8558 (tp40) cc_final: 0.7585 (tp-100) REVERT: A 527 LEU cc_start: 0.8582 (mt) cc_final: 0.8330 (mt) REVERT: A 537 LEU cc_start: 0.7541 (mt) cc_final: 0.7323 (tp) REVERT: A 540 LYS cc_start: 0.7724 (tttm) cc_final: 0.6980 (tptp) REVERT: A 545 ASN cc_start: 0.8192 (m-40) cc_final: 0.7985 (m-40) REVERT: A 555 ASP cc_start: 0.7074 (t0) cc_final: 0.6715 (t70) REVERT: A 558 GLU cc_start: 0.7288 (tt0) cc_final: 0.7032 (tm-30) REVERT: A 559 TYR cc_start: 0.7166 (m-80) cc_final: 0.6458 (m-80) REVERT: A 567 LYS cc_start: 0.7838 (mttt) cc_final: 0.7386 (mttt) REVERT: A 577 ILE cc_start: 0.8517 (mm) cc_final: 0.8264 (mm) REVERT: A 578 LYS cc_start: 0.8780 (mmtp) cc_final: 0.8353 (mmtp) REVERT: A 632 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8797 (mtmt) REVERT: A 641 ASN cc_start: 0.8515 (m-40) cc_final: 0.8141 (m110) REVERT: A 644 HIS cc_start: 0.7551 (m170) cc_final: 0.7250 (m170) REVERT: A 646 LEU cc_start: 0.8594 (tp) cc_final: 0.8345 (tt) REVERT: A 657 TYR cc_start: 0.7615 (m-80) cc_final: 0.7103 (m-80) REVERT: A 667 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8442 (mtpt) REVERT: A 675 LYS cc_start: 0.8044 (mmtp) cc_final: 0.7603 (mmtp) REVERT: A 732 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7211 (tm-30) REVERT: B 7 THR cc_start: 0.8820 (m) cc_final: 0.8470 (p) REVERT: B 9 LEU cc_start: 0.7974 (mt) cc_final: 0.7712 (mt) REVERT: B 32 PHE cc_start: 0.7446 (p90) cc_final: 0.7237 (p90) REVERT: B 35 ILE cc_start: 0.8395 (mt) cc_final: 0.8026 (pt) REVERT: B 55 VAL cc_start: 0.8404 (t) cc_final: 0.8167 (t) REVERT: B 63 ARG cc_start: 0.7793 (mtm180) cc_final: 0.6690 (ppt170) REVERT: B 77 ILE cc_start: 0.8027 (mt) cc_final: 0.7731 (tt) REVERT: B 81 ASP cc_start: 0.7936 (p0) cc_final: 0.7179 (m-30) REVERT: B 83 MET cc_start: 0.8423 (mmm) cc_final: 0.7368 (mmm) REVERT: B 84 GLU cc_start: 0.8288 (tt0) cc_final: 0.7781 (tt0) REVERT: B 87 TRP cc_start: 0.7852 (m-10) cc_final: 0.7631 (m-90) REVERT: B 88 HIS cc_start: 0.7964 (t-90) cc_final: 0.7678 (t-170) REVERT: B 94 GLU cc_start: 0.7842 (tp30) cc_final: 0.7482 (tp30) REVERT: B 95 LEU cc_start: 0.8776 (mt) cc_final: 0.8548 (mt) REVERT: B 100 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7759 (mm-30) REVERT: B 101 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8009 (mm-30) REVERT: B 102 HIS cc_start: 0.8313 (m-70) cc_final: 0.7646 (m90) REVERT: B 105 LEU cc_start: 0.8636 (tt) cc_final: 0.8385 (tp) REVERT: B 106 LEU cc_start: 0.7963 (mt) cc_final: 0.7613 (mp) REVERT: B 111 LEU cc_start: 0.8067 (mt) cc_final: 0.7830 (mp) REVERT: B 114 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7647 (mtpt) REVERT: B 117 ARG cc_start: 0.8456 (ttm110) cc_final: 0.8083 (ttm170) REVERT: B 118 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7506 (mt-10) REVERT: B 119 LYS cc_start: 0.8545 (tptt) cc_final: 0.7718 (mmmt) REVERT: B 120 MET cc_start: 0.8713 (ttm) cc_final: 0.7608 (ttm) REVERT: B 124 MET cc_start: 0.8514 (mmm) cc_final: 0.7522 (mmm) REVERT: B 129 ASN cc_start: 0.7395 (t0) cc_final: 0.6794 (t0) REVERT: B 135 VAL cc_start: 0.8664 (t) cc_final: 0.7871 (p) REVERT: B 143 LEU cc_start: 0.8594 (tp) cc_final: 0.8270 (tp) REVERT: B 177 MET cc_start: 0.6912 (mtt) cc_final: 0.6670 (mtm) REVERT: B 181 LEU cc_start: 0.7852 (tp) cc_final: 0.7496 (mp) REVERT: B 184 ARG cc_start: 0.7452 (tpp80) cc_final: 0.6971 (mtp85) REVERT: B 186 LEU cc_start: 0.8493 (mt) cc_final: 0.8197 (mm) REVERT: B 187 THR cc_start: 0.8494 (m) cc_final: 0.8091 (p) REVERT: B 188 ASP cc_start: 0.7742 (m-30) cc_final: 0.7277 (m-30) REVERT: B 190 LEU cc_start: 0.8514 (tp) cc_final: 0.7682 (tp) REVERT: B 194 LEU cc_start: 0.8416 (mt) cc_final: 0.7907 (mt) REVERT: B 204 THR cc_start: 0.7974 (m) cc_final: 0.6334 (p) REVERT: B 209 ILE cc_start: 0.8659 (mm) cc_final: 0.8102 (mm) REVERT: B 210 VAL cc_start: 0.8876 (t) cc_final: 0.8673 (t) REVERT: B 211 ARG cc_start: 0.7673 (ttp80) cc_final: 0.7405 (ttp80) REVERT: B 212 ASP cc_start: 0.8265 (m-30) cc_final: 0.7478 (m-30) REVERT: B 213 ILE cc_start: 0.8657 (mt) cc_final: 0.8356 (mt) REVERT: B 215 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6136 (mt-10) REVERT: B 216 LYS cc_start: 0.8102 (mttt) cc_final: 0.7766 (mttt) REVERT: B 241 TYR cc_start: 0.8285 (t80) cc_final: 0.7991 (t80) REVERT: B 242 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7532 (tm-30) REVERT: B 243 LEU cc_start: 0.8031 (mt) cc_final: 0.7566 (mt) REVERT: B 247 GLN cc_start: 0.7026 (mp10) cc_final: 0.6357 (mm-40) REVERT: B 260 GLU cc_start: 0.7829 (tp30) cc_final: 0.7188 (tp30) REVERT: B 262 LEU cc_start: 0.8207 (mt) cc_final: 0.7998 (mt) REVERT: B 272 SER cc_start: 0.7938 (m) cc_final: 0.7531 (t) REVERT: B 281 ASN cc_start: 0.7893 (m-40) cc_final: 0.7576 (m-40) REVERT: B 283 ILE cc_start: 0.7769 (mt) cc_final: 0.7485 (mt) REVERT: B 287 ASP cc_start: 0.7543 (m-30) cc_final: 0.7196 (m-30) REVERT: B 293 ASP cc_start: 0.7521 (m-30) cc_final: 0.7248 (m-30) REVERT: B 295 TYR cc_start: 0.6750 (m-80) cc_final: 0.6466 (m-80) REVERT: B 300 MET cc_start: 0.7744 (mmm) cc_final: 0.7019 (mmp) REVERT: B 313 ARG cc_start: 0.8140 (tpt-90) cc_final: 0.7863 (tpt170) REVERT: B 314 MET cc_start: 0.7712 (tpp) cc_final: 0.7159 (tpp) REVERT: B 341 TRP cc_start: 0.7961 (t60) cc_final: 0.7624 (t60) REVERT: B 347 LEU cc_start: 0.7662 (tp) cc_final: 0.7433 (tp) REVERT: B 357 TRP cc_start: 0.7875 (m100) cc_final: 0.7573 (m100) REVERT: C 31 PHE cc_start: 0.8413 (p90) cc_final: 0.7973 (p90) REVERT: C 34 ILE cc_start: 0.7984 (mt) cc_final: 0.7571 (mt) REVERT: C 50 LYS cc_start: 0.7707 (mttt) cc_final: 0.7433 (mttm) REVERT: C 53 TYR cc_start: 0.7168 (m-80) cc_final: 0.6867 (m-80) REVERT: C 61 LYS cc_start: 0.8269 (mttm) cc_final: 0.7542 (mttm) REVERT: C 67 LEU cc_start: 0.8085 (mt) cc_final: 0.7852 (mt) REVERT: C 78 ASN cc_start: 0.7011 (t0) cc_final: 0.6358 (t0) REVERT: C 82 MET cc_start: 0.7398 (mmm) cc_final: 0.7026 (mmm) REVERT: C 85 ILE cc_start: 0.8369 (pt) cc_final: 0.7832 (pt) REVERT: C 90 PHE cc_start: 0.7842 (m-80) cc_final: 0.7363 (m-80) REVERT: C 102 PRO cc_start: 0.6616 (Cg_exo) cc_final: 0.5948 (Cg_endo) REVERT: C 110 LEU cc_start: 0.8009 (mt) cc_final: 0.7697 (mp) REVERT: C 111 ASN cc_start: 0.7383 (m-40) cc_final: 0.7164 (m-40) REVERT: C 118 LYS cc_start: 0.8370 (tptt) cc_final: 0.7846 (tptt) REVERT: C 119 MET cc_start: 0.8428 (ttm) cc_final: 0.7976 (ttm) REVERT: C 121 GLN cc_start: 0.8399 (tt0) cc_final: 0.7948 (tm-30) REVERT: C 123 MET cc_start: 0.8143 (tpp) cc_final: 0.7428 (tpp) REVERT: C 137 GLN cc_start: 0.7787 (mt0) cc_final: 0.7301 (mp10) REVERT: C 148 THR cc_start: 0.7746 (p) cc_final: 0.7503 (p) REVERT: C 151 ILE cc_start: 0.8681 (tt) cc_final: 0.8446 (tt) REVERT: C 165 ILE cc_start: 0.8393 (mt) cc_final: 0.8188 (mm) REVERT: C 166 TYR cc_start: 0.7958 (t80) cc_final: 0.7258 (t80) REVERT: C 175 ILE cc_start: 0.7542 (pt) cc_final: 0.6771 (mt) REVERT: C 176 MET cc_start: 0.6131 (mtt) cc_final: 0.5632 (mtt) REVERT: C 190 MET cc_start: 0.7899 (mtm) cc_final: 0.7458 (mtm) REVERT: C 205 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7368 (mt-10) REVERT: C 212 ILE cc_start: 0.8862 (mt) cc_final: 0.8581 (mt) REVERT: C 215 LYS cc_start: 0.8792 (mttm) cc_final: 0.8322 (mmmm) REVERT: C 247 VAL cc_start: 0.7898 (t) cc_final: 0.7688 (p) REVERT: C 259 GLU cc_start: 0.7437 (tp30) cc_final: 0.7150 (tp30) REVERT: C 261 LEU cc_start: 0.8144 (mt) cc_final: 0.7781 (mp) REVERT: C 271 SER cc_start: 0.8689 (m) cc_final: 0.8214 (t) REVERT: C 277 THR cc_start: 0.7014 (p) cc_final: 0.6489 (p) REVERT: C 281 SER cc_start: 0.8345 (t) cc_final: 0.7666 (p) REVERT: C 283 MET cc_start: 0.7711 (mmm) cc_final: 0.7504 (mmm) REVERT: C 291 LYS cc_start: 0.8557 (mtpt) cc_final: 0.8012 (mptt) REVERT: C 299 MET cc_start: 0.7367 (mmm) cc_final: 0.7010 (mmm) REVERT: C 305 MET cc_start: 0.7590 (mmm) cc_final: 0.6906 (mmt) REVERT: C 314 GLN cc_start: 0.8908 (tt0) cc_final: 0.8684 (tt0) REVERT: C 324 THR cc_start: 0.8547 (p) cc_final: 0.8179 (p) REVERT: C 328 LYS cc_start: 0.8424 (mttt) cc_final: 0.8019 (mttt) REVERT: C 334 GLU cc_start: 0.7836 (mm-30) cc_final: 0.6966 (tp30) REVERT: C 337 TYR cc_start: 0.6907 (m-10) cc_final: 0.6689 (m-10) REVERT: C 349 LEU cc_start: 0.8503 (tp) cc_final: 0.8023 (tp) REVERT: D 8 LEU cc_start: 0.8314 (mt) cc_final: 0.7825 (mm) REVERT: D 9 VAL cc_start: 0.7507 (m) cc_final: 0.7227 (p) REVERT: D 24 ASP cc_start: 0.6226 (m-30) cc_final: 0.5908 (m-30) REVERT: D 34 ILE cc_start: 0.8678 (mt) cc_final: 0.8333 (mm) REVERT: D 47 MET cc_start: 0.7080 (ttm) cc_final: 0.6872 (ttm) REVERT: D 54 VAL cc_start: 0.8303 (t) cc_final: 0.7984 (m) REVERT: D 76 ILE cc_start: 0.8068 (mt) cc_final: 0.7389 (mt) REVERT: D 79 TRP cc_start: 0.7738 (m100) cc_final: 0.6902 (m100) REVERT: D 82 MET cc_start: 0.7725 (mmm) cc_final: 0.7501 (mmm) REVERT: D 84 LYS cc_start: 0.8580 (tttt) cc_final: 0.8186 (tttt) REVERT: D 86 TRP cc_start: 0.7658 (m-10) cc_final: 0.7260 (m-10) REVERT: D 87 HIS cc_start: 0.8366 (t-90) cc_final: 0.8144 (t-90) REVERT: D 92 ASN cc_start: 0.7033 (m-40) cc_final: 0.6779 (m-40) REVERT: D 99 GLU cc_start: 0.7755 (mp0) cc_final: 0.7538 (mp0) REVERT: D 100 GLU cc_start: 0.7978 (tp30) cc_final: 0.7332 (tp30) REVERT: D 116 ARG cc_start: 0.8272 (ttm110) cc_final: 0.7921 (ttm110) REVERT: D 118 LYS cc_start: 0.8937 (tptt) cc_final: 0.8160 (tptt) REVERT: D 122 ILE cc_start: 0.8582 (mt) cc_final: 0.7215 (tp) REVERT: D 123 MET cc_start: 0.8018 (mmt) cc_final: 0.7750 (mmp) REVERT: D 133 TYR cc_start: 0.7828 (t80) cc_final: 0.7031 (t80) REVERT: D 134 VAL cc_start: 0.8079 (t) cc_final: 0.7505 (p) REVERT: D 153 LEU cc_start: 0.8229 (tp) cc_final: 0.7147 (pp) REVERT: D 159 VAL cc_start: 0.7585 (p) cc_final: 0.6996 (m) REVERT: D 166 TYR cc_start: 0.8012 (t80) cc_final: 0.7725 (t80) REVERT: D 175 ILE cc_start: 0.7479 (pt) cc_final: 0.6311 (mp) REVERT: D 176 MET cc_start: 0.6381 (mtp) cc_final: 0.5467 (mtp) REVERT: D 184 ASP cc_start: 0.8188 (m-30) cc_final: 0.7881 (m-30) REVERT: D 190 MET cc_start: 0.8005 (mtm) cc_final: 0.7770 (mtt) REVERT: D 206 ARG cc_start: 0.8194 (ttm170) cc_final: 0.7812 (ttm-80) REVERT: D 211 ASP cc_start: 0.7894 (m-30) cc_final: 0.7463 (m-30) REVERT: D 222 ASP cc_start: 0.8422 (t0) cc_final: 0.7692 (t70) REVERT: D 238 LYS cc_start: 0.7406 (mmmt) cc_final: 0.7180 (mmtm) REVERT: D 253 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7091 (mp0) REVERT: D 274 ILE cc_start: 0.7693 (pt) cc_final: 0.7456 (pt) REVERT: D 275 HIS cc_start: 0.7883 (p-80) cc_final: 0.7295 (p-80) REVERT: D 280 ASN cc_start: 0.7280 (t0) cc_final: 0.6918 (t0) REVERT: D 281 SER cc_start: 0.8216 (p) cc_final: 0.7902 (m) REVERT: D 282 ILE cc_start: 0.8202 (mt) cc_final: 0.7858 (mt) REVERT: D 294 TYR cc_start: 0.7031 (m-80) cc_final: 0.6707 (m-80) REVERT: D 313 MET cc_start: 0.8644 (tpt) cc_final: 0.7897 (tpt) REVERT: D 315 LYS cc_start: 0.8562 (ttpp) cc_final: 0.8279 (ttpp) REVERT: D 320 LEU cc_start: 0.8362 (mt) cc_final: 0.7767 (mt) REVERT: D 324 THR cc_start: 0.7883 (p) cc_final: 0.7637 (t) REVERT: D 359 LYS cc_start: 0.7966 (tttt) cc_final: 0.7681 (tttt) REVERT: D 361 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7661 (mt-10) outliers start: 3 outliers final: 2 residues processed: 805 average time/residue: 0.1428 time to fit residues: 158.2625 Evaluate side-chains 756 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 754 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0370 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 264 GLN A 307 HIS A 395 GLN A 424 HIS A 458 ASN A 560 GLN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 HIS B 116 ASN B 372 HIS C 101 HIS C 111 ASN C 162 ASN C 353 GLN D 40 HIS D 73 HIS D 92 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.109868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.089589 restraints weight = 40676.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.093210 restraints weight = 22911.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.095700 restraints weight = 14738.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.097469 restraints weight = 10311.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.098661 restraints weight = 7703.856| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15117 Z= 0.143 Angle : 0.669 12.640 20466 Z= 0.341 Chirality : 0.044 0.186 2241 Planarity : 0.005 0.041 2622 Dihedral : 11.477 159.738 2062 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.06 % Allowed : 1.89 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.09 (0.19), residues: 1838 helix: 0.51 (0.17), residues: 843 sheet: -0.47 (0.29), residues: 299 loop : -0.02 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 700 TYR 0.033 0.002 TYR A 477 PHE 0.020 0.002 PHE B 128 TRP 0.024 0.002 TRP A 414 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00295 (15117) covalent geometry : angle 0.66942 (20466) hydrogen bonds : bond 0.04569 ( 729) hydrogen bonds : angle 5.12586 ( 2013) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 805 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8731 (mttp) cc_final: 0.8318 (mttp) REVERT: A 88 ASN cc_start: 0.8856 (m110) cc_final: 0.8488 (m-40) REVERT: A 125 ASN cc_start: 0.8048 (t0) cc_final: 0.7826 (m-40) REVERT: A 132 MET cc_start: 0.3369 (ppp) cc_final: 0.2933 (ppp) REVERT: A 140 PHE cc_start: 0.8293 (m-10) cc_final: 0.7879 (m-10) REVERT: A 148 LYS cc_start: 0.9045 (tttt) cc_final: 0.8763 (tptp) REVERT: A 149 GLN cc_start: 0.8431 (mt0) cc_final: 0.8121 (mm-40) REVERT: A 150 MET cc_start: 0.7911 (ttp) cc_final: 0.7508 (ttp) REVERT: A 159 ILE cc_start: 0.8030 (mp) cc_final: 0.7825 (tp) REVERT: A 174 LYS cc_start: 0.8463 (pttp) cc_final: 0.7817 (ttpp) REVERT: A 178 ARG cc_start: 0.8698 (mmm-85) cc_final: 0.8447 (mmm-85) REVERT: A 210 LYS cc_start: 0.6998 (tmtt) cc_final: 0.6280 (tptp) REVERT: A 219 ARG cc_start: 0.6900 (mmp-170) cc_final: 0.6445 (mmm-85) REVERT: A 223 TYR cc_start: 0.8028 (t80) cc_final: 0.7549 (t80) REVERT: A 228 PHE cc_start: 0.7708 (m-80) cc_final: 0.7446 (m-80) REVERT: A 251 PHE cc_start: 0.7011 (t80) cc_final: 0.6768 (t80) REVERT: A 259 TYR cc_start: 0.6901 (m-80) cc_final: 0.6401 (m-10) REVERT: A 273 GLU cc_start: 0.8754 (mp0) cc_final: 0.7386 (tm-30) REVERT: A 285 PHE cc_start: 0.7898 (m-80) cc_final: 0.7427 (m-80) REVERT: A 307 HIS cc_start: 0.8553 (m90) cc_final: 0.7966 (m-70) REVERT: A 312 CYS cc_start: 0.8604 (m) cc_final: 0.8287 (m) REVERT: A 319 GLU cc_start: 0.8111 (tt0) cc_final: 0.7707 (tp30) REVERT: A 323 MET cc_start: 0.8273 (mmp) cc_final: 0.7638 (mmp) REVERT: A 327 ARG cc_start: 0.8020 (ttt180) cc_final: 0.7352 (ptm-80) REVERT: A 328 ILE cc_start: 0.8473 (mt) cc_final: 0.8232 (mt) REVERT: A 354 HIS cc_start: 0.7653 (t70) cc_final: 0.7047 (t-170) REVERT: A 362 ASP cc_start: 0.8719 (m-30) cc_final: 0.8441 (m-30) REVERT: A 369 GLU cc_start: 0.8178 (mp0) cc_final: 0.7741 (mp0) REVERT: A 371 MET cc_start: 0.8288 (mmm) cc_final: 0.8085 (mmm) REVERT: A 372 CYS cc_start: 0.8971 (t) cc_final: 0.8356 (p) REVERT: A 389 LYS cc_start: 0.8619 (mmtp) cc_final: 0.8242 (tppt) REVERT: A 395 GLN cc_start: 0.8354 (mm110) cc_final: 0.7570 (mt0) REVERT: A 405 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8184 (mtmt) REVERT: A 408 TYR cc_start: 0.8484 (t80) cc_final: 0.8030 (t80) REVERT: A 414 TRP cc_start: 0.8197 (t60) cc_final: 0.7577 (t60) REVERT: A 427 VAL cc_start: 0.8345 (t) cc_final: 0.8120 (p) REVERT: A 433 ILE cc_start: 0.7627 (mt) cc_final: 0.7374 (mp) REVERT: A 452 PHE cc_start: 0.8517 (t80) cc_final: 0.8311 (t80) REVERT: A 453 CYS cc_start: 0.8731 (m) cc_final: 0.8389 (p) REVERT: A 455 ASN cc_start: 0.8917 (m-40) cc_final: 0.7870 (m110) REVERT: A 456 TYR cc_start: 0.8126 (t80) cc_final: 0.7658 (t80) REVERT: A 458 ASN cc_start: 0.8637 (m-40) cc_final: 0.8341 (m110) REVERT: A 459 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 460 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8284 (mmmt) REVERT: A 461 LEU cc_start: 0.8898 (mt) cc_final: 0.8648 (tp) REVERT: A 466 ASN cc_start: 0.8557 (m-40) cc_final: 0.8103 (m-40) REVERT: A 469 VAL cc_start: 0.8790 (t) cc_final: 0.8562 (m) REVERT: A 471 LYS cc_start: 0.9251 (tttt) cc_final: 0.9026 (tptp) REVERT: A 472 LEU cc_start: 0.8631 (tp) cc_final: 0.8353 (tp) REVERT: A 475 GLU cc_start: 0.8742 (tp30) cc_final: 0.8313 (tp30) REVERT: A 499 ILE cc_start: 0.8762 (mt) cc_final: 0.8513 (mm) REVERT: A 500 GLU cc_start: 0.7911 (pt0) cc_final: 0.6834 (pt0) REVERT: A 508 LEU cc_start: 0.8352 (mt) cc_final: 0.8071 (mt) REVERT: A 509 LEU cc_start: 0.8045 (tp) cc_final: 0.7802 (tp) REVERT: A 511 GLU cc_start: 0.8205 (tt0) cc_final: 0.7160 (tt0) REVERT: A 526 LYS cc_start: 0.8851 (mttt) cc_final: 0.8486 (mmtt) REVERT: A 527 LEU cc_start: 0.8732 (mt) cc_final: 0.8496 (mt) REVERT: A 533 ASN cc_start: 0.7938 (t0) cc_final: 0.7735 (t0) REVERT: A 548 PHE cc_start: 0.7969 (p90) cc_final: 0.7706 (p90) REVERT: A 552 HIS cc_start: 0.6476 (m-70) cc_final: 0.5520 (m-70) REVERT: A 555 ASP cc_start: 0.7017 (t0) cc_final: 0.6677 (t0) REVERT: A 557 VAL cc_start: 0.7405 (t) cc_final: 0.5777 (t) REVERT: A 558 GLU cc_start: 0.7343 (tt0) cc_final: 0.7131 (tm-30) REVERT: A 573 PHE cc_start: 0.7580 (m-80) cc_final: 0.7360 (m-80) REVERT: A 577 ILE cc_start: 0.8492 (mm) cc_final: 0.8248 (mm) REVERT: A 578 LYS cc_start: 0.8795 (mmtp) cc_final: 0.8439 (mmtp) REVERT: A 585 PHE cc_start: 0.6739 (t80) cc_final: 0.6176 (t80) REVERT: A 632 LYS cc_start: 0.9120 (mtmt) cc_final: 0.8771 (mtmt) REVERT: A 641 ASN cc_start: 0.8838 (m-40) cc_final: 0.8399 (m110) REVERT: A 644 HIS cc_start: 0.7660 (m170) cc_final: 0.7404 (m170) REVERT: A 647 MET cc_start: 0.7953 (tpt) cc_final: 0.7465 (tpt) REVERT: A 654 THR cc_start: 0.7699 (m) cc_final: 0.7427 (m) REVERT: A 675 LYS cc_start: 0.8479 (mmtp) cc_final: 0.8199 (mptt) REVERT: A 700 ARG cc_start: 0.6854 (ttp80) cc_final: 0.6540 (tmm160) REVERT: B 7 THR cc_start: 0.8723 (m) cc_final: 0.8518 (m) REVERT: B 9 LEU cc_start: 0.8066 (mt) cc_final: 0.7803 (mt) REVERT: B 32 PHE cc_start: 0.7365 (p90) cc_final: 0.6935 (p90) REVERT: B 35 ILE cc_start: 0.8394 (mt) cc_final: 0.8017 (mm) REVERT: B 51 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7679 (mtpp) REVERT: B 77 ILE cc_start: 0.8178 (mt) cc_final: 0.7868 (mt) REVERT: B 81 ASP cc_start: 0.8324 (p0) cc_final: 0.6663 (m-30) REVERT: B 83 MET cc_start: 0.8441 (mmm) cc_final: 0.7214 (mmm) REVERT: B 84 GLU cc_start: 0.8353 (tt0) cc_final: 0.8013 (tt0) REVERT: B 85 LYS cc_start: 0.8851 (mttm) cc_final: 0.8532 (mttm) REVERT: B 87 TRP cc_start: 0.7943 (m-10) cc_final: 0.7592 (m-90) REVERT: B 88 HIS cc_start: 0.8201 (t-90) cc_final: 0.7942 (t-170) REVERT: B 93 ASN cc_start: 0.7749 (m-40) cc_final: 0.7480 (m-40) REVERT: B 101 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8130 (mm-30) REVERT: B 102 HIS cc_start: 0.8353 (m-70) cc_final: 0.7849 (m90) REVERT: B 108 GLU cc_start: 0.7175 (mt-10) cc_final: 0.5295 (mt-10) REVERT: B 117 ARG cc_start: 0.8434 (ttm110) cc_final: 0.7478 (ttm110) REVERT: B 119 LYS cc_start: 0.8546 (tptt) cc_final: 0.7875 (mmmt) REVERT: B 120 MET cc_start: 0.8620 (ttm) cc_final: 0.7946 (ttm) REVERT: B 123 ILE cc_start: 0.8794 (mt) cc_final: 0.8290 (tp) REVERT: B 128 PHE cc_start: 0.7784 (m-10) cc_final: 0.7432 (m-10) REVERT: B 134 TYR cc_start: 0.8138 (t80) cc_final: 0.7918 (t80) REVERT: B 144 TYR cc_start: 0.7573 (m-80) cc_final: 0.7262 (m-10) REVERT: B 180 ASP cc_start: 0.6676 (m-30) cc_final: 0.6175 (t70) REVERT: B 181 LEU cc_start: 0.8050 (tp) cc_final: 0.7744 (mm) REVERT: B 184 ARG cc_start: 0.7639 (tpp80) cc_final: 0.6985 (mtp85) REVERT: B 185 ASP cc_start: 0.8393 (m-30) cc_final: 0.8064 (m-30) REVERT: B 186 LEU cc_start: 0.8538 (mt) cc_final: 0.8249 (mm) REVERT: B 187 THR cc_start: 0.8548 (m) cc_final: 0.8136 (p) REVERT: B 188 ASP cc_start: 0.7916 (m-30) cc_final: 0.7326 (m-30) REVERT: B 190 LEU cc_start: 0.8454 (tp) cc_final: 0.7797 (tp) REVERT: B 194 LEU cc_start: 0.8644 (mt) cc_final: 0.8155 (mt) REVERT: B 208 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7643 (mm-30) REVERT: B 209 ILE cc_start: 0.8758 (mm) cc_final: 0.8377 (mm) REVERT: B 211 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7658 (ttp80) REVERT: B 212 ASP cc_start: 0.8331 (m-30) cc_final: 0.7628 (m-30) REVERT: B 213 ILE cc_start: 0.8819 (mt) cc_final: 0.8519 (mt) REVERT: B 215 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6829 (mt-10) REVERT: B 243 LEU cc_start: 0.7912 (mt) cc_final: 0.7487 (mt) REVERT: B 247 GLN cc_start: 0.7544 (mm110) cc_final: 0.6939 (tp40) REVERT: B 254 GLU cc_start: 0.8245 (mp0) cc_final: 0.7832 (mp0) REVERT: B 255 ARG cc_start: 0.7758 (mtp85) cc_final: 0.7506 (mtp85) REVERT: B 257 ARG cc_start: 0.7891 (mtp180) cc_final: 0.7630 (mtp85) REVERT: B 263 PHE cc_start: 0.8583 (m-10) cc_final: 0.8322 (m-80) REVERT: B 283 ILE cc_start: 0.7582 (mt) cc_final: 0.7319 (tt) REVERT: B 295 TYR cc_start: 0.6849 (m-80) cc_final: 0.6573 (m-80) REVERT: B 300 MET cc_start: 0.7731 (mmm) cc_final: 0.7162 (mmp) REVERT: B 314 MET cc_start: 0.7673 (tpp) cc_final: 0.7204 (tpp) REVERT: B 350 LEU cc_start: 0.8136 (mp) cc_final: 0.7851 (mp) REVERT: C 9 VAL cc_start: 0.7722 (t) cc_final: 0.7508 (p) REVERT: C 12 ASN cc_start: 0.7546 (m110) cc_final: 0.6779 (m110) REVERT: C 16 LEU cc_start: 0.6969 (tp) cc_final: 0.6643 (tp) REVERT: C 17 VAL cc_start: 0.7840 (m) cc_final: 0.7422 (p) REVERT: C 18 LYS cc_start: 0.7124 (mppt) cc_final: 0.6589 (mppt) REVERT: C 31 PHE cc_start: 0.8392 (p90) cc_final: 0.8181 (p90) REVERT: C 34 ILE cc_start: 0.7911 (mt) cc_final: 0.7689 (mt) REVERT: C 50 LYS cc_start: 0.7967 (mttt) cc_final: 0.7583 (mttt) REVERT: C 67 LEU cc_start: 0.7938 (mt) cc_final: 0.7698 (mt) REVERT: C 78 ASN cc_start: 0.7280 (t0) cc_final: 0.6627 (t0) REVERT: C 81 ASP cc_start: 0.7913 (m-30) cc_final: 0.7685 (m-30) REVERT: C 82 MET cc_start: 0.8110 (mmm) cc_final: 0.7621 (mmm) REVERT: C 85 ILE cc_start: 0.8659 (pt) cc_final: 0.8417 (pt) REVERT: C 87 HIS cc_start: 0.8652 (t-90) cc_final: 0.8214 (t-90) REVERT: C 92 ASN cc_start: 0.7977 (m-40) cc_final: 0.7727 (m-40) REVERT: C 105 LEU cc_start: 0.7966 (mt) cc_final: 0.7418 (mt) REVERT: C 111 ASN cc_start: 0.7906 (m110) cc_final: 0.7399 (m-40) REVERT: C 113 LYS cc_start: 0.7949 (mttp) cc_final: 0.7740 (mttp) REVERT: C 115 ASN cc_start: 0.7755 (t0) cc_final: 0.7376 (t0) REVERT: C 116 ARG cc_start: 0.8401 (ttm110) cc_final: 0.7742 (ttm170) REVERT: C 118 LYS cc_start: 0.8293 (tptt) cc_final: 0.8076 (tptt) REVERT: C 119 MET cc_start: 0.8550 (ttm) cc_final: 0.7953 (ttm) REVERT: C 121 GLN cc_start: 0.8535 (tt0) cc_final: 0.7738 (tm-30) REVERT: C 123 MET cc_start: 0.8020 (tpp) cc_final: 0.7478 (tpp) REVERT: C 128 ASN cc_start: 0.8480 (m-40) cc_final: 0.8223 (m-40) REVERT: C 136 ILE cc_start: 0.8149 (mm) cc_final: 0.7930 (mm) REVERT: C 137 GLN cc_start: 0.7745 (mt0) cc_final: 0.7310 (mp10) REVERT: C 139 VAL cc_start: 0.8600 (m) cc_final: 0.8346 (p) REVERT: C 148 THR cc_start: 0.7893 (p) cc_final: 0.7636 (p) REVERT: C 152 VAL cc_start: 0.8239 (t) cc_final: 0.7862 (p) REVERT: C 165 ILE cc_start: 0.8531 (mt) cc_final: 0.8155 (mm) REVERT: C 166 TYR cc_start: 0.7970 (t80) cc_final: 0.7635 (t80) REVERT: C 175 ILE cc_start: 0.7617 (pt) cc_final: 0.6839 (mt) REVERT: C 176 MET cc_start: 0.6479 (mtt) cc_final: 0.6124 (mtt) REVERT: C 205 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7138 (mt-10) REVERT: C 208 ILE cc_start: 0.8503 (mp) cc_final: 0.8284 (mp) REVERT: C 209 VAL cc_start: 0.8634 (t) cc_final: 0.8386 (t) REVERT: C 210 ARG cc_start: 0.8422 (ttp-110) cc_final: 0.7738 (ttp-110) REVERT: C 212 ILE cc_start: 0.8828 (mt) cc_final: 0.8601 (mt) REVERT: C 213 LYS cc_start: 0.8607 (ttpt) cc_final: 0.8202 (ttpp) REVERT: C 215 LYS cc_start: 0.8818 (mttm) cc_final: 0.8514 (mtpp) REVERT: C 222 ASP cc_start: 0.7054 (t0) cc_final: 0.6530 (t0) REVERT: C 225 ASN cc_start: 0.8665 (m110) cc_final: 0.8453 (m-40) REVERT: C 238 LYS cc_start: 0.8059 (mmtm) cc_final: 0.7655 (mmtt) REVERT: C 269 MET cc_start: 0.7140 (mtm) cc_final: 0.6700 (mtm) REVERT: C 271 SER cc_start: 0.8693 (m) cc_final: 0.8226 (t) REVERT: C 278 THR cc_start: 0.7860 (m) cc_final: 0.7097 (p) REVERT: C 279 TYR cc_start: 0.7857 (t80) cc_final: 0.7586 (t80) REVERT: C 283 MET cc_start: 0.7679 (mmm) cc_final: 0.7249 (mmp) REVERT: C 291 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8204 (mptt) REVERT: C 297 ASN cc_start: 0.8077 (m-40) cc_final: 0.7689 (m-40) REVERT: C 299 MET cc_start: 0.8006 (mmm) cc_final: 0.7611 (mmm) REVERT: C 305 MET cc_start: 0.7387 (mmm) cc_final: 0.7058 (mmt) REVERT: C 314 GLN cc_start: 0.8843 (tt0) cc_final: 0.8621 (tt0) REVERT: C 326 LYS cc_start: 0.7720 (mmtt) cc_final: 0.7411 (mmtt) REVERT: C 328 LYS cc_start: 0.8417 (mttt) cc_final: 0.7919 (mttt) REVERT: C 330 ILE cc_start: 0.8402 (mp) cc_final: 0.8200 (mp) REVERT: C 334 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7447 (tp30) REVERT: C 337 TYR cc_start: 0.6739 (m-10) cc_final: 0.6388 (m-10) REVERT: C 349 LEU cc_start: 0.8517 (tp) cc_final: 0.8244 (tp) REVERT: C 356 TRP cc_start: 0.6050 (m100) cc_final: 0.5482 (m100) REVERT: C 371 HIS cc_start: 0.7772 (m-70) cc_final: 0.6856 (m-70) REVERT: C 372 ARG cc_start: 0.8001 (mtm-85) cc_final: 0.7784 (mtm-85) REVERT: D 24 ASP cc_start: 0.6466 (m-30) cc_final: 0.6001 (m-30) REVERT: D 41 GLN cc_start: 0.7031 (tp40) cc_final: 0.6748 (tp40) REVERT: D 44 MET cc_start: 0.6270 (mmm) cc_final: 0.5985 (mmm) REVERT: D 47 MET cc_start: 0.6769 (ttm) cc_final: 0.6482 (ttm) REVERT: D 54 VAL cc_start: 0.8244 (t) cc_final: 0.7819 (m) REVERT: D 64 ILE cc_start: 0.8357 (mm) cc_final: 0.8132 (mm) REVERT: D 76 ILE cc_start: 0.8028 (mt) cc_final: 0.7244 (mt) REVERT: D 78 ASN cc_start: 0.8051 (t0) cc_final: 0.7734 (t0) REVERT: D 79 TRP cc_start: 0.7613 (m100) cc_final: 0.6830 (m100) REVERT: D 84 LYS cc_start: 0.8597 (tttt) cc_final: 0.8315 (tptt) REVERT: D 92 ASN cc_start: 0.7204 (m110) cc_final: 0.6957 (m110) REVERT: D 95 ARG cc_start: 0.8511 (ptp90) cc_final: 0.8191 (ptp90) REVERT: D 99 GLU cc_start: 0.7808 (mp0) cc_final: 0.7588 (mp0) REVERT: D 100 GLU cc_start: 0.7908 (tp30) cc_final: 0.7405 (tp30) REVERT: D 107 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6262 (mt-10) REVERT: D 116 ARG cc_start: 0.8408 (ttm110) cc_final: 0.7986 (ttm110) REVERT: D 123 MET cc_start: 0.8204 (mmp) cc_final: 0.7984 (mmp) REVERT: D 133 TYR cc_start: 0.7924 (t80) cc_final: 0.7069 (t80) REVERT: D 134 VAL cc_start: 0.8182 (t) cc_final: 0.7799 (p) REVERT: D 153 LEU cc_start: 0.8123 (tp) cc_final: 0.7408 (tt) REVERT: D 165 ILE cc_start: 0.7886 (mm) cc_final: 0.7628 (tp) REVERT: D 175 ILE cc_start: 0.7780 (pt) cc_final: 0.6731 (mp) REVERT: D 176 MET cc_start: 0.6569 (mtp) cc_final: 0.5978 (mtp) REVERT: D 183 ARG cc_start: 0.7886 (ttm170) cc_final: 0.7290 (ttm-80) REVERT: D 184 ASP cc_start: 0.8228 (m-30) cc_final: 0.7997 (m-30) REVERT: D 188 TYR cc_start: 0.7576 (t80) cc_final: 0.7305 (t80) REVERT: D 190 MET cc_start: 0.7793 (mtm) cc_final: 0.7478 (mtt) REVERT: D 205 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7188 (mt-10) REVERT: D 206 ARG cc_start: 0.8342 (ttm170) cc_final: 0.8101 (ttm-80) REVERT: D 207 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7495 (mm-30) REVERT: D 210 ARG cc_start: 0.8351 (ttp80) cc_final: 0.8127 (tmm-80) REVERT: D 211 ASP cc_start: 0.7986 (m-30) cc_final: 0.7118 (m-30) REVERT: D 222 ASP cc_start: 0.8454 (t0) cc_final: 0.8135 (t70) REVERT: D 223 PHE cc_start: 0.7414 (t80) cc_final: 0.7204 (t80) REVERT: D 238 LYS cc_start: 0.7705 (mmmt) cc_final: 0.7301 (mmmm) REVERT: D 253 GLU cc_start: 0.7423 (mp0) cc_final: 0.7088 (mp0) REVERT: D 255 PHE cc_start: 0.8062 (p90) cc_final: 0.7802 (p90) REVERT: D 256 ARG cc_start: 0.7899 (mtp180) cc_final: 0.7147 (mtp180) REVERT: D 279 TYR cc_start: 0.7874 (t80) cc_final: 0.7622 (t80) REVERT: D 280 ASN cc_start: 0.7496 (t0) cc_final: 0.6899 (t0) REVERT: D 294 TYR cc_start: 0.7089 (m-80) cc_final: 0.6614 (m-80) REVERT: D 299 MET cc_start: 0.7566 (mmm) cc_final: 0.7364 (mmm) REVERT: D 303 THR cc_start: 0.7724 (m) cc_final: 0.7166 (p) REVERT: D 313 MET cc_start: 0.8557 (tpt) cc_final: 0.7818 (tpt) REVERT: D 315 LYS cc_start: 0.8838 (ttpp) cc_final: 0.8311 (ttpp) REVERT: D 316 GLU cc_start: 0.7761 (mm-30) cc_final: 0.6956 (mm-30) REVERT: D 320 LEU cc_start: 0.8729 (mt) cc_final: 0.8310 (mt) REVERT: D 325 MET cc_start: 0.6812 (ttm) cc_final: 0.6445 (ttm) REVERT: D 361 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7758 (mt-10) outliers start: 1 outliers final: 1 residues processed: 805 average time/residue: 0.1423 time to fit residues: 156.7901 Evaluate side-chains 724 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 723 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 56 optimal weight: 0.0270 chunk 33 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 6 optimal weight: 0.0010 chunk 91 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.5646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 HIS ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 ASN B 50 GLN B 298 ASN B 372 HIS ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.106061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.086423 restraints weight = 40401.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089839 restraints weight = 23088.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.092200 restraints weight = 14930.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.093889 restraints weight = 10495.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.095034 restraints weight = 7857.346| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15117 Z= 0.146 Angle : 0.638 10.845 20466 Z= 0.323 Chirality : 0.043 0.195 2241 Planarity : 0.005 0.053 2622 Dihedral : 10.776 163.992 2062 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.20), residues: 1838 helix: 0.98 (0.18), residues: 834 sheet: -0.21 (0.30), residues: 293 loop : 0.23 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 676 TYR 0.020 0.002 TYR A 477 PHE 0.018 0.002 PHE B 263 TRP 0.032 0.002 TRP A 374 HIS 0.011 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00291 (15117) covalent geometry : angle 0.63770 (20466) hydrogen bonds : bond 0.04189 ( 729) hydrogen bonds : angle 4.84419 ( 2013) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 758 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASN cc_start: 0.8768 (m110) cc_final: 0.8529 (m-40) REVERT: A 103 CYS cc_start: 0.7388 (m) cc_final: 0.7060 (m) REVERT: A 132 MET cc_start: 0.3301 (ppp) cc_final: 0.2807 (ppp) REVERT: A 140 PHE cc_start: 0.8303 (m-10) cc_final: 0.7826 (m-10) REVERT: A 150 MET cc_start: 0.7942 (ttp) cc_final: 0.7610 (ttp) REVERT: A 153 ASP cc_start: 0.8348 (t70) cc_final: 0.8039 (t0) REVERT: A 159 ILE cc_start: 0.7974 (mp) cc_final: 0.7695 (tp) REVERT: A 203 MET cc_start: 0.8616 (ptp) cc_final: 0.8255 (ptp) REVERT: A 210 LYS cc_start: 0.7096 (tmtt) cc_final: 0.6599 (tppt) REVERT: A 225 GLU cc_start: 0.7156 (pm20) cc_final: 0.6334 (pm20) REVERT: A 228 PHE cc_start: 0.7665 (m-80) cc_final: 0.7321 (m-80) REVERT: A 239 MET cc_start: 0.6997 (tpt) cc_final: 0.6683 (tpt) REVERT: A 262 PHE cc_start: 0.8350 (m-80) cc_final: 0.7914 (m-80) REVERT: A 285 PHE cc_start: 0.7892 (m-80) cc_final: 0.7519 (m-80) REVERT: A 312 CYS cc_start: 0.8627 (m) cc_final: 0.8340 (m) REVERT: A 319 GLU cc_start: 0.8224 (tt0) cc_final: 0.7880 (tp30) REVERT: A 323 MET cc_start: 0.8264 (mmp) cc_final: 0.7491 (mmp) REVERT: A 328 ILE cc_start: 0.8477 (mt) cc_final: 0.8173 (mm) REVERT: A 371 MET cc_start: 0.8181 (mmm) cc_final: 0.7978 (mmm) REVERT: A 372 CYS cc_start: 0.8938 (t) cc_final: 0.8405 (p) REVERT: A 374 TRP cc_start: 0.8538 (m100) cc_final: 0.8182 (m100) REVERT: A 385 GLU cc_start: 0.7743 (tp30) cc_final: 0.7165 (tm-30) REVERT: A 389 LYS cc_start: 0.8637 (mmtp) cc_final: 0.8406 (tppt) REVERT: A 400 ARG cc_start: 0.8094 (ttp-170) cc_final: 0.7662 (ttt-90) REVERT: A 405 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8488 (mtmt) REVERT: A 408 TYR cc_start: 0.8440 (t80) cc_final: 0.8176 (t80) REVERT: A 413 ASN cc_start: 0.8624 (m110) cc_final: 0.8334 (m110) REVERT: A 414 TRP cc_start: 0.7832 (t60) cc_final: 0.7532 (t60) REVERT: A 443 THR cc_start: 0.6722 (t) cc_final: 0.6106 (t) REVERT: A 450 GLU cc_start: 0.8467 (mp0) cc_final: 0.8167 (pm20) REVERT: A 452 PHE cc_start: 0.8692 (t80) cc_final: 0.8445 (t80) REVERT: A 453 CYS cc_start: 0.8619 (m) cc_final: 0.8360 (p) REVERT: A 455 ASN cc_start: 0.8739 (m-40) cc_final: 0.7702 (m110) REVERT: A 459 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7676 (mm-30) REVERT: A 460 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8442 (mmmt) REVERT: A 461 LEU cc_start: 0.8924 (mt) cc_final: 0.8642 (tp) REVERT: A 466 ASN cc_start: 0.8579 (m-40) cc_final: 0.8088 (m-40) REVERT: A 468 HIS cc_start: 0.8400 (t-90) cc_final: 0.8080 (t-90) REVERT: A 469 VAL cc_start: 0.8802 (t) cc_final: 0.8349 (m) REVERT: A 471 LYS cc_start: 0.9326 (tttt) cc_final: 0.8978 (tptp) REVERT: A 472 LEU cc_start: 0.8688 (tp) cc_final: 0.8469 (pp) REVERT: A 499 ILE cc_start: 0.8910 (mt) cc_final: 0.8322 (tp) REVERT: A 501 SER cc_start: 0.7931 (m) cc_final: 0.7477 (p) REVERT: A 502 LYS cc_start: 0.8165 (mmtp) cc_final: 0.7865 (mmtp) REVERT: A 508 LEU cc_start: 0.8383 (mt) cc_final: 0.8145 (mt) REVERT: A 511 GLU cc_start: 0.8086 (tt0) cc_final: 0.7414 (tt0) REVERT: A 515 MET cc_start: 0.6410 (tpt) cc_final: 0.6203 (tpt) REVERT: A 526 LYS cc_start: 0.8862 (mttt) cc_final: 0.8412 (mmtt) REVERT: A 533 ASN cc_start: 0.7876 (t0) cc_final: 0.7544 (t0) REVERT: A 555 ASP cc_start: 0.7060 (t0) cc_final: 0.6585 (t70) REVERT: A 577 ILE cc_start: 0.8431 (mm) cc_final: 0.8184 (mm) REVERT: A 581 LYS cc_start: 0.8958 (tttt) cc_final: 0.8689 (mtpp) REVERT: A 586 LYS cc_start: 0.8346 (mtmm) cc_final: 0.7897 (mmmt) REVERT: A 588 LEU cc_start: 0.8992 (mt) cc_final: 0.8782 (mt) REVERT: A 592 PHE cc_start: 0.7730 (m-80) cc_final: 0.7467 (m-10) REVERT: A 632 LYS cc_start: 0.9106 (mtmt) cc_final: 0.8811 (pttm) REVERT: A 641 ASN cc_start: 0.8908 (m-40) cc_final: 0.8555 (m110) REVERT: A 647 MET cc_start: 0.7971 (tpt) cc_final: 0.7545 (tpt) REVERT: A 648 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 650 LEU cc_start: 0.8730 (mt) cc_final: 0.8498 (mt) REVERT: A 673 ASP cc_start: 0.7401 (t0) cc_final: 0.7116 (t0) REVERT: A 675 LYS cc_start: 0.8529 (mmtp) cc_final: 0.8088 (mptt) REVERT: A 676 ARG cc_start: 0.8416 (tpp-160) cc_final: 0.7977 (tpp80) REVERT: A 680 GLN cc_start: 0.8325 (mm110) cc_final: 0.7827 (mm-40) REVERT: B 7 THR cc_start: 0.8661 (m) cc_final: 0.8420 (m) REVERT: B 9 LEU cc_start: 0.8103 (mt) cc_final: 0.7852 (mt) REVERT: B 32 PHE cc_start: 0.7657 (p90) cc_final: 0.7348 (p90) REVERT: B 35 ILE cc_start: 0.8586 (mt) cc_final: 0.8230 (mm) REVERT: B 45 MET cc_start: 0.7026 (ptt) cc_final: 0.6743 (ptt) REVERT: B 69 LYS cc_start: 0.7983 (mttt) cc_final: 0.7780 (mttt) REVERT: B 81 ASP cc_start: 0.8522 (p0) cc_final: 0.7058 (m-30) REVERT: B 83 MET cc_start: 0.8446 (mmm) cc_final: 0.7487 (mmm) REVERT: B 84 GLU cc_start: 0.8311 (tt0) cc_final: 0.8091 (tt0) REVERT: B 85 LYS cc_start: 0.8829 (mttm) cc_final: 0.8488 (mttm) REVERT: B 87 TRP cc_start: 0.8033 (m-10) cc_final: 0.7582 (m-90) REVERT: B 88 HIS cc_start: 0.8209 (t-90) cc_final: 0.7864 (t-170) REVERT: B 93 ASN cc_start: 0.7803 (m-40) cc_final: 0.7581 (m-40) REVERT: B 101 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8171 (mm-30) REVERT: B 102 HIS cc_start: 0.8343 (m-70) cc_final: 0.7797 (m90) REVERT: B 108 GLU cc_start: 0.7035 (mt-10) cc_final: 0.5603 (mt-10) REVERT: B 114 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7996 (mtmt) REVERT: B 116 ASN cc_start: 0.8355 (t0) cc_final: 0.8074 (t0) REVERT: B 117 ARG cc_start: 0.8288 (ttm110) cc_final: 0.7307 (ttm110) REVERT: B 119 LYS cc_start: 0.8622 (tptt) cc_final: 0.7878 (mmmt) REVERT: B 120 MET cc_start: 0.8640 (ttm) cc_final: 0.7985 (ttm) REVERT: B 123 ILE cc_start: 0.8823 (mt) cc_final: 0.8328 (tp) REVERT: B 177 MET cc_start: 0.7289 (mtt) cc_final: 0.6696 (mtm) REVERT: B 178 ARG cc_start: 0.7837 (ttt180) cc_final: 0.7533 (ttm-80) REVERT: B 180 ASP cc_start: 0.6728 (m-30) cc_final: 0.6356 (t70) REVERT: B 181 LEU cc_start: 0.8014 (tp) cc_final: 0.7715 (mm) REVERT: B 184 ARG cc_start: 0.7804 (tpp80) cc_final: 0.6981 (mtp85) REVERT: B 185 ASP cc_start: 0.8434 (m-30) cc_final: 0.8153 (m-30) REVERT: B 186 LEU cc_start: 0.8692 (mt) cc_final: 0.8420 (mm) REVERT: B 187 THR cc_start: 0.8649 (m) cc_final: 0.8227 (p) REVERT: B 188 ASP cc_start: 0.7986 (m-30) cc_final: 0.7418 (m-30) REVERT: B 190 LEU cc_start: 0.8551 (tp) cc_final: 0.7844 (tp) REVERT: B 194 LEU cc_start: 0.8851 (mt) cc_final: 0.8262 (mt) REVERT: B 208 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7490 (mm-30) REVERT: B 213 ILE cc_start: 0.8868 (mt) cc_final: 0.8667 (tp) REVERT: B 215 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7272 (mt-10) REVERT: B 216 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7699 (mtmm) REVERT: B 241 TYR cc_start: 0.7958 (t80) cc_final: 0.7534 (t80) REVERT: B 243 LEU cc_start: 0.8013 (mt) cc_final: 0.7721 (mt) REVERT: B 247 GLN cc_start: 0.7747 (mm110) cc_final: 0.7269 (tp-100) REVERT: B 248 VAL cc_start: 0.8510 (t) cc_final: 0.8065 (p) REVERT: B 254 GLU cc_start: 0.8102 (mp0) cc_final: 0.7669 (mp0) REVERT: B 263 PHE cc_start: 0.8521 (m-10) cc_final: 0.8174 (m-80) REVERT: B 272 SER cc_start: 0.8092 (m) cc_final: 0.7742 (t) REVERT: B 281 ASN cc_start: 0.8106 (m-40) cc_final: 0.7895 (m-40) REVERT: B 283 ILE cc_start: 0.7764 (mt) cc_final: 0.7551 (tt) REVERT: B 285 LYS cc_start: 0.8282 (tttp) cc_final: 0.8014 (tttp) REVERT: B 292 LYS cc_start: 0.7654 (pttm) cc_final: 0.7283 (pttm) REVERT: B 293 ASP cc_start: 0.7732 (m-30) cc_final: 0.7523 (m-30) REVERT: B 295 TYR cc_start: 0.6827 (m-80) cc_final: 0.6545 (m-80) REVERT: B 300 MET cc_start: 0.7692 (mmm) cc_final: 0.7205 (mmp) REVERT: B 314 MET cc_start: 0.7696 (tpp) cc_final: 0.7098 (tpp) REVERT: B 362 GLU cc_start: 0.9062 (tt0) cc_final: 0.8726 (tt0) REVERT: C 12 ASN cc_start: 0.7457 (m110) cc_final: 0.6814 (m110) REVERT: C 16 LEU cc_start: 0.7018 (tp) cc_final: 0.6647 (tp) REVERT: C 17 VAL cc_start: 0.7929 (m) cc_final: 0.7678 (p) REVERT: C 28 ARG cc_start: 0.8249 (ptm160) cc_final: 0.7525 (ptt90) REVERT: C 50 LYS cc_start: 0.8080 (mttt) cc_final: 0.7720 (mttt) REVERT: C 76 ILE cc_start: 0.7957 (mt) cc_final: 0.7753 (mt) REVERT: C 78 ASN cc_start: 0.7276 (t0) cc_final: 0.6391 (t0) REVERT: C 81 ASP cc_start: 0.7835 (m-30) cc_final: 0.7454 (m-30) REVERT: C 82 MET cc_start: 0.8104 (mmm) cc_final: 0.7117 (mmm) REVERT: C 86 TRP cc_start: 0.7870 (m-10) cc_final: 0.7182 (m-10) REVERT: C 105 LEU cc_start: 0.8065 (mt) cc_final: 0.7820 (mm) REVERT: C 111 ASN cc_start: 0.7948 (m110) cc_final: 0.7385 (m-40) REVERT: C 113 LYS cc_start: 0.8152 (mttp) cc_final: 0.7880 (mttp) REVERT: C 115 ASN cc_start: 0.7753 (t0) cc_final: 0.7391 (t0) REVERT: C 116 ARG cc_start: 0.8261 (ttm110) cc_final: 0.7927 (mtp180) REVERT: C 119 MET cc_start: 0.8635 (ttm) cc_final: 0.8119 (ttm) REVERT: C 121 GLN cc_start: 0.8537 (tt0) cc_final: 0.7863 (tm-30) REVERT: C 123 MET cc_start: 0.8023 (tpp) cc_final: 0.7457 (tpp) REVERT: C 125 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7014 (mm-30) REVERT: C 137 GLN cc_start: 0.7837 (mt0) cc_final: 0.7466 (mp10) REVERT: C 139 VAL cc_start: 0.8592 (m) cc_final: 0.8373 (p) REVERT: C 148 THR cc_start: 0.7901 (p) cc_final: 0.7646 (p) REVERT: C 151 ILE cc_start: 0.8667 (tt) cc_final: 0.8453 (tt) REVERT: C 152 VAL cc_start: 0.8315 (t) cc_final: 0.8002 (p) REVERT: C 154 ASP cc_start: 0.6724 (t70) cc_final: 0.6507 (t0) REVERT: C 165 ILE cc_start: 0.8634 (mt) cc_final: 0.8219 (mm) REVERT: C 166 TYR cc_start: 0.7904 (t80) cc_final: 0.7597 (t80) REVERT: C 171 LEU cc_start: 0.8153 (mp) cc_final: 0.7914 (mp) REVERT: C 175 ILE cc_start: 0.7730 (pt) cc_final: 0.6990 (mt) REVERT: C 176 MET cc_start: 0.6463 (mtt) cc_final: 0.6125 (mtt) REVERT: C 187 ASP cc_start: 0.8070 (m-30) cc_final: 0.7832 (m-30) REVERT: C 195 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7036 (mt-10) REVERT: C 198 TYR cc_start: 0.7216 (m-10) cc_final: 0.6576 (m-80) REVERT: C 205 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7248 (mt-10) REVERT: C 206 ARG cc_start: 0.8200 (ttm110) cc_final: 0.7908 (ttm110) REVERT: C 208 ILE cc_start: 0.8547 (mp) cc_final: 0.8307 (mp) REVERT: C 209 VAL cc_start: 0.8683 (t) cc_final: 0.8444 (t) REVERT: C 210 ARG cc_start: 0.8355 (ptm-80) cc_final: 0.7762 (ttp80) REVERT: C 212 ILE cc_start: 0.8866 (mt) cc_final: 0.8663 (mt) REVERT: C 213 LYS cc_start: 0.8618 (ttpt) cc_final: 0.8128 (ttpp) REVERT: C 214 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7265 (mt-10) REVERT: C 215 LYS cc_start: 0.8842 (mttm) cc_final: 0.8506 (mtpp) REVERT: C 222 ASP cc_start: 0.7208 (t0) cc_final: 0.6641 (t0) REVERT: C 238 LYS cc_start: 0.8085 (mmtm) cc_final: 0.7730 (mmtt) REVERT: C 255 PHE cc_start: 0.8476 (p90) cc_final: 0.8194 (p90) REVERT: C 259 GLU cc_start: 0.7599 (tp30) cc_final: 0.7253 (tp30) REVERT: C 278 THR cc_start: 0.7823 (m) cc_final: 0.7539 (p) REVERT: C 284 LYS cc_start: 0.8046 (tppt) cc_final: 0.7615 (tptt) REVERT: C 291 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8237 (mptt) REVERT: C 297 ASN cc_start: 0.7773 (m-40) cc_final: 0.7457 (m-40) REVERT: C 299 MET cc_start: 0.7999 (mmm) cc_final: 0.7577 (mmm) REVERT: C 305 MET cc_start: 0.7455 (mmm) cc_final: 0.7003 (mmt) REVERT: C 306 TYR cc_start: 0.7605 (m-80) cc_final: 0.7368 (m-10) REVERT: C 313 MET cc_start: 0.8674 (mmt) cc_final: 0.8403 (mmt) REVERT: C 314 GLN cc_start: 0.8846 (tt0) cc_final: 0.8131 (mm-40) REVERT: C 325 MET cc_start: 0.7099 (mpp) cc_final: 0.6731 (mpp) REVERT: C 328 LYS cc_start: 0.8450 (mttt) cc_final: 0.7941 (mttt) REVERT: C 356 TRP cc_start: 0.6076 (m100) cc_final: 0.5470 (m100) REVERT: C 371 HIS cc_start: 0.7880 (m-70) cc_final: 0.7289 (m-70) REVERT: D 8 LEU cc_start: 0.8239 (mt) cc_final: 0.7874 (mm) REVERT: D 24 ASP cc_start: 0.6675 (m-30) cc_final: 0.6162 (m-30) REVERT: D 34 ILE cc_start: 0.8795 (mt) cc_final: 0.8002 (tp) REVERT: D 41 GLN cc_start: 0.7220 (tp40) cc_final: 0.6937 (tp40) REVERT: D 47 MET cc_start: 0.6788 (ttm) cc_final: 0.6447 (ttm) REVERT: D 50 LYS cc_start: 0.7758 (ttmt) cc_final: 0.7535 (ttmt) REVERT: D 54 VAL cc_start: 0.8367 (t) cc_final: 0.7937 (m) REVERT: D 61 LYS cc_start: 0.7703 (mmtp) cc_final: 0.7470 (mmtp) REVERT: D 64 ILE cc_start: 0.8488 (mm) cc_final: 0.8259 (mm) REVERT: D 76 ILE cc_start: 0.8058 (mt) cc_final: 0.7299 (mt) REVERT: D 78 ASN cc_start: 0.8202 (t0) cc_final: 0.7776 (t0) REVERT: D 79 TRP cc_start: 0.7775 (m100) cc_final: 0.7197 (m100) REVERT: D 84 LYS cc_start: 0.8623 (tttt) cc_final: 0.8347 (tptt) REVERT: D 92 ASN cc_start: 0.7253 (m110) cc_final: 0.7000 (m110) REVERT: D 99 GLU cc_start: 0.7741 (mp0) cc_final: 0.7540 (mp0) REVERT: D 100 GLU cc_start: 0.7844 (tp30) cc_final: 0.7195 (tp30) REVERT: D 107 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6665 (mt-10) REVERT: D 133 TYR cc_start: 0.8046 (t80) cc_final: 0.7359 (t80) REVERT: D 134 VAL cc_start: 0.8223 (t) cc_final: 0.7952 (p) REVERT: D 153 LEU cc_start: 0.8009 (tp) cc_final: 0.7424 (tt) REVERT: D 176 MET cc_start: 0.6571 (mtp) cc_final: 0.5820 (mtp) REVERT: D 184 ASP cc_start: 0.8216 (m-30) cc_final: 0.8001 (m-30) REVERT: D 188 TYR cc_start: 0.7659 (t80) cc_final: 0.7411 (t80) REVERT: D 190 MET cc_start: 0.7778 (mtm) cc_final: 0.7571 (mtt) REVERT: D 192 ILE cc_start: 0.7832 (mm) cc_final: 0.7084 (mm) REVERT: D 195 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6604 (mt-10) REVERT: D 205 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7155 (mt-10) REVERT: D 206 ARG cc_start: 0.8280 (ttm170) cc_final: 0.7899 (ttm-80) REVERT: D 207 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7187 (mm-30) REVERT: D 210 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8036 (ttp80) REVERT: D 211 ASP cc_start: 0.8052 (m-30) cc_final: 0.7165 (m-30) REVERT: D 214 GLU cc_start: 0.7963 (tt0) cc_final: 0.7739 (tt0) REVERT: D 222 ASP cc_start: 0.8449 (t0) cc_final: 0.8180 (t0) REVERT: D 238 LYS cc_start: 0.7951 (mmmt) cc_final: 0.7561 (mmmm) REVERT: D 253 GLU cc_start: 0.7252 (mp0) cc_final: 0.6913 (mp0) REVERT: D 267 ILE cc_start: 0.7638 (pt) cc_final: 0.7256 (pt) REVERT: D 276 GLU cc_start: 0.8633 (tp30) cc_final: 0.8377 (tp30) REVERT: D 280 ASN cc_start: 0.7596 (t0) cc_final: 0.6337 (t0) REVERT: D 281 SER cc_start: 0.8361 (p) cc_final: 0.7527 (p) REVERT: D 282 ILE cc_start: 0.8342 (mt) cc_final: 0.8034 (mt) REVERT: D 284 LYS cc_start: 0.8238 (mmpt) cc_final: 0.7938 (mmpt) REVERT: D 294 TYR cc_start: 0.6979 (m-80) cc_final: 0.6471 (m-80) REVERT: D 298 VAL cc_start: 0.8182 (t) cc_final: 0.7844 (m) REVERT: D 299 MET cc_start: 0.7571 (mmm) cc_final: 0.7363 (mmm) REVERT: D 303 THR cc_start: 0.7796 (m) cc_final: 0.6930 (p) REVERT: D 306 TYR cc_start: 0.7133 (m-80) cc_final: 0.6592 (m-10) REVERT: D 312 ARG cc_start: 0.8093 (tpt-90) cc_final: 0.6761 (tpt170) REVERT: D 313 MET cc_start: 0.8376 (tpt) cc_final: 0.7810 (tpt) REVERT: D 315 LYS cc_start: 0.8817 (ttpp) cc_final: 0.8373 (ttpp) REVERT: D 316 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7117 (mm-30) REVERT: D 317 ILE cc_start: 0.8759 (mm) cc_final: 0.8459 (mm) REVERT: D 320 LEU cc_start: 0.8794 (mt) cc_final: 0.8388 (mt) REVERT: D 325 MET cc_start: 0.6838 (ttm) cc_final: 0.6441 (ttm) REVERT: D 361 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7777 (mt-10) outliers start: 0 outliers final: 0 residues processed: 758 average time/residue: 0.1337 time to fit residues: 140.9347 Evaluate side-chains 707 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 707 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 116 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 372 HIS ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 161 HIS C 296 ASN D 12 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.102129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.083131 restraints weight = 40596.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.086459 restraints weight = 22664.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.088790 restraints weight = 14466.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090403 restraints weight = 10076.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.091583 restraints weight = 7496.203| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15117 Z= 0.200 Angle : 0.683 11.202 20466 Z= 0.354 Chirality : 0.046 0.247 2241 Planarity : 0.005 0.049 2622 Dihedral : 10.456 163.133 2062 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.40 (0.19), residues: 1838 helix: 0.77 (0.18), residues: 841 sheet: -0.27 (0.30), residues: 289 loop : 0.10 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 37 TYR 0.025 0.002 TYR B 54 PHE 0.021 0.002 PHE A 548 TRP 0.017 0.002 TRP A 414 HIS 0.012 0.002 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00390 (15117) covalent geometry : angle 0.68329 (20466) hydrogen bonds : bond 0.04540 ( 729) hydrogen bonds : angle 4.98748 ( 2013) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 756 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9216 (tt) cc_final: 0.8841 (tp) REVERT: A 88 ASN cc_start: 0.8692 (m110) cc_final: 0.8359 (m110) REVERT: A 90 ARG cc_start: 0.8244 (ttp-110) cc_final: 0.7887 (ttp-110) REVERT: A 132 MET cc_start: 0.2964 (ppp) cc_final: 0.2661 (ppp) REVERT: A 140 PHE cc_start: 0.8260 (m-10) cc_final: 0.7696 (m-10) REVERT: A 145 GLU cc_start: 0.8815 (tt0) cc_final: 0.8609 (tt0) REVERT: A 178 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8294 (mmm-85) REVERT: A 210 LYS cc_start: 0.7165 (tmtt) cc_final: 0.6687 (tppt) REVERT: A 228 PHE cc_start: 0.7379 (m-80) cc_final: 0.6917 (m-10) REVERT: A 262 PHE cc_start: 0.8409 (m-80) cc_final: 0.7967 (m-80) REVERT: A 273 GLU cc_start: 0.8854 (mp0) cc_final: 0.7439 (tm-30) REVERT: A 285 PHE cc_start: 0.8013 (m-80) cc_final: 0.7740 (m-80) REVERT: A 304 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7966 (mm-30) REVERT: A 323 MET cc_start: 0.8109 (mmp) cc_final: 0.7894 (mmp) REVERT: A 328 ILE cc_start: 0.8549 (mt) cc_final: 0.8264 (mm) REVERT: A 342 SER cc_start: 0.8499 (t) cc_final: 0.8070 (t) REVERT: A 354 HIS cc_start: 0.7881 (t70) cc_final: 0.7190 (t-90) REVERT: A 363 LEU cc_start: 0.8106 (mt) cc_final: 0.7317 (mt) REVERT: A 364 MET cc_start: 0.7163 (mmt) cc_final: 0.6375 (mmt) REVERT: A 372 CYS cc_start: 0.8861 (t) cc_final: 0.8503 (p) REVERT: A 374 TRP cc_start: 0.8601 (m100) cc_final: 0.8227 (m100) REVERT: A 385 GLU cc_start: 0.7635 (tp30) cc_final: 0.7020 (tm-30) REVERT: A 389 LYS cc_start: 0.8666 (mmtp) cc_final: 0.8394 (tppt) REVERT: A 393 LYS cc_start: 0.8480 (tttt) cc_final: 0.8204 (mmmt) REVERT: A 400 ARG cc_start: 0.8123 (ttp-170) cc_final: 0.7483 (tmm160) REVERT: A 410 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8104 (mtpt) REVERT: A 413 ASN cc_start: 0.8690 (m110) cc_final: 0.8412 (m-40) REVERT: A 414 TRP cc_start: 0.7814 (t60) cc_final: 0.7600 (t60) REVERT: A 450 GLU cc_start: 0.8566 (mp0) cc_final: 0.8353 (pm20) REVERT: A 453 CYS cc_start: 0.8601 (m) cc_final: 0.8401 (p) REVERT: A 459 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 460 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8439 (mmmt) REVERT: A 461 LEU cc_start: 0.8929 (mt) cc_final: 0.8685 (pp) REVERT: A 464 GLN cc_start: 0.8854 (tt0) cc_final: 0.7970 (tm-30) REVERT: A 465 PHE cc_start: 0.8599 (t80) cc_final: 0.8331 (t80) REVERT: A 466 ASN cc_start: 0.8567 (m-40) cc_final: 0.8256 (m-40) REVERT: A 469 VAL cc_start: 0.8988 (t) cc_final: 0.8534 (m) REVERT: A 476 GLU cc_start: 0.8609 (tp30) cc_final: 0.8090 (tp30) REVERT: A 499 ILE cc_start: 0.8948 (mt) cc_final: 0.8200 (tp) REVERT: A 501 SER cc_start: 0.8143 (m) cc_final: 0.7723 (p) REVERT: A 502 LYS cc_start: 0.8353 (mmtp) cc_final: 0.8030 (mmtp) REVERT: A 506 LEU cc_start: 0.8328 (tp) cc_final: 0.7997 (pp) REVERT: A 507 ASP cc_start: 0.8337 (m-30) cc_final: 0.7977 (m-30) REVERT: A 508 LEU cc_start: 0.8436 (mt) cc_final: 0.8181 (mt) REVERT: A 511 GLU cc_start: 0.8279 (tt0) cc_final: 0.7435 (tt0) REVERT: A 514 LYS cc_start: 0.7834 (tmmt) cc_final: 0.7542 (tmmt) REVERT: A 526 LYS cc_start: 0.8782 (mttt) cc_final: 0.8270 (mmtt) REVERT: A 533 ASN cc_start: 0.7694 (t0) cc_final: 0.7446 (t0) REVERT: A 545 ASN cc_start: 0.8352 (m-40) cc_final: 0.8123 (m-40) REVERT: A 551 LYS cc_start: 0.8124 (tttt) cc_final: 0.7851 (tptp) REVERT: A 574 GLU cc_start: 0.7816 (pm20) cc_final: 0.7558 (pm20) REVERT: A 578 LYS cc_start: 0.8848 (mtpp) cc_final: 0.8573 (mtpp) REVERT: A 581 LYS cc_start: 0.8963 (tttt) cc_final: 0.8718 (mtpp) REVERT: A 629 LYS cc_start: 0.8576 (tptp) cc_final: 0.8245 (tptp) REVERT: A 632 LYS cc_start: 0.9094 (mtmt) cc_final: 0.8623 (ptpp) REVERT: A 641 ASN cc_start: 0.8860 (m-40) cc_final: 0.8478 (m110) REVERT: A 644 HIS cc_start: 0.7925 (m90) cc_final: 0.7423 (m90) REVERT: A 647 MET cc_start: 0.8065 (tpt) cc_final: 0.7588 (tpt) REVERT: A 648 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8097 (tm-30) REVERT: A 657 TYR cc_start: 0.7391 (m-80) cc_final: 0.6798 (m-80) REVERT: A 673 ASP cc_start: 0.7455 (t0) cc_final: 0.7248 (t0) REVERT: A 675 LYS cc_start: 0.8465 (mmtp) cc_final: 0.7990 (mptt) REVERT: A 691 ARG cc_start: 0.8144 (ptm-80) cc_final: 0.7942 (ptm-80) REVERT: B 32 PHE cc_start: 0.7809 (p90) cc_final: 0.7455 (p90) REVERT: B 35 ILE cc_start: 0.8611 (mt) cc_final: 0.8299 (mm) REVERT: B 55 VAL cc_start: 0.8399 (t) cc_final: 0.8008 (m) REVERT: B 81 ASP cc_start: 0.8566 (p0) cc_final: 0.7233 (m-30) REVERT: B 83 MET cc_start: 0.8547 (mmm) cc_final: 0.7971 (mmm) REVERT: B 84 GLU cc_start: 0.8438 (tt0) cc_final: 0.8212 (tt0) REVERT: B 85 LYS cc_start: 0.8716 (mttm) cc_final: 0.8304 (mttm) REVERT: B 87 TRP cc_start: 0.7986 (m-10) cc_final: 0.7746 (m-90) REVERT: B 92 TYR cc_start: 0.7856 (m-80) cc_final: 0.7229 (m-80) REVERT: B 93 ASN cc_start: 0.7856 (m-40) cc_final: 0.7641 (m-40) REVERT: B 101 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8150 (mm-30) REVERT: B 102 HIS cc_start: 0.8447 (m-70) cc_final: 0.7783 (m90) REVERT: B 114 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8179 (mtmt) REVERT: B 116 ASN cc_start: 0.8292 (t0) cc_final: 0.8006 (t0) REVERT: B 117 ARG cc_start: 0.8330 (ttm110) cc_final: 0.7694 (ttm110) REVERT: B 119 LYS cc_start: 0.8692 (tptt) cc_final: 0.7853 (mmmt) REVERT: B 120 MET cc_start: 0.8617 (ttm) cc_final: 0.8045 (ttm) REVERT: B 123 ILE cc_start: 0.8847 (mt) cc_final: 0.8228 (tp) REVERT: B 127 THR cc_start: 0.8692 (m) cc_final: 0.7749 (t) REVERT: B 128 PHE cc_start: 0.8316 (m-10) cc_final: 0.7983 (m-10) REVERT: B 156 SER cc_start: 0.7312 (t) cc_final: 0.7063 (t) REVERT: B 177 MET cc_start: 0.7271 (mtt) cc_final: 0.6948 (mtm) REVERT: B 180 ASP cc_start: 0.6767 (m-30) cc_final: 0.6118 (t70) REVERT: B 184 ARG cc_start: 0.7859 (tpp80) cc_final: 0.7281 (mtp85) REVERT: B 185 ASP cc_start: 0.8358 (m-30) cc_final: 0.7975 (m-30) REVERT: B 186 LEU cc_start: 0.8776 (mt) cc_final: 0.8455 (mm) REVERT: B 188 ASP cc_start: 0.7979 (m-30) cc_final: 0.7498 (m-30) REVERT: B 194 LEU cc_start: 0.8906 (mt) cc_final: 0.8697 (tp) REVERT: B 199 TYR cc_start: 0.7389 (m-10) cc_final: 0.6831 (m-10) REVERT: B 208 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7742 (mm-30) REVERT: B 211 ARG cc_start: 0.8488 (ttp80) cc_final: 0.7929 (ttp80) REVERT: B 215 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7049 (mt-10) REVERT: B 223 ASP cc_start: 0.8144 (t70) cc_final: 0.7807 (t70) REVERT: B 225 GLU cc_start: 0.8230 (tm-30) cc_final: 0.8014 (pp20) REVERT: B 243 LEU cc_start: 0.8009 (mt) cc_final: 0.7734 (mt) REVERT: B 247 GLN cc_start: 0.7818 (mm110) cc_final: 0.7043 (mp10) REVERT: B 248 VAL cc_start: 0.8535 (t) cc_final: 0.8254 (p) REVERT: B 253 ASN cc_start: 0.8371 (p0) cc_final: 0.8132 (p0) REVERT: B 254 GLU cc_start: 0.8111 (mp0) cc_final: 0.7496 (mp0) REVERT: B 263 PHE cc_start: 0.8598 (m-10) cc_final: 0.8302 (m-80) REVERT: B 272 SER cc_start: 0.8292 (m) cc_final: 0.7859 (t) REVERT: B 283 ILE cc_start: 0.7955 (mt) cc_final: 0.7657 (tt) REVERT: B 284 MET cc_start: 0.7479 (mmm) cc_final: 0.7045 (mmm) REVERT: B 285 LYS cc_start: 0.8392 (tttp) cc_final: 0.8147 (tttp) REVERT: B 292 LYS cc_start: 0.7908 (pttm) cc_final: 0.7593 (pttm) REVERT: B 295 TYR cc_start: 0.6866 (m-80) cc_final: 0.6608 (m-80) REVERT: B 300 MET cc_start: 0.7647 (mmm) cc_final: 0.7197 (mmp) REVERT: B 314 MET cc_start: 0.7688 (tpp) cc_final: 0.7178 (tpp) REVERT: B 347 LEU cc_start: 0.8083 (tp) cc_final: 0.7746 (tp) REVERT: B 350 LEU cc_start: 0.7921 (mp) cc_final: 0.7699 (mt) REVERT: B 362 GLU cc_start: 0.9083 (tt0) cc_final: 0.8790 (tt0) REVERT: C 8 LEU cc_start: 0.7915 (mt) cc_final: 0.7689 (mt) REVERT: C 28 ARG cc_start: 0.8305 (ptm160) cc_final: 0.6770 (ptt90) REVERT: C 34 ILE cc_start: 0.8029 (mt) cc_final: 0.7806 (tp) REVERT: C 50 LYS cc_start: 0.8212 (mttt) cc_final: 0.7812 (mttt) REVERT: C 62 ARG cc_start: 0.5451 (ppt170) cc_final: 0.4227 (ppt170) REVERT: C 76 ILE cc_start: 0.8052 (mt) cc_final: 0.7702 (mt) REVERT: C 78 ASN cc_start: 0.7531 (t0) cc_final: 0.6323 (t0) REVERT: C 81 ASP cc_start: 0.7888 (m-30) cc_final: 0.7267 (m-30) REVERT: C 82 MET cc_start: 0.8011 (mmm) cc_final: 0.7274 (mmm) REVERT: C 86 TRP cc_start: 0.7949 (m-10) cc_final: 0.7147 (m-10) REVERT: C 90 PHE cc_start: 0.7954 (m-10) cc_final: 0.7602 (m-80) REVERT: C 93 GLU cc_start: 0.8218 (tp30) cc_final: 0.7953 (tp30) REVERT: C 99 GLU cc_start: 0.7040 (mp0) cc_final: 0.6791 (mp0) REVERT: C 111 ASN cc_start: 0.8015 (m-40) cc_final: 0.7544 (m-40) REVERT: C 113 LYS cc_start: 0.8307 (mttp) cc_final: 0.8067 (mttp) REVERT: C 115 ASN cc_start: 0.7800 (t0) cc_final: 0.7519 (t0) REVERT: C 116 ARG cc_start: 0.8239 (ttm110) cc_final: 0.7984 (mtp85) REVERT: C 119 MET cc_start: 0.8670 (ttm) cc_final: 0.8143 (ttm) REVERT: C 127 PHE cc_start: 0.8338 (m-10) cc_final: 0.7917 (m-10) REVERT: C 137 GLN cc_start: 0.7923 (mt0) cc_final: 0.7603 (mp10) REVERT: C 151 ILE cc_start: 0.8742 (tt) cc_final: 0.8538 (tt) REVERT: C 152 VAL cc_start: 0.8398 (t) cc_final: 0.8080 (p) REVERT: C 154 ASP cc_start: 0.6926 (t70) cc_final: 0.6429 (t0) REVERT: C 176 MET cc_start: 0.6684 (mtt) cc_final: 0.6427 (mtt) REVERT: C 190 MET cc_start: 0.7911 (mtm) cc_final: 0.7589 (mtm) REVERT: C 192 ILE cc_start: 0.7943 (pt) cc_final: 0.7338 (pt) REVERT: C 198 TYR cc_start: 0.7589 (m-10) cc_final: 0.7137 (m-80) REVERT: C 205 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7343 (mt-10) REVERT: C 210 ARG cc_start: 0.8265 (ptm-80) cc_final: 0.7943 (ttp80) REVERT: C 212 ILE cc_start: 0.8683 (mt) cc_final: 0.8469 (mt) REVERT: C 213 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8181 (ttpp) REVERT: C 214 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7650 (mt-10) REVERT: C 215 LYS cc_start: 0.8778 (mttm) cc_final: 0.8441 (mmmm) REVERT: C 222 ASP cc_start: 0.7338 (t0) cc_final: 0.7088 (t0) REVERT: C 238 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7800 (mmtt) REVERT: C 253 GLU cc_start: 0.7165 (mp0) cc_final: 0.6846 (mp0) REVERT: C 256 ARG cc_start: 0.7821 (ttm170) cc_final: 0.7123 (ttm-80) REVERT: C 261 LEU cc_start: 0.8309 (mt) cc_final: 0.8097 (mt) REVERT: C 278 THR cc_start: 0.7827 (m) cc_final: 0.7485 (p) REVERT: C 279 TYR cc_start: 0.7972 (t80) cc_final: 0.7579 (t80) REVERT: C 283 MET cc_start: 0.7802 (mmp) cc_final: 0.7187 (mmp) REVERT: C 284 LYS cc_start: 0.8191 (tppt) cc_final: 0.7932 (tppt) REVERT: C 286 ASP cc_start: 0.8040 (t0) cc_final: 0.7835 (t0) REVERT: C 291 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8365 (mptt) REVERT: C 294 TYR cc_start: 0.7686 (m-80) cc_final: 0.7436 (m-80) REVERT: C 299 MET cc_start: 0.7905 (mmm) cc_final: 0.7392 (mmm) REVERT: C 305 MET cc_start: 0.7561 (mmm) cc_final: 0.6987 (mmt) REVERT: C 306 TYR cc_start: 0.7651 (m-80) cc_final: 0.7446 (m-10) REVERT: C 313 MET cc_start: 0.8673 (mmt) cc_final: 0.8469 (mmt) REVERT: C 316 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8298 (mm-30) REVERT: C 326 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7872 (mmtt) REVERT: C 328 LYS cc_start: 0.8565 (mttt) cc_final: 0.8180 (mttt) REVERT: C 330 ILE cc_start: 0.8806 (mp) cc_final: 0.8564 (mm) REVERT: C 336 LYS cc_start: 0.8155 (pttp) cc_final: 0.7620 (ptmm) REVERT: C 349 LEU cc_start: 0.8635 (tp) cc_final: 0.8354 (tp) REVERT: C 356 TRP cc_start: 0.6337 (m100) cc_final: 0.5865 (m100) REVERT: C 361 GLU cc_start: 0.8757 (tt0) cc_final: 0.8045 (tt0) REVERT: D 24 ASP cc_start: 0.6879 (m-30) cc_final: 0.6327 (m-30) REVERT: D 34 ILE cc_start: 0.8867 (mt) cc_final: 0.8106 (tp) REVERT: D 47 MET cc_start: 0.6848 (ttm) cc_final: 0.6529 (ttm) REVERT: D 50 LYS cc_start: 0.7870 (ttmt) cc_final: 0.7553 (ttmt) REVERT: D 54 VAL cc_start: 0.8534 (t) cc_final: 0.8017 (m) REVERT: D 76 ILE cc_start: 0.8129 (mt) cc_final: 0.7581 (mt) REVERT: D 78 ASN cc_start: 0.8180 (t0) cc_final: 0.7890 (t0) REVERT: D 79 TRP cc_start: 0.8043 (m100) cc_final: 0.7386 (m100) REVERT: D 84 LYS cc_start: 0.8644 (tttt) cc_final: 0.8419 (tptt) REVERT: D 99 GLU cc_start: 0.7748 (mp0) cc_final: 0.7533 (mp0) REVERT: D 100 GLU cc_start: 0.7916 (tp30) cc_final: 0.7244 (tp30) REVERT: D 118 LYS cc_start: 0.8864 (tptt) cc_final: 0.8337 (tptt) REVERT: D 122 ILE cc_start: 0.8644 (mt) cc_final: 0.7957 (mt) REVERT: D 133 TYR cc_start: 0.8128 (t80) cc_final: 0.7662 (t80) REVERT: D 153 LEU cc_start: 0.8019 (tp) cc_final: 0.7315 (tt) REVERT: D 176 MET cc_start: 0.6691 (mtp) cc_final: 0.6006 (mtp) REVERT: D 192 ILE cc_start: 0.7931 (mm) cc_final: 0.7264 (mm) REVERT: D 195 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6440 (mt-10) REVERT: D 206 ARG cc_start: 0.8312 (ttm170) cc_final: 0.7999 (mtp-110) REVERT: D 207 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7425 (mm-30) REVERT: D 208 ILE cc_start: 0.8257 (mm) cc_final: 0.8002 (mm) REVERT: D 210 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8163 (ttp80) REVERT: D 211 ASP cc_start: 0.8036 (m-30) cc_final: 0.7224 (m-30) REVERT: D 222 ASP cc_start: 0.8582 (t0) cc_final: 0.8342 (t0) REVERT: D 223 PHE cc_start: 0.7435 (t80) cc_final: 0.7133 (t80) REVERT: D 238 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7770 (mmmm) REVERT: D 253 GLU cc_start: 0.7283 (mp0) cc_final: 0.6985 (mp0) REVERT: D 269 MET cc_start: 0.7211 (mtt) cc_final: 0.6992 (mtt) REVERT: D 276 GLU cc_start: 0.8584 (tp30) cc_final: 0.8328 (tp30) REVERT: D 280 ASN cc_start: 0.7853 (t0) cc_final: 0.6563 (t0) REVERT: D 281 SER cc_start: 0.8504 (p) cc_final: 0.7827 (p) REVERT: D 282 ILE cc_start: 0.8416 (mt) cc_final: 0.8206 (mt) REVERT: D 284 LYS cc_start: 0.8446 (mmpt) cc_final: 0.8166 (mmpt) REVERT: D 294 TYR cc_start: 0.7205 (m-80) cc_final: 0.6573 (m-80) REVERT: D 298 VAL cc_start: 0.8354 (t) cc_final: 0.7992 (m) REVERT: D 299 MET cc_start: 0.7535 (mmm) cc_final: 0.7299 (mmm) REVERT: D 300 SER cc_start: 0.7403 (t) cc_final: 0.6773 (p) REVERT: D 306 TYR cc_start: 0.7312 (m-80) cc_final: 0.7001 (m-10) REVERT: D 313 MET cc_start: 0.8386 (tpt) cc_final: 0.7854 (tpt) REVERT: D 315 LYS cc_start: 0.8843 (ttpp) cc_final: 0.8326 (ttpp) REVERT: D 316 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7193 (mm-30) REVERT: D 317 ILE cc_start: 0.8891 (mm) cc_final: 0.8600 (mm) REVERT: D 320 LEU cc_start: 0.8848 (mt) cc_final: 0.8538 (mt) REVERT: D 325 MET cc_start: 0.6962 (ttm) cc_final: 0.6594 (ttm) REVERT: D 361 GLU cc_start: 0.8575 (mt-10) cc_final: 0.7917 (mt-10) outliers start: 0 outliers final: 0 residues processed: 756 average time/residue: 0.1410 time to fit residues: 146.7864 Evaluate side-chains 704 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 704 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 128 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 GLN A 474 GLN ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 HIS B 372 HIS ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS D 40 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.102646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.083434 restraints weight = 40188.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.086832 restraints weight = 22473.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089168 restraints weight = 14296.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.090787 restraints weight = 9939.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.091961 restraints weight = 7411.143| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15117 Z= 0.141 Angle : 0.644 11.278 20466 Z= 0.324 Chirality : 0.044 0.194 2241 Planarity : 0.005 0.060 2622 Dihedral : 10.237 164.034 2062 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: 0.68 (0.20), residues: 1838 helix: 1.04 (0.18), residues: 818 sheet: -0.19 (0.30), residues: 291 loop : 0.24 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 659 TYR 0.023 0.002 TYR A 456 PHE 0.022 0.001 PHE A 452 TRP 0.015 0.002 TRP A 414 HIS 0.008 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00293 (15117) covalent geometry : angle 0.64403 (20466) hydrogen bonds : bond 0.03962 ( 729) hydrogen bonds : angle 4.78306 ( 2013) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 737 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7331 (pp20) REVERT: A 86 LEU cc_start: 0.9257 (tt) cc_final: 0.8943 (tp) REVERT: A 88 ASN cc_start: 0.8687 (m110) cc_final: 0.8233 (m110) REVERT: A 90 ARG cc_start: 0.8344 (ttp-110) cc_final: 0.7968 (ttp-110) REVERT: A 113 TYR cc_start: 0.7199 (m-80) cc_final: 0.6408 (m-80) REVERT: A 132 MET cc_start: 0.2928 (ppp) cc_final: 0.2607 (ppp) REVERT: A 140 PHE cc_start: 0.8223 (m-10) cc_final: 0.7661 (m-10) REVERT: A 148 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8672 (mmtt) REVERT: A 150 MET cc_start: 0.8246 (ttp) cc_final: 0.7819 (ttp) REVERT: A 155 ARG cc_start: 0.7465 (ttt90) cc_final: 0.7223 (ttt90) REVERT: A 158 SER cc_start: 0.6530 (t) cc_final: 0.6053 (m) REVERT: A 178 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8188 (mmm-85) REVERT: A 228 PHE cc_start: 0.7431 (m-80) cc_final: 0.7017 (m-80) REVERT: A 233 ARG cc_start: 0.7538 (tpt170) cc_final: 0.7331 (tpt170) REVERT: A 285 PHE cc_start: 0.7958 (m-80) cc_final: 0.7705 (m-80) REVERT: A 304 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7782 (mm-30) REVERT: A 328 ILE cc_start: 0.8545 (mt) cc_final: 0.8242 (mm) REVERT: A 354 HIS cc_start: 0.7880 (t70) cc_final: 0.7211 (t-170) REVERT: A 359 ILE cc_start: 0.8073 (mt) cc_final: 0.7788 (tp) REVERT: A 363 LEU cc_start: 0.8123 (mt) cc_final: 0.7814 (mt) REVERT: A 369 GLU cc_start: 0.8421 (mp0) cc_final: 0.8140 (mp0) REVERT: A 372 CYS cc_start: 0.8879 (t) cc_final: 0.8452 (p) REVERT: A 374 TRP cc_start: 0.8574 (m100) cc_final: 0.8268 (m100) REVERT: A 385 GLU cc_start: 0.7631 (tp30) cc_final: 0.7092 (tm-30) REVERT: A 389 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8324 (tppt) REVERT: A 400 ARG cc_start: 0.8115 (ttp-170) cc_final: 0.7719 (tmm160) REVERT: A 410 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8018 (mtpt) REVERT: A 413 ASN cc_start: 0.8597 (m110) cc_final: 0.8290 (m-40) REVERT: A 453 CYS cc_start: 0.8625 (m) cc_final: 0.8324 (p) REVERT: A 455 ASN cc_start: 0.8700 (m-40) cc_final: 0.7423 (m110) REVERT: A 459 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 460 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8439 (mmmt) REVERT: A 461 LEU cc_start: 0.8912 (mt) cc_final: 0.8666 (pp) REVERT: A 466 ASN cc_start: 0.8544 (m-40) cc_final: 0.8200 (m-40) REVERT: A 468 HIS cc_start: 0.8305 (t-90) cc_final: 0.8083 (t-90) REVERT: A 469 VAL cc_start: 0.8893 (t) cc_final: 0.8564 (m) REVERT: A 499 ILE cc_start: 0.8936 (mt) cc_final: 0.8428 (tt) REVERT: A 501 SER cc_start: 0.8225 (m) cc_final: 0.7803 (p) REVERT: A 502 LYS cc_start: 0.8346 (mmtp) cc_final: 0.8035 (mmtp) REVERT: A 507 ASP cc_start: 0.8349 (m-30) cc_final: 0.8041 (m-30) REVERT: A 508 LEU cc_start: 0.8389 (mt) cc_final: 0.8102 (mt) REVERT: A 511 GLU cc_start: 0.8228 (tt0) cc_final: 0.7069 (tt0) REVERT: A 515 MET cc_start: 0.6472 (tpt) cc_final: 0.6246 (tpt) REVERT: A 522 THR cc_start: 0.7808 (p) cc_final: 0.7424 (p) REVERT: A 526 LYS cc_start: 0.8768 (mttt) cc_final: 0.7873 (mmmt) REVERT: A 545 ASN cc_start: 0.8427 (m-40) cc_final: 0.8130 (m-40) REVERT: A 557 VAL cc_start: 0.8120 (t) cc_final: 0.7845 (t) REVERT: A 574 GLU cc_start: 0.7793 (pm20) cc_final: 0.7467 (pm20) REVERT: A 575 GLU cc_start: 0.7584 (pm20) cc_final: 0.7112 (pm20) REVERT: A 578 LYS cc_start: 0.8841 (mtpp) cc_final: 0.8605 (mtpp) REVERT: A 581 LYS cc_start: 0.8974 (tttt) cc_final: 0.8693 (mtpp) REVERT: A 632 LYS cc_start: 0.9082 (mtmt) cc_final: 0.8824 (pttm) REVERT: A 641 ASN cc_start: 0.8884 (m-40) cc_final: 0.8603 (m110) REVERT: A 644 HIS cc_start: 0.8041 (m90) cc_final: 0.7484 (m90) REVERT: A 647 MET cc_start: 0.7972 (tpt) cc_final: 0.7443 (tpt) REVERT: A 650 LEU cc_start: 0.8745 (mt) cc_final: 0.8540 (mt) REVERT: A 653 THR cc_start: 0.8351 (p) cc_final: 0.7955 (p) REVERT: A 667 LYS cc_start: 0.8806 (ptpp) cc_final: 0.8387 (tptp) REVERT: A 673 ASP cc_start: 0.7569 (t0) cc_final: 0.7290 (t0) REVERT: A 675 LYS cc_start: 0.8480 (mmtp) cc_final: 0.8025 (mptt) REVERT: A 732 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7595 (tp30) REVERT: B 29 ARG cc_start: 0.7655 (ttm110) cc_final: 0.7404 (ttm110) REVERT: B 32 PHE cc_start: 0.7786 (p90) cc_final: 0.7397 (p90) REVERT: B 35 ILE cc_start: 0.8606 (mt) cc_final: 0.8294 (mm) REVERT: B 51 LYS cc_start: 0.7585 (ptpp) cc_final: 0.7270 (pttp) REVERT: B 55 VAL cc_start: 0.8396 (t) cc_final: 0.8076 (m) REVERT: B 81 ASP cc_start: 0.8528 (p0) cc_final: 0.7369 (m-30) REVERT: B 83 MET cc_start: 0.8441 (mmm) cc_final: 0.7313 (mmm) REVERT: B 84 GLU cc_start: 0.8432 (tt0) cc_final: 0.8194 (tt0) REVERT: B 85 LYS cc_start: 0.8697 (mttm) cc_final: 0.8249 (mttm) REVERT: B 87 TRP cc_start: 0.8064 (m-10) cc_final: 0.7568 (m-90) REVERT: B 93 ASN cc_start: 0.7870 (m-40) cc_final: 0.7651 (m-40) REVERT: B 101 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8118 (mm-30) REVERT: B 102 HIS cc_start: 0.8452 (m-70) cc_final: 0.7836 (m90) REVERT: B 108 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6368 (mt-10) REVERT: B 114 LYS cc_start: 0.8462 (mtmt) cc_final: 0.8166 (mtmt) REVERT: B 117 ARG cc_start: 0.8303 (ttm110) cc_final: 0.7555 (ttm110) REVERT: B 119 LYS cc_start: 0.8610 (tptt) cc_final: 0.7781 (mmmt) REVERT: B 120 MET cc_start: 0.8562 (ttm) cc_final: 0.8046 (ttm) REVERT: B 123 ILE cc_start: 0.8820 (mt) cc_final: 0.8060 (tp) REVERT: B 127 THR cc_start: 0.8658 (m) cc_final: 0.7690 (p) REVERT: B 128 PHE cc_start: 0.8245 (m-10) cc_final: 0.7763 (m-10) REVERT: B 144 TYR cc_start: 0.7430 (m-80) cc_final: 0.7151 (m-80) REVERT: B 168 GLU cc_start: 0.7222 (mm-30) cc_final: 0.7005 (mm-30) REVERT: B 180 ASP cc_start: 0.6719 (m-30) cc_final: 0.6072 (t70) REVERT: B 184 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7094 (mtp85) REVERT: B 185 ASP cc_start: 0.8331 (m-30) cc_final: 0.7958 (m-30) REVERT: B 188 ASP cc_start: 0.8012 (m-30) cc_final: 0.7538 (m-30) REVERT: B 194 LEU cc_start: 0.9000 (mt) cc_final: 0.8662 (mm) REVERT: B 199 TYR cc_start: 0.7411 (m-10) cc_final: 0.6439 (m-10) REVERT: B 208 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7766 (mm-30) REVERT: B 211 ARG cc_start: 0.8498 (ttp80) cc_final: 0.7928 (ttp80) REVERT: B 215 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7001 (mt-10) REVERT: B 243 LEU cc_start: 0.7934 (mt) cc_final: 0.7587 (mt) REVERT: B 247 GLN cc_start: 0.7884 (mm110) cc_final: 0.7541 (tp-100) REVERT: B 248 VAL cc_start: 0.8594 (t) cc_final: 0.8158 (p) REVERT: B 254 GLU cc_start: 0.8028 (mp0) cc_final: 0.7694 (mp0) REVERT: B 264 GLN cc_start: 0.8196 (mt0) cc_final: 0.7557 (mp10) REVERT: B 272 SER cc_start: 0.8277 (m) cc_final: 0.7890 (t) REVERT: B 283 ILE cc_start: 0.7930 (mt) cc_final: 0.7606 (tt) REVERT: B 285 LYS cc_start: 0.8380 (tttp) cc_final: 0.8170 (tttp) REVERT: B 287 ASP cc_start: 0.7560 (m-30) cc_final: 0.7226 (m-30) REVERT: B 292 LYS cc_start: 0.7945 (pttm) cc_final: 0.7601 (pttm) REVERT: B 295 TYR cc_start: 0.6847 (m-80) cc_final: 0.6570 (m-80) REVERT: B 300 MET cc_start: 0.7611 (mmm) cc_final: 0.7317 (mmm) REVERT: B 306 MET cc_start: 0.7276 (mmm) cc_final: 0.7030 (mmm) REVERT: B 314 MET cc_start: 0.7637 (tpp) cc_final: 0.7124 (tpp) REVERT: B 315 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7887 (tm-30) REVERT: B 347 LEU cc_start: 0.8107 (tp) cc_final: 0.7777 (tp) REVERT: B 355 GLN cc_start: 0.8315 (pm20) cc_final: 0.7957 (pm20) REVERT: B 356 MET cc_start: 0.8609 (mpp) cc_final: 0.7900 (mpp) REVERT: B 362 GLU cc_start: 0.9013 (tt0) cc_final: 0.8723 (tt0) REVERT: C 16 LEU cc_start: 0.7168 (tp) cc_final: 0.6781 (tp) REVERT: C 18 LYS cc_start: 0.7400 (mtmm) cc_final: 0.7027 (mtmm) REVERT: C 28 ARG cc_start: 0.8234 (ptm160) cc_final: 0.7989 (ptm160) REVERT: C 50 LYS cc_start: 0.8262 (mttt) cc_final: 0.7898 (mttt) REVERT: C 59 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8486 (tm-30) REVERT: C 61 LYS cc_start: 0.8393 (mttm) cc_final: 0.7801 (mttm) REVERT: C 76 ILE cc_start: 0.8113 (mt) cc_final: 0.7891 (mt) REVERT: C 78 ASN cc_start: 0.7629 (t0) cc_final: 0.6388 (t0) REVERT: C 81 ASP cc_start: 0.7911 (m-30) cc_final: 0.7152 (m-30) REVERT: C 82 MET cc_start: 0.7973 (mmm) cc_final: 0.7200 (mmm) REVERT: C 86 TRP cc_start: 0.7925 (m-10) cc_final: 0.7279 (m-10) REVERT: C 99 GLU cc_start: 0.7001 (mp0) cc_final: 0.6660 (mp0) REVERT: C 111 ASN cc_start: 0.8108 (m-40) cc_final: 0.7601 (m-40) REVERT: C 113 LYS cc_start: 0.8358 (mttp) cc_final: 0.7834 (mttp) REVERT: C 117 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8084 (mt-10) REVERT: C 119 MET cc_start: 0.8683 (ttm) cc_final: 0.8217 (ttm) REVERT: C 127 PHE cc_start: 0.8328 (m-10) cc_final: 0.7948 (m-10) REVERT: C 137 GLN cc_start: 0.7884 (mt0) cc_final: 0.7534 (mp10) REVERT: C 152 VAL cc_start: 0.8317 (t) cc_final: 0.7970 (p) REVERT: C 154 ASP cc_start: 0.6810 (t70) cc_final: 0.6262 (t0) REVERT: C 161 HIS cc_start: 0.7383 (p90) cc_final: 0.7179 (p-80) REVERT: C 165 ILE cc_start: 0.8594 (mt) cc_final: 0.8278 (mm) REVERT: C 176 MET cc_start: 0.6572 (mtt) cc_final: 0.6294 (mtt) REVERT: C 198 TYR cc_start: 0.7676 (m-10) cc_final: 0.7295 (m-80) REVERT: C 205 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7424 (mt-10) REVERT: C 208 ILE cc_start: 0.8538 (mp) cc_final: 0.8327 (mm) REVERT: C 210 ARG cc_start: 0.8204 (ptm-80) cc_final: 0.7876 (ttp80) REVERT: C 213 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8171 (ttpp) REVERT: C 214 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7701 (mt-10) REVERT: C 215 LYS cc_start: 0.8691 (mttm) cc_final: 0.8373 (mmmm) REVERT: C 238 LYS cc_start: 0.7984 (mmtm) cc_final: 0.7424 (mmtt) REVERT: C 253 GLU cc_start: 0.7129 (mp0) cc_final: 0.6564 (mp0) REVERT: C 256 ARG cc_start: 0.7805 (ttm170) cc_final: 0.7148 (ttm-80) REVERT: C 278 THR cc_start: 0.7890 (m) cc_final: 0.7621 (p) REVERT: C 279 TYR cc_start: 0.8029 (t80) cc_final: 0.7588 (t80) REVERT: C 283 MET cc_start: 0.7737 (mmp) cc_final: 0.7125 (mmp) REVERT: C 284 LYS cc_start: 0.8215 (tppt) cc_final: 0.7756 (tptt) REVERT: C 291 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8360 (mptt) REVERT: C 294 TYR cc_start: 0.7598 (m-80) cc_final: 0.7284 (m-80) REVERT: C 297 ASN cc_start: 0.7860 (m-40) cc_final: 0.7608 (m-40) REVERT: C 299 MET cc_start: 0.7876 (mmm) cc_final: 0.7392 (mmm) REVERT: C 306 TYR cc_start: 0.7675 (m-80) cc_final: 0.7459 (m-10) REVERT: C 314 GLN cc_start: 0.8805 (tt0) cc_final: 0.8044 (mm-40) REVERT: C 316 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8161 (mm-30) REVERT: C 325 MET cc_start: 0.7205 (mpp) cc_final: 0.6743 (mpp) REVERT: C 328 LYS cc_start: 0.8726 (mttt) cc_final: 0.8233 (mttt) REVERT: C 335 ARG cc_start: 0.7202 (mpp-170) cc_final: 0.6267 (mpt180) REVERT: C 336 LYS cc_start: 0.8054 (pttp) cc_final: 0.7466 (ptmm) REVERT: C 349 LEU cc_start: 0.8592 (tp) cc_final: 0.8331 (tp) REVERT: C 356 TRP cc_start: 0.6407 (m100) cc_final: 0.5944 (m100) REVERT: C 361 GLU cc_start: 0.8734 (tt0) cc_final: 0.8031 (tt0) REVERT: D 24 ASP cc_start: 0.6865 (m-30) cc_final: 0.6314 (m-30) REVERT: D 43 VAL cc_start: 0.7861 (t) cc_final: 0.7548 (p) REVERT: D 47 MET cc_start: 0.6861 (ttm) cc_final: 0.6411 (ttm) REVERT: D 50 LYS cc_start: 0.7877 (ttmt) cc_final: 0.7587 (ttmt) REVERT: D 54 VAL cc_start: 0.8503 (t) cc_final: 0.8036 (m) REVERT: D 61 LYS cc_start: 0.8138 (mtpp) cc_final: 0.7790 (mmtp) REVERT: D 76 ILE cc_start: 0.8123 (mt) cc_final: 0.7652 (mt) REVERT: D 78 ASN cc_start: 0.8152 (t0) cc_final: 0.7684 (t0) REVERT: D 79 TRP cc_start: 0.8054 (m100) cc_final: 0.7747 (m100) REVERT: D 82 MET cc_start: 0.7960 (mmm) cc_final: 0.7610 (mmm) REVERT: D 84 LYS cc_start: 0.8658 (tttt) cc_final: 0.8370 (tptt) REVERT: D 86 TRP cc_start: 0.7793 (m-10) cc_final: 0.7506 (m-10) REVERT: D 100 GLU cc_start: 0.7884 (tp30) cc_final: 0.7110 (tp30) REVERT: D 111 ASN cc_start: 0.7632 (t0) cc_final: 0.7194 (t0) REVERT: D 118 LYS cc_start: 0.8831 (tptt) cc_final: 0.8449 (tptt) REVERT: D 122 ILE cc_start: 0.8595 (mt) cc_final: 0.7919 (tp) REVERT: D 123 MET cc_start: 0.7913 (mmp) cc_final: 0.7696 (mmp) REVERT: D 133 TYR cc_start: 0.8150 (t80) cc_final: 0.7769 (t80) REVERT: D 137 GLN cc_start: 0.8282 (mt0) cc_final: 0.7913 (mp10) REVERT: D 153 LEU cc_start: 0.7990 (tp) cc_final: 0.7477 (tp) REVERT: D 176 MET cc_start: 0.6637 (mtp) cc_final: 0.5991 (mtp) REVERT: D 202 THR cc_start: 0.7244 (p) cc_final: 0.6497 (t) REVERT: D 205 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7485 (mt-10) REVERT: D 206 ARG cc_start: 0.8285 (ttm170) cc_final: 0.7964 (mtp-110) REVERT: D 207 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7306 (mm-30) REVERT: D 208 ILE cc_start: 0.8233 (mm) cc_final: 0.7962 (mm) REVERT: D 210 ARG cc_start: 0.8399 (ttp80) cc_final: 0.8125 (ttp80) REVERT: D 211 ASP cc_start: 0.7986 (m-30) cc_final: 0.7181 (m-30) REVERT: D 222 ASP cc_start: 0.8501 (t0) cc_final: 0.8148 (t0) REVERT: D 223 PHE cc_start: 0.7445 (t80) cc_final: 0.7190 (t80) REVERT: D 238 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7793 (mmmm) REVERT: D 253 GLU cc_start: 0.7466 (mp0) cc_final: 0.7177 (mp0) REVERT: D 276 GLU cc_start: 0.8503 (tp30) cc_final: 0.8280 (tp30) REVERT: D 280 ASN cc_start: 0.7791 (t0) cc_final: 0.6656 (t0) REVERT: D 281 SER cc_start: 0.8474 (p) cc_final: 0.7798 (p) REVERT: D 282 ILE cc_start: 0.8475 (mt) cc_final: 0.8244 (mt) REVERT: D 284 LYS cc_start: 0.8414 (mmpt) cc_final: 0.8199 (mmpt) REVERT: D 294 TYR cc_start: 0.7071 (m-80) cc_final: 0.6492 (m-80) REVERT: D 300 SER cc_start: 0.7421 (t) cc_final: 0.6872 (p) REVERT: D 306 TYR cc_start: 0.7318 (m-80) cc_final: 0.7051 (m-10) REVERT: D 313 MET cc_start: 0.8387 (tpt) cc_final: 0.7852 (tpt) REVERT: D 315 LYS cc_start: 0.8845 (ttpp) cc_final: 0.8526 (ttpp) REVERT: D 316 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7254 (mm-30) REVERT: D 317 ILE cc_start: 0.8831 (mm) cc_final: 0.8542 (mm) REVERT: D 325 MET cc_start: 0.6944 (ttm) cc_final: 0.6622 (ttm) REVERT: D 361 GLU cc_start: 0.8581 (mt-10) cc_final: 0.7878 (mt-10) outliers start: 0 outliers final: 0 residues processed: 737 average time/residue: 0.1479 time to fit residues: 149.5363 Evaluate side-chains 692 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 692 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 75 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 406 HIS A 458 ASN A 464 GLN ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 GLN B 174 HIS B 372 HIS C 92 ASN C 115 ASN C 225 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.082417 restraints weight = 40224.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.085768 restraints weight = 22430.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.088063 restraints weight = 14280.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.089605 restraints weight = 9911.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.090790 restraints weight = 7417.101| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15117 Z= 0.156 Angle : 0.644 11.741 20466 Z= 0.326 Chirality : 0.044 0.164 2241 Planarity : 0.005 0.062 2622 Dihedral : 10.089 167.108 2062 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.06 % Allowed : 1.45 % Favored : 98.49 % 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: 0.68 (0.20), residues: 1838 helix: 0.94 (0.18), residues: 830 sheet: -0.12 (0.30), residues: 288 loop : 0.33 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 63 TYR 0.028 0.002 TYR B 189 PHE 0.021 0.001 PHE B 125 TRP 0.020 0.002 TRP A 414 HIS 0.015 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00313 (15117) covalent geometry : angle 0.64380 (20466) hydrogen bonds : bond 0.03989 ( 729) hydrogen bonds : angle 4.76656 ( 2013) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 744 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.8372 (ttp-110) cc_final: 0.8039 (ttp-110) REVERT: A 127 TYR cc_start: 0.7817 (m-80) cc_final: 0.7499 (m-80) REVERT: A 132 MET cc_start: 0.2744 (ppp) cc_final: 0.2418 (ppp) REVERT: A 140 PHE cc_start: 0.8130 (m-10) cc_final: 0.7760 (m-10) REVERT: A 144 GLU cc_start: 0.8152 (tp30) cc_final: 0.7249 (tp30) REVERT: A 148 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8684 (pttt) REVERT: A 150 MET cc_start: 0.8144 (ttp) cc_final: 0.7782 (ttp) REVERT: A 155 ARG cc_start: 0.7506 (ttt90) cc_final: 0.7275 (ttt-90) REVERT: A 158 SER cc_start: 0.6863 (t) cc_final: 0.6296 (m) REVERT: A 178 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8158 (mmm-85) REVERT: A 203 MET cc_start: 0.8507 (ptp) cc_final: 0.8295 (ptp) REVERT: A 228 PHE cc_start: 0.7312 (m-80) cc_final: 0.6972 (m-10) REVERT: A 233 ARG cc_start: 0.7599 (tpt170) cc_final: 0.6924 (tpt-90) REVERT: A 241 THR cc_start: 0.7429 (t) cc_final: 0.7084 (t) REVERT: A 262 PHE cc_start: 0.8326 (m-80) cc_final: 0.7930 (m-80) REVERT: A 304 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7914 (mm-30) REVERT: A 312 CYS cc_start: 0.8733 (m) cc_final: 0.8509 (m) REVERT: A 328 ILE cc_start: 0.8483 (mt) cc_final: 0.8164 (mm) REVERT: A 332 ILE cc_start: 0.8472 (pt) cc_final: 0.8256 (pt) REVERT: A 354 HIS cc_start: 0.7886 (t70) cc_final: 0.7189 (t-170) REVERT: A 363 LEU cc_start: 0.8201 (mt) cc_final: 0.7889 (mt) REVERT: A 369 GLU cc_start: 0.8439 (mp0) cc_final: 0.8098 (pm20) REVERT: A 372 CYS cc_start: 0.8866 (t) cc_final: 0.8505 (p) REVERT: A 374 TRP cc_start: 0.8602 (m100) cc_final: 0.8265 (m100) REVERT: A 385 GLU cc_start: 0.7595 (tp30) cc_final: 0.6982 (tm-30) REVERT: A 389 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8324 (tppt) REVERT: A 393 LYS cc_start: 0.8464 (tttt) cc_final: 0.7918 (tptt) REVERT: A 400 ARG cc_start: 0.8192 (ttp-170) cc_final: 0.7714 (tmm160) REVERT: A 406 HIS cc_start: 0.8832 (t-170) cc_final: 0.7399 (t70) REVERT: A 410 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8165 (mmtt) REVERT: A 413 ASN cc_start: 0.8553 (m110) cc_final: 0.8233 (m-40) REVERT: A 453 CYS cc_start: 0.8645 (m) cc_final: 0.8405 (p) REVERT: A 455 ASN cc_start: 0.8615 (m-40) cc_final: 0.7843 (m-40) REVERT: A 459 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 460 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8471 (mmmt) REVERT: A 461 LEU cc_start: 0.8933 (mt) cc_final: 0.8659 (pp) REVERT: A 464 GLN cc_start: 0.8809 (tt0) cc_final: 0.7695 (tm-30) REVERT: A 466 ASN cc_start: 0.8549 (m-40) cc_final: 0.8230 (m-40) REVERT: A 468 HIS cc_start: 0.8239 (t-90) cc_final: 0.7833 (t-90) REVERT: A 469 VAL cc_start: 0.8917 (t) cc_final: 0.8647 (m) REVERT: A 473 GLU cc_start: 0.8556 (tp30) cc_final: 0.7938 (tm-30) REVERT: A 499 ILE cc_start: 0.9016 (mt) cc_final: 0.8652 (tt) REVERT: A 501 SER cc_start: 0.8051 (m) cc_final: 0.7763 (p) REVERT: A 502 LYS cc_start: 0.8408 (mmtp) cc_final: 0.8033 (mmtp) REVERT: A 507 ASP cc_start: 0.8494 (m-30) cc_final: 0.8254 (m-30) REVERT: A 508 LEU cc_start: 0.8437 (mt) cc_final: 0.8207 (mt) REVERT: A 511 GLU cc_start: 0.8155 (tt0) cc_final: 0.7297 (tt0) REVERT: A 515 MET cc_start: 0.6555 (tpt) cc_final: 0.6327 (tpt) REVERT: A 522 THR cc_start: 0.7885 (p) cc_final: 0.7576 (p) REVERT: A 526 LYS cc_start: 0.8812 (mttt) cc_final: 0.7896 (mmtt) REVERT: A 545 ASN cc_start: 0.8341 (m-40) cc_final: 0.8110 (m-40) REVERT: A 569 LYS cc_start: 0.8078 (mttt) cc_final: 0.7696 (mmtm) REVERT: A 574 GLU cc_start: 0.7764 (pm20) cc_final: 0.7399 (pm20) REVERT: A 575 GLU cc_start: 0.7600 (pm20) cc_final: 0.6900 (pm20) REVERT: A 577 ILE cc_start: 0.8497 (mm) cc_final: 0.8217 (mm) REVERT: A 578 LYS cc_start: 0.8845 (mtpp) cc_final: 0.8481 (mtmm) REVERT: A 581 LYS cc_start: 0.8967 (tttt) cc_final: 0.8710 (mtpp) REVERT: A 592 PHE cc_start: 0.7832 (m-80) cc_final: 0.7569 (m-80) REVERT: A 629 LYS cc_start: 0.8589 (tptp) cc_final: 0.8183 (tptp) REVERT: A 632 LYS cc_start: 0.9060 (mtmt) cc_final: 0.8796 (pttm) REVERT: A 641 ASN cc_start: 0.8953 (m-40) cc_final: 0.8690 (m110) REVERT: A 644 HIS cc_start: 0.8068 (m90) cc_final: 0.7781 (m90) REVERT: A 647 MET cc_start: 0.7941 (tpt) cc_final: 0.7482 (tpt) REVERT: A 650 LEU cc_start: 0.8740 (mt) cc_final: 0.8527 (mt) REVERT: A 651 ASN cc_start: 0.8612 (t0) cc_final: 0.8367 (t0) REVERT: A 653 THR cc_start: 0.8308 (p) cc_final: 0.8047 (p) REVERT: A 657 TYR cc_start: 0.7529 (m-80) cc_final: 0.7054 (m-80) REVERT: A 673 ASP cc_start: 0.7657 (t0) cc_final: 0.7391 (t0) REVERT: A 675 LYS cc_start: 0.8496 (mmtp) cc_final: 0.7996 (mptt) REVERT: A 732 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7557 (tp30) REVERT: B 29 ARG cc_start: 0.7728 (ttm110) cc_final: 0.7494 (ptp-110) REVERT: B 35 ILE cc_start: 0.8509 (mt) cc_final: 0.8129 (mm) REVERT: B 51 LYS cc_start: 0.7642 (ptpp) cc_final: 0.7322 (pttp) REVERT: B 81 ASP cc_start: 0.8605 (p0) cc_final: 0.7551 (m-30) REVERT: B 83 MET cc_start: 0.8470 (mmm) cc_final: 0.7108 (tmm) REVERT: B 85 LYS cc_start: 0.8728 (mttm) cc_final: 0.8265 (mttm) REVERT: B 86 ILE cc_start: 0.8500 (mm) cc_final: 0.8276 (tp) REVERT: B 87 TRP cc_start: 0.8103 (m-10) cc_final: 0.7556 (m-90) REVERT: B 94 GLU cc_start: 0.7978 (tp30) cc_final: 0.7615 (tp30) REVERT: B 95 LEU cc_start: 0.8813 (mm) cc_final: 0.8354 (mm) REVERT: B 101 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8127 (mm-30) REVERT: B 102 HIS cc_start: 0.8468 (m-70) cc_final: 0.7961 (m-70) REVERT: B 114 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8187 (mtmt) REVERT: B 116 ASN cc_start: 0.8249 (t0) cc_final: 0.8025 (t0) REVERT: B 117 ARG cc_start: 0.8261 (ttm110) cc_final: 0.7924 (ttm170) REVERT: B 119 LYS cc_start: 0.8709 (tptt) cc_final: 0.7734 (mmmt) REVERT: B 120 MET cc_start: 0.8599 (ttm) cc_final: 0.8074 (ttm) REVERT: B 122 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8456 (tm-30) REVERT: B 123 ILE cc_start: 0.8872 (mt) cc_final: 0.8268 (tp) REVERT: B 127 THR cc_start: 0.8677 (m) cc_final: 0.7628 (t) REVERT: B 128 PHE cc_start: 0.8232 (m-10) cc_final: 0.7776 (m-10) REVERT: B 144 TYR cc_start: 0.7540 (m-80) cc_final: 0.7227 (m-80) REVERT: B 166 ILE cc_start: 0.8522 (mt) cc_final: 0.8134 (mm) REVERT: B 176 ILE cc_start: 0.7236 (pt) cc_final: 0.7021 (mt) REVERT: B 177 MET cc_start: 0.7236 (mtt) cc_final: 0.6798 (mtm) REVERT: B 180 ASP cc_start: 0.6699 (m-30) cc_final: 0.6057 (t70) REVERT: B 184 ARG cc_start: 0.7927 (tpp80) cc_final: 0.7487 (mmm-85) REVERT: B 185 ASP cc_start: 0.8311 (m-30) cc_final: 0.7968 (m-30) REVERT: B 188 ASP cc_start: 0.8010 (m-30) cc_final: 0.7544 (m-30) REVERT: B 192 LYS cc_start: 0.8608 (tttt) cc_final: 0.8328 (tttt) REVERT: B 194 LEU cc_start: 0.8975 (mt) cc_final: 0.8585 (mm) REVERT: B 196 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7275 (mt-10) REVERT: B 208 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7876 (mm-30) REVERT: B 211 ARG cc_start: 0.8501 (ttp80) cc_final: 0.7977 (ttp80) REVERT: B 212 ASP cc_start: 0.8266 (m-30) cc_final: 0.8033 (m-30) REVERT: B 214 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8405 (ttmm) REVERT: B 215 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7003 (mt-10) REVERT: B 242 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6849 (tm-30) REVERT: B 254 GLU cc_start: 0.8041 (mp0) cc_final: 0.7808 (mp0) REVERT: B 255 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7857 (mtp85) REVERT: B 262 LEU cc_start: 0.8423 (mt) cc_final: 0.8216 (mm) REVERT: B 264 GLN cc_start: 0.8222 (mt0) cc_final: 0.7564 (mp10) REVERT: B 272 SER cc_start: 0.8403 (m) cc_final: 0.7969 (t) REVERT: B 281 ASN cc_start: 0.8087 (m-40) cc_final: 0.7845 (m-40) REVERT: B 283 ILE cc_start: 0.7958 (mt) cc_final: 0.7612 (tt) REVERT: B 284 MET cc_start: 0.7644 (mmm) cc_final: 0.7153 (mmm) REVERT: B 285 LYS cc_start: 0.8421 (tttp) cc_final: 0.8140 (tttp) REVERT: B 287 ASP cc_start: 0.7570 (m-30) cc_final: 0.7331 (m-30) REVERT: B 292 LYS cc_start: 0.7982 (pttm) cc_final: 0.7631 (pttm) REVERT: B 295 TYR cc_start: 0.6880 (m-80) cc_final: 0.6660 (m-80) REVERT: B 300 MET cc_start: 0.7650 (mmm) cc_final: 0.7389 (mmm) REVERT: B 306 MET cc_start: 0.7292 (mmm) cc_final: 0.7020 (mmm) REVERT: B 314 MET cc_start: 0.7644 (tpp) cc_final: 0.7157 (tpp) REVERT: B 347 LEU cc_start: 0.7848 (tp) cc_final: 0.7536 (tp) REVERT: B 355 GLN cc_start: 0.8327 (pm20) cc_final: 0.7993 (pm20) REVERT: B 356 MET cc_start: 0.8556 (mpp) cc_final: 0.7934 (mpp) REVERT: B 358 ILE cc_start: 0.7625 (mt) cc_final: 0.6842 (mm) REVERT: B 362 GLU cc_start: 0.9019 (tt0) cc_final: 0.8656 (tt0) REVERT: C 16 LEU cc_start: 0.7075 (tp) cc_final: 0.6569 (mt) REVERT: C 50 LYS cc_start: 0.8300 (mttt) cc_final: 0.7916 (mttt) REVERT: C 78 ASN cc_start: 0.7620 (t0) cc_final: 0.6368 (t0) REVERT: C 81 ASP cc_start: 0.7852 (m-30) cc_final: 0.7109 (m-30) REVERT: C 82 MET cc_start: 0.8007 (mmm) cc_final: 0.7116 (mmm) REVERT: C 86 TRP cc_start: 0.7942 (m-10) cc_final: 0.7407 (m-10) REVERT: C 104 LEU cc_start: 0.8596 (tp) cc_final: 0.8302 (tp) REVERT: C 105 LEU cc_start: 0.8040 (mm) cc_final: 0.7620 (mm) REVERT: C 111 ASN cc_start: 0.8041 (m-40) cc_final: 0.7563 (m-40) REVERT: C 113 LYS cc_start: 0.8405 (mttp) cc_final: 0.7128 (mttp) REVERT: C 119 MET cc_start: 0.8677 (ttm) cc_final: 0.8170 (ttm) REVERT: C 125 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7685 (mt-10) REVERT: C 152 VAL cc_start: 0.8307 (t) cc_final: 0.8060 (p) REVERT: C 165 ILE cc_start: 0.8600 (mt) cc_final: 0.8259 (mm) REVERT: C 176 MET cc_start: 0.6509 (mtt) cc_final: 0.6298 (mtt) REVERT: C 178 LEU cc_start: 0.8241 (tp) cc_final: 0.7998 (tp) REVERT: C 190 MET cc_start: 0.7836 (mtm) cc_final: 0.7515 (mtm) REVERT: C 198 TYR cc_start: 0.7837 (m-10) cc_final: 0.7633 (m-80) REVERT: C 205 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7287 (mt-10) REVERT: C 208 ILE cc_start: 0.8587 (mp) cc_final: 0.8365 (mp) REVERT: C 210 ARG cc_start: 0.8225 (ptm-80) cc_final: 0.7845 (ttp80) REVERT: C 213 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8175 (ttpp) REVERT: C 214 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7647 (mt-10) REVERT: C 215 LYS cc_start: 0.8666 (mttm) cc_final: 0.8325 (mmmm) REVERT: C 253 GLU cc_start: 0.7111 (mp0) cc_final: 0.6356 (mp0) REVERT: C 256 ARG cc_start: 0.7781 (ttm170) cc_final: 0.7168 (ttm-80) REVERT: C 261 LEU cc_start: 0.8296 (mt) cc_final: 0.7990 (mm) REVERT: C 278 THR cc_start: 0.7876 (m) cc_final: 0.7594 (p) REVERT: C 279 TYR cc_start: 0.8003 (t80) cc_final: 0.7505 (t80) REVERT: C 283 MET cc_start: 0.7797 (mmp) cc_final: 0.7260 (mmp) REVERT: C 284 LYS cc_start: 0.8242 (tppt) cc_final: 0.7815 (tppt) REVERT: C 288 ASP cc_start: 0.8022 (m-30) cc_final: 0.7780 (p0) REVERT: C 291 LYS cc_start: 0.8765 (mtpt) cc_final: 0.8353 (mptt) REVERT: C 294 TYR cc_start: 0.7610 (m-80) cc_final: 0.7388 (m-80) REVERT: C 296 ASN cc_start: 0.8316 (m110) cc_final: 0.8102 (m110) REVERT: C 299 MET cc_start: 0.7886 (mmm) cc_final: 0.7325 (mmm) REVERT: C 305 MET cc_start: 0.7666 (mmt) cc_final: 0.7373 (mmt) REVERT: C 325 MET cc_start: 0.7264 (mpp) cc_final: 0.6897 (mpp) REVERT: C 326 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7743 (mmmt) REVERT: C 328 LYS cc_start: 0.8702 (mttt) cc_final: 0.8281 (mttt) REVERT: C 330 ILE cc_start: 0.8831 (mp) cc_final: 0.8463 (pt) REVERT: C 336 LYS cc_start: 0.8228 (pttp) cc_final: 0.7571 (ptmm) REVERT: C 349 LEU cc_start: 0.8627 (tp) cc_final: 0.8362 (tp) REVERT: C 356 TRP cc_start: 0.6588 (m100) cc_final: 0.6166 (m100) REVERT: C 360 GLN cc_start: 0.9005 (pm20) cc_final: 0.8590 (pm20) REVERT: D 24 ASP cc_start: 0.6975 (m-30) cc_final: 0.6311 (m-30) REVERT: D 43 VAL cc_start: 0.7884 (t) cc_final: 0.7610 (p) REVERT: D 50 LYS cc_start: 0.7917 (ttmt) cc_final: 0.7666 (ttmt) REVERT: D 54 VAL cc_start: 0.8516 (t) cc_final: 0.8120 (m) REVERT: D 61 LYS cc_start: 0.8107 (mtpp) cc_final: 0.7570 (mmtp) REVERT: D 76 ILE cc_start: 0.8145 (mt) cc_final: 0.7582 (mt) REVERT: D 78 ASN cc_start: 0.8188 (t0) cc_final: 0.7675 (t0) REVERT: D 79 TRP cc_start: 0.8145 (m100) cc_final: 0.7386 (m100) REVERT: D 82 MET cc_start: 0.7927 (mmm) cc_final: 0.7719 (mmm) REVERT: D 84 LYS cc_start: 0.8671 (tttt) cc_final: 0.8371 (tptt) REVERT: D 100 GLU cc_start: 0.7877 (tp30) cc_final: 0.7136 (tp30) REVERT: D 118 LYS cc_start: 0.8846 (tptt) cc_final: 0.8439 (tptt) REVERT: D 122 ILE cc_start: 0.8613 (mt) cc_final: 0.7930 (tp) REVERT: D 137 GLN cc_start: 0.8253 (mt0) cc_final: 0.7935 (mp10) REVERT: D 153 LEU cc_start: 0.7949 (tp) cc_final: 0.7515 (tp) REVERT: D 166 TYR cc_start: 0.8009 (t80) cc_final: 0.7731 (t80) REVERT: D 176 MET cc_start: 0.6675 (mtp) cc_final: 0.6062 (mtp) REVERT: D 202 THR cc_start: 0.7206 (p) cc_final: 0.6371 (t) REVERT: D 205 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7465 (mt-10) REVERT: D 206 ARG cc_start: 0.8367 (ttm170) cc_final: 0.8094 (mtp-110) REVERT: D 208 ILE cc_start: 0.8226 (mm) cc_final: 0.7989 (mm) REVERT: D 210 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8026 (ttp80) REVERT: D 211 ASP cc_start: 0.7997 (m-30) cc_final: 0.7198 (m-30) REVERT: D 223 PHE cc_start: 0.7461 (t80) cc_final: 0.7200 (t80) REVERT: D 238 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7871 (mmmm) REVERT: D 253 GLU cc_start: 0.7578 (mp0) cc_final: 0.7310 (mp0) REVERT: D 280 ASN cc_start: 0.7925 (t0) cc_final: 0.6846 (t0) REVERT: D 281 SER cc_start: 0.8508 (p) cc_final: 0.7883 (p) REVERT: D 282 ILE cc_start: 0.8467 (mt) cc_final: 0.8266 (mt) REVERT: D 284 LYS cc_start: 0.8476 (mmpt) cc_final: 0.8242 (mmpt) REVERT: D 294 TYR cc_start: 0.7184 (m-80) cc_final: 0.6541 (m-80) REVERT: D 299 MET cc_start: 0.7511 (mmm) cc_final: 0.7264 (mmm) REVERT: D 300 SER cc_start: 0.7466 (t) cc_final: 0.6962 (p) REVERT: D 306 TYR cc_start: 0.7343 (m-80) cc_final: 0.7106 (m-10) REVERT: D 313 MET cc_start: 0.8385 (tpt) cc_final: 0.7869 (tpt) REVERT: D 315 LYS cc_start: 0.8807 (ttpp) cc_final: 0.8496 (ttpp) REVERT: D 316 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7329 (mm-30) REVERT: D 317 ILE cc_start: 0.8886 (mm) cc_final: 0.8604 (mm) REVERT: D 325 MET cc_start: 0.7004 (ttm) cc_final: 0.6680 (ttm) REVERT: D 340 TRP cc_start: 0.7931 (t60) cc_final: 0.6794 (t60) REVERT: D 361 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7910 (mt-10) outliers start: 1 outliers final: 1 residues processed: 744 average time/residue: 0.1474 time to fit residues: 150.4489 Evaluate side-chains 700 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 699 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 80 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 139 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 HIS C 73 HIS ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS C 225 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS D 371 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.100582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.082061 restraints weight = 40259.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.085401 restraints weight = 22347.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087699 restraints weight = 14136.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.089068 restraints weight = 9774.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.090310 restraints weight = 7482.836| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.6450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15117 Z= 0.156 Angle : 0.664 10.624 20466 Z= 0.335 Chirality : 0.045 0.175 2241 Planarity : 0.005 0.049 2622 Dihedral : 9.885 173.247 2062 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 0.60 (0.20), residues: 1838 helix: 0.91 (0.18), residues: 819 sheet: -0.14 (0.30), residues: 287 loop : 0.25 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 37 TYR 0.025 0.002 TYR C 166 PHE 0.027 0.001 PHE A 465 TRP 0.024 0.002 TRP A 414 HIS 0.015 0.002 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00315 (15117) covalent geometry : angle 0.66438 (20466) hydrogen bonds : bond 0.04018 ( 729) hydrogen bonds : angle 4.80960 ( 2013) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 746 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASN cc_start: 0.8751 (m110) cc_final: 0.8327 (m110) REVERT: A 90 ARG cc_start: 0.8412 (ttp-110) cc_final: 0.8002 (ttp-110) REVERT: A 127 TYR cc_start: 0.7916 (m-10) cc_final: 0.7501 (m-80) REVERT: A 140 PHE cc_start: 0.8068 (m-10) cc_final: 0.7668 (m-10) REVERT: A 145 GLU cc_start: 0.8705 (tt0) cc_final: 0.8135 (tm-30) REVERT: A 148 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8701 (mmtt) REVERT: A 150 MET cc_start: 0.8195 (ttp) cc_final: 0.7813 (ttp) REVERT: A 155 ARG cc_start: 0.7524 (ttt90) cc_final: 0.7254 (ttt90) REVERT: A 158 SER cc_start: 0.6906 (t) cc_final: 0.6577 (m) REVERT: A 178 ARG cc_start: 0.8641 (mmm-85) cc_final: 0.8074 (ttp80) REVERT: A 228 PHE cc_start: 0.7314 (m-80) cc_final: 0.7044 (m-80) REVERT: A 246 LYS cc_start: 0.8836 (mmtm) cc_final: 0.8333 (mmmt) REVERT: A 262 PHE cc_start: 0.8264 (m-80) cc_final: 0.7821 (m-80) REVERT: A 274 PHE cc_start: 0.7961 (m-10) cc_final: 0.7706 (m-80) REVERT: A 304 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7833 (mm-30) REVERT: A 312 CYS cc_start: 0.8739 (m) cc_final: 0.8531 (m) REVERT: A 323 MET cc_start: 0.8083 (mmm) cc_final: 0.7701 (mmm) REVERT: A 328 ILE cc_start: 0.8528 (mt) cc_final: 0.8237 (mm) REVERT: A 332 ILE cc_start: 0.8548 (pt) cc_final: 0.8326 (pt) REVERT: A 363 LEU cc_start: 0.8196 (mt) cc_final: 0.7755 (pp) REVERT: A 369 GLU cc_start: 0.8438 (mp0) cc_final: 0.8028 (pm20) REVERT: A 372 CYS cc_start: 0.8897 (t) cc_final: 0.8494 (p) REVERT: A 374 TRP cc_start: 0.8608 (m100) cc_final: 0.8322 (m100) REVERT: A 385 GLU cc_start: 0.7553 (tp30) cc_final: 0.6967 (tm-30) REVERT: A 389 LYS cc_start: 0.8615 (mmtp) cc_final: 0.8093 (tppt) REVERT: A 393 LYS cc_start: 0.8453 (tttt) cc_final: 0.7917 (tptt) REVERT: A 400 ARG cc_start: 0.8152 (ttp-170) cc_final: 0.7683 (tmm160) REVERT: A 406 HIS cc_start: 0.8787 (t-170) cc_final: 0.7740 (t70) REVERT: A 410 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8053 (mttt) REVERT: A 413 ASN cc_start: 0.8606 (m110) cc_final: 0.8310 (m-40) REVERT: A 453 CYS cc_start: 0.8683 (m) cc_final: 0.8352 (p) REVERT: A 455 ASN cc_start: 0.8657 (m-40) cc_final: 0.7673 (m-40) REVERT: A 459 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 460 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8488 (mmmt) REVERT: A 461 LEU cc_start: 0.8919 (mt) cc_final: 0.8675 (pp) REVERT: A 464 GLN cc_start: 0.8820 (tt0) cc_final: 0.7622 (tm-30) REVERT: A 466 ASN cc_start: 0.8540 (m-40) cc_final: 0.8217 (m-40) REVERT: A 467 MET cc_start: 0.8148 (tmm) cc_final: 0.7861 (tmm) REVERT: A 469 VAL cc_start: 0.8923 (t) cc_final: 0.8665 (m) REVERT: A 478 MET cc_start: 0.8262 (ttt) cc_final: 0.7959 (ttt) REVERT: A 499 ILE cc_start: 0.8988 (mt) cc_final: 0.8601 (tt) REVERT: A 501 SER cc_start: 0.8054 (m) cc_final: 0.7748 (p) REVERT: A 502 LYS cc_start: 0.8446 (mmtp) cc_final: 0.8043 (mmtp) REVERT: A 507 ASP cc_start: 0.8512 (m-30) cc_final: 0.8297 (m-30) REVERT: A 508 LEU cc_start: 0.8440 (mt) cc_final: 0.8213 (mt) REVERT: A 511 GLU cc_start: 0.8117 (tt0) cc_final: 0.7416 (tt0) REVERT: A 575 GLU cc_start: 0.7687 (pm20) cc_final: 0.7181 (pm20) REVERT: A 577 ILE cc_start: 0.8509 (mm) cc_final: 0.8272 (mm) REVERT: A 578 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8530 (mtmm) REVERT: A 581 LYS cc_start: 0.8957 (tttt) cc_final: 0.8722 (mtpp) REVERT: A 592 PHE cc_start: 0.7771 (m-80) cc_final: 0.7170 (m-10) REVERT: A 630 GLU cc_start: 0.8357 (tt0) cc_final: 0.7866 (tt0) REVERT: A 632 LYS cc_start: 0.9090 (mtmt) cc_final: 0.8811 (pttm) REVERT: A 641 ASN cc_start: 0.8983 (m-40) cc_final: 0.8184 (m110) REVERT: A 644 HIS cc_start: 0.8209 (m90) cc_final: 0.7529 (m170) REVERT: A 647 MET cc_start: 0.7996 (tpt) cc_final: 0.7462 (tpt) REVERT: A 648 GLU cc_start: 0.8789 (pt0) cc_final: 0.8443 (tm-30) REVERT: A 651 ASN cc_start: 0.8649 (t0) cc_final: 0.8358 (t0) REVERT: A 653 THR cc_start: 0.8324 (p) cc_final: 0.8029 (p) REVERT: A 657 TYR cc_start: 0.7516 (m-80) cc_final: 0.6863 (m-80) REVERT: A 673 ASP cc_start: 0.7675 (t0) cc_final: 0.7100 (t0) REVERT: A 675 LYS cc_start: 0.8517 (mmtp) cc_final: 0.7986 (mptt) REVERT: B 12 ASP cc_start: 0.7235 (t70) cc_final: 0.6724 (p0) REVERT: B 26 ASP cc_start: 0.7457 (m-30) cc_final: 0.7248 (m-30) REVERT: B 51 LYS cc_start: 0.7677 (ptpp) cc_final: 0.7397 (pttp) REVERT: B 83 MET cc_start: 0.8383 (mmm) cc_final: 0.7417 (tmm) REVERT: B 84 GLU cc_start: 0.8460 (tt0) cc_final: 0.8163 (tt0) REVERT: B 85 LYS cc_start: 0.8701 (mttm) cc_final: 0.8220 (mttm) REVERT: B 87 TRP cc_start: 0.8126 (m-10) cc_final: 0.7471 (m-10) REVERT: B 93 ASN cc_start: 0.7932 (m-40) cc_final: 0.7709 (m-40) REVERT: B 101 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8077 (mm-30) REVERT: B 114 LYS cc_start: 0.8513 (mtmt) cc_final: 0.8278 (mtmt) REVERT: B 117 ARG cc_start: 0.8276 (ttm110) cc_final: 0.8034 (ttm170) REVERT: B 119 LYS cc_start: 0.8648 (tptt) cc_final: 0.7868 (tptt) REVERT: B 120 MET cc_start: 0.8550 (ttm) cc_final: 0.8087 (ttm) REVERT: B 123 ILE cc_start: 0.8831 (mt) cc_final: 0.8244 (tp) REVERT: B 127 THR cc_start: 0.8665 (m) cc_final: 0.7665 (p) REVERT: B 128 PHE cc_start: 0.8206 (m-10) cc_final: 0.7822 (m-10) REVERT: B 144 TYR cc_start: 0.7554 (m-80) cc_final: 0.7168 (m-80) REVERT: B 166 ILE cc_start: 0.8567 (mt) cc_final: 0.8162 (mm) REVERT: B 180 ASP cc_start: 0.6732 (m-30) cc_final: 0.5948 (t70) REVERT: B 184 ARG cc_start: 0.7937 (tpp80) cc_final: 0.7437 (mmm-85) REVERT: B 185 ASP cc_start: 0.8278 (m-30) cc_final: 0.7944 (m-30) REVERT: B 188 ASP cc_start: 0.7968 (m-30) cc_final: 0.7728 (t0) REVERT: B 192 LYS cc_start: 0.8583 (tttt) cc_final: 0.8212 (tttt) REVERT: B 194 LEU cc_start: 0.9060 (mt) cc_final: 0.8700 (mm) REVERT: B 208 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7824 (mm-30) REVERT: B 211 ARG cc_start: 0.8486 (ttp80) cc_final: 0.7973 (ttp80) REVERT: B 214 LYS cc_start: 0.8756 (ttpt) cc_final: 0.8417 (ttmm) REVERT: B 215 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7043 (mt-10) REVERT: B 248 VAL cc_start: 0.8579 (t) cc_final: 0.8364 (p) REVERT: B 255 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7922 (mtp85) REVERT: B 264 GLN cc_start: 0.7954 (mt0) cc_final: 0.7472 (mp10) REVERT: B 272 SER cc_start: 0.8441 (m) cc_final: 0.8013 (t) REVERT: B 283 ILE cc_start: 0.7928 (mt) cc_final: 0.7595 (tt) REVERT: B 284 MET cc_start: 0.7699 (mmm) cc_final: 0.7196 (mmm) REVERT: B 285 LYS cc_start: 0.8418 (tttp) cc_final: 0.8115 (tttp) REVERT: B 287 ASP cc_start: 0.7575 (m-30) cc_final: 0.7061 (p0) REVERT: B 292 LYS cc_start: 0.7979 (pttm) cc_final: 0.7653 (pttm) REVERT: B 295 TYR cc_start: 0.6903 (m-80) cc_final: 0.6666 (m-80) REVERT: B 300 MET cc_start: 0.7622 (mmm) cc_final: 0.7309 (mmm) REVERT: B 314 MET cc_start: 0.7636 (tpp) cc_final: 0.7162 (tpp) REVERT: B 355 GLN cc_start: 0.8354 (pm20) cc_final: 0.8028 (pm20) REVERT: B 356 MET cc_start: 0.8543 (mpp) cc_final: 0.7953 (mpp) REVERT: B 358 ILE cc_start: 0.7625 (mt) cc_final: 0.6989 (mm) REVERT: B 362 GLU cc_start: 0.8944 (tt0) cc_final: 0.8626 (tt0) REVERT: B 373 ARG cc_start: 0.8109 (mtm-85) cc_final: 0.7887 (mtm-85) REVERT: C 16 LEU cc_start: 0.7042 (tp) cc_final: 0.6587 (mt) REVERT: C 28 ARG cc_start: 0.8186 (ptt90) cc_final: 0.7375 (ptt90) REVERT: C 37 ARG cc_start: 0.7271 (mmm-85) cc_final: 0.6830 (mmm-85) REVERT: C 50 LYS cc_start: 0.8312 (mttt) cc_final: 0.7932 (mttt) REVERT: C 62 ARG cc_start: 0.5203 (ppt170) cc_final: 0.4413 (ppt170) REVERT: C 78 ASN cc_start: 0.7574 (t0) cc_final: 0.6241 (t0) REVERT: C 81 ASP cc_start: 0.7859 (m-30) cc_final: 0.7070 (m-30) REVERT: C 82 MET cc_start: 0.8071 (mmm) cc_final: 0.7291 (mmm) REVERT: C 99 GLU cc_start: 0.7054 (mp0) cc_final: 0.6638 (mp0) REVERT: C 104 LEU cc_start: 0.8585 (tp) cc_final: 0.8240 (tp) REVERT: C 105 LEU cc_start: 0.7976 (mm) cc_final: 0.7671 (mm) REVERT: C 111 ASN cc_start: 0.8132 (m-40) cc_final: 0.7397 (m110) REVERT: C 113 LYS cc_start: 0.8204 (mttp) cc_final: 0.7838 (mttp) REVERT: C 117 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8150 (mt-10) REVERT: C 119 MET cc_start: 0.8737 (ttm) cc_final: 0.8298 (ttm) REVERT: C 127 PHE cc_start: 0.8395 (m-10) cc_final: 0.8118 (m-10) REVERT: C 152 VAL cc_start: 0.8279 (t) cc_final: 0.7985 (m) REVERT: C 165 ILE cc_start: 0.8531 (mt) cc_final: 0.8162 (mm) REVERT: C 176 MET cc_start: 0.6583 (mtt) cc_final: 0.6283 (mtt) REVERT: C 178 LEU cc_start: 0.8240 (tp) cc_final: 0.7967 (tp) REVERT: C 185 LEU cc_start: 0.8358 (mt) cc_final: 0.8063 (mm) REVERT: C 190 MET cc_start: 0.7790 (mtm) cc_final: 0.7365 (mtm) REVERT: C 205 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7308 (mt-10) REVERT: C 206 ARG cc_start: 0.8157 (ttm110) cc_final: 0.7758 (ttp80) REVERT: C 208 ILE cc_start: 0.8595 (mp) cc_final: 0.8285 (mp) REVERT: C 210 ARG cc_start: 0.8243 (ptm-80) cc_final: 0.7809 (ttp80) REVERT: C 213 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8174 (ttpp) REVERT: C 214 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7374 (mt-10) REVERT: C 215 LYS cc_start: 0.8659 (mttm) cc_final: 0.8317 (mmmm) REVERT: C 238 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7461 (mmtt) REVERT: C 242 LEU cc_start: 0.8305 (mm) cc_final: 0.7748 (mt) REVERT: C 256 ARG cc_start: 0.7793 (ttm170) cc_final: 0.7146 (ttm-80) REVERT: C 261 LEU cc_start: 0.8292 (mt) cc_final: 0.8043 (mm) REVERT: C 276 GLU cc_start: 0.7401 (pm20) cc_final: 0.7037 (pm20) REVERT: C 278 THR cc_start: 0.7800 (m) cc_final: 0.7555 (m) REVERT: C 279 TYR cc_start: 0.8056 (t80) cc_final: 0.7671 (t80) REVERT: C 282 ILE cc_start: 0.8305 (mt) cc_final: 0.7643 (mm) REVERT: C 283 MET cc_start: 0.7836 (mmp) cc_final: 0.7426 (mmp) REVERT: C 284 LYS cc_start: 0.8224 (tppt) cc_final: 0.7774 (tppt) REVERT: C 288 ASP cc_start: 0.8071 (m-30) cc_final: 0.7833 (p0) REVERT: C 291 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8357 (mptt) REVERT: C 292 ASP cc_start: 0.8484 (m-30) cc_final: 0.8246 (m-30) REVERT: C 294 TYR cc_start: 0.7618 (m-80) cc_final: 0.7374 (m-80) REVERT: C 297 ASN cc_start: 0.7930 (m-40) cc_final: 0.7696 (m-40) REVERT: C 299 MET cc_start: 0.7925 (mmm) cc_final: 0.7406 (mmm) REVERT: C 305 MET cc_start: 0.7736 (mmm) cc_final: 0.7278 (mmm) REVERT: C 316 GLU cc_start: 0.8268 (tp30) cc_final: 0.7468 (tp30) REVERT: C 320 LEU cc_start: 0.8401 (mt) cc_final: 0.8144 (mt) REVERT: C 325 MET cc_start: 0.7228 (mpp) cc_final: 0.6913 (mpp) REVERT: C 326 LYS cc_start: 0.8172 (mmtm) cc_final: 0.7801 (mmmt) REVERT: C 328 LYS cc_start: 0.8711 (mttt) cc_final: 0.8305 (mttt) REVERT: C 330 ILE cc_start: 0.8873 (mp) cc_final: 0.8471 (pt) REVERT: C 336 LYS cc_start: 0.8335 (pttp) cc_final: 0.7626 (ptmm) REVERT: C 349 LEU cc_start: 0.8719 (tp) cc_final: 0.8485 (tp) REVERT: C 356 TRP cc_start: 0.6747 (m100) cc_final: 0.6431 (m100) REVERT: D 34 ILE cc_start: 0.9000 (mt) cc_final: 0.8274 (tp) REVERT: D 43 VAL cc_start: 0.7997 (t) cc_final: 0.7650 (p) REVERT: D 50 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7723 (ttmt) REVERT: D 54 VAL cc_start: 0.8588 (t) cc_final: 0.8265 (m) REVERT: D 61 LYS cc_start: 0.8090 (mtpp) cc_final: 0.7462 (mtpp) REVERT: D 76 ILE cc_start: 0.8159 (mt) cc_final: 0.7593 (mt) REVERT: D 78 ASN cc_start: 0.8185 (t0) cc_final: 0.7666 (t0) REVERT: D 79 TRP cc_start: 0.8223 (m100) cc_final: 0.7440 (m100) REVERT: D 100 GLU cc_start: 0.7864 (tp30) cc_final: 0.7113 (tp30) REVERT: D 107 GLU cc_start: 0.6213 (tt0) cc_final: 0.5342 (tt0) REVERT: D 116 ARG cc_start: 0.8152 (ttm110) cc_final: 0.7179 (ttm110) REVERT: D 118 LYS cc_start: 0.8825 (tptt) cc_final: 0.8296 (tptt) REVERT: D 122 ILE cc_start: 0.8579 (mt) cc_final: 0.7634 (mt) REVERT: D 137 GLN cc_start: 0.8319 (mt0) cc_final: 0.8037 (mp10) REVERT: D 153 LEU cc_start: 0.8058 (tp) cc_final: 0.7501 (tp) REVERT: D 157 ASP cc_start: 0.6299 (t0) cc_final: 0.6078 (t0) REVERT: D 166 TYR cc_start: 0.7986 (t80) cc_final: 0.7703 (t80) REVERT: D 176 MET cc_start: 0.6709 (mtp) cc_final: 0.6067 (mtp) REVERT: D 190 MET cc_start: 0.8072 (mtt) cc_final: 0.7736 (mmt) REVERT: D 194 THR cc_start: 0.8177 (m) cc_final: 0.7890 (p) REVERT: D 202 THR cc_start: 0.7212 (p) cc_final: 0.6470 (t) REVERT: D 205 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7473 (mt-10) REVERT: D 206 ARG cc_start: 0.8313 (ttm170) cc_final: 0.8063 (mtp-110) REVERT: D 210 ARG cc_start: 0.8418 (ttp80) cc_final: 0.8003 (ttp80) REVERT: D 211 ASP cc_start: 0.8020 (m-30) cc_final: 0.7217 (m-30) REVERT: D 238 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7935 (mmmm) REVERT: D 253 GLU cc_start: 0.7453 (mp0) cc_final: 0.7242 (mp0) REVERT: D 269 MET cc_start: 0.7427 (mtt) cc_final: 0.7188 (mtt) REVERT: D 280 ASN cc_start: 0.7999 (t0) cc_final: 0.6990 (t0) REVERT: D 281 SER cc_start: 0.8540 (p) cc_final: 0.7939 (p) REVERT: D 284 LYS cc_start: 0.8489 (mmpt) cc_final: 0.8233 (mmpt) REVERT: D 294 TYR cc_start: 0.7265 (m-80) cc_final: 0.6896 (m-80) REVERT: D 299 MET cc_start: 0.7524 (mmm) cc_final: 0.7314 (mmm) REVERT: D 300 SER cc_start: 0.7431 (t) cc_final: 0.6983 (p) REVERT: D 306 TYR cc_start: 0.7367 (m-80) cc_final: 0.7149 (m-10) REVERT: D 312 ARG cc_start: 0.8100 (tpt-90) cc_final: 0.6860 (tpp-160) REVERT: D 313 MET cc_start: 0.8383 (tpt) cc_final: 0.7840 (tpt) REVERT: D 315 LYS cc_start: 0.8797 (ttpp) cc_final: 0.8387 (ttpp) REVERT: D 316 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7360 (mm-30) REVERT: D 317 ILE cc_start: 0.8869 (mm) cc_final: 0.8603 (mm) REVERT: D 325 MET cc_start: 0.6961 (ttm) cc_final: 0.6659 (ttm) REVERT: D 340 TRP cc_start: 0.7951 (t60) cc_final: 0.6774 (t60) outliers start: 0 outliers final: 0 residues processed: 746 average time/residue: 0.1516 time to fit residues: 153.8354 Evaluate side-chains 695 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 695 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 123 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 GLN B 372 HIS C 73 HIS ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.097974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.079501 restraints weight = 40707.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.082782 restraints weight = 22502.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.085021 restraints weight = 14246.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.086571 restraints weight = 9854.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.087658 restraints weight = 7312.912| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.6958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 15117 Z= 0.260 Angle : 0.754 11.134 20466 Z= 0.392 Chirality : 0.048 0.214 2241 Planarity : 0.006 0.071 2622 Dihedral : 9.919 177.005 2062 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.06 % Allowed : 0.88 % Favored : 99.06 % 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: 0.13 (0.19), residues: 1838 helix: 0.59 (0.18), residues: 814 sheet: -0.50 (0.29), residues: 293 loop : -0.04 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 659 TYR 0.021 0.002 TYR A 439 PHE 0.025 0.002 PHE B 32 TRP 0.046 0.003 TRP A 523 HIS 0.020 0.002 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00502 (15117) covalent geometry : angle 0.75405 (20466) hydrogen bonds : bond 0.04919 ( 729) hydrogen bonds : angle 5.23774 ( 2013) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 752 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7463 (tp) cc_final: 0.7242 (tp) REVERT: A 89 LEU cc_start: 0.8911 (mt) cc_final: 0.8486 (pp) REVERT: A 90 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.8173 (ttp-110) REVERT: A 116 LEU cc_start: 0.8265 (tp) cc_final: 0.7298 (tp) REVERT: A 123 ILE cc_start: 0.8372 (mp) cc_final: 0.7614 (mt) REVERT: A 127 TYR cc_start: 0.7995 (m-10) cc_final: 0.7626 (m-80) REVERT: A 140 PHE cc_start: 0.8101 (m-10) cc_final: 0.7717 (m-10) REVERT: A 148 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8695 (mmtt) REVERT: A 150 MET cc_start: 0.8153 (ttp) cc_final: 0.7801 (ttp) REVERT: A 158 SER cc_start: 0.6868 (t) cc_final: 0.6477 (m) REVERT: A 178 ARG cc_start: 0.8649 (ttt-90) cc_final: 0.8264 (mmm-85) REVERT: A 179 TYR cc_start: 0.8067 (t80) cc_final: 0.7673 (t80) REVERT: A 216 ASN cc_start: 0.7214 (t0) cc_final: 0.6995 (t0) REVERT: A 231 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7175 (ttp80) REVERT: A 233 ARG cc_start: 0.7832 (tpt-90) cc_final: 0.7313 (tpt-90) REVERT: A 243 LEU cc_start: 0.8155 (mt) cc_final: 0.7928 (mt) REVERT: A 246 LYS cc_start: 0.8830 (mmtm) cc_final: 0.8381 (mmmt) REVERT: A 262 PHE cc_start: 0.8329 (m-80) cc_final: 0.7845 (m-80) REVERT: A 278 ARG cc_start: 0.8183 (mmp80) cc_final: 0.7978 (mmt180) REVERT: A 304 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8021 (mm-30) REVERT: A 312 CYS cc_start: 0.8818 (m) cc_final: 0.8607 (m) REVERT: A 323 MET cc_start: 0.8105 (mmm) cc_final: 0.7712 (mmm) REVERT: A 328 ILE cc_start: 0.8529 (mt) cc_final: 0.8259 (mm) REVERT: A 354 HIS cc_start: 0.8061 (t70) cc_final: 0.7348 (t70) REVERT: A 363 LEU cc_start: 0.8343 (mt) cc_final: 0.7925 (pp) REVERT: A 369 GLU cc_start: 0.8473 (mp0) cc_final: 0.8131 (pm20) REVERT: A 372 CYS cc_start: 0.8960 (t) cc_final: 0.8589 (p) REVERT: A 374 TRP cc_start: 0.8643 (m100) cc_final: 0.8195 (m100) REVERT: A 385 GLU cc_start: 0.7598 (tp30) cc_final: 0.7109 (tm-30) REVERT: A 389 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8203 (tppt) REVERT: A 393 LYS cc_start: 0.8662 (tttt) cc_final: 0.8198 (tppt) REVERT: A 400 ARG cc_start: 0.8197 (ttp-170) cc_final: 0.7634 (ttp80) REVERT: A 401 ASP cc_start: 0.7881 (m-30) cc_final: 0.7544 (m-30) REVERT: A 406 HIS cc_start: 0.8798 (t-170) cc_final: 0.8575 (t70) REVERT: A 410 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8176 (mmmt) REVERT: A 413 ASN cc_start: 0.8636 (m110) cc_final: 0.8300 (m-40) REVERT: A 436 LEU cc_start: 0.8066 (tp) cc_final: 0.7842 (tp) REVERT: A 438 ILE cc_start: 0.7956 (tp) cc_final: 0.7609 (tp) REVERT: A 453 CYS cc_start: 0.8680 (m) cc_final: 0.8354 (p) REVERT: A 458 ASN cc_start: 0.8515 (m110) cc_final: 0.8073 (m110) REVERT: A 459 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7567 (mm-30) REVERT: A 460 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8504 (mmmt) REVERT: A 461 LEU cc_start: 0.8959 (mt) cc_final: 0.8724 (pp) REVERT: A 464 GLN cc_start: 0.8851 (tt0) cc_final: 0.7794 (tm-30) REVERT: A 466 ASN cc_start: 0.8637 (m-40) cc_final: 0.8368 (m-40) REVERT: A 467 MET cc_start: 0.8160 (tmm) cc_final: 0.7903 (tmm) REVERT: A 468 HIS cc_start: 0.8303 (t-90) cc_final: 0.7830 (t-90) REVERT: A 469 VAL cc_start: 0.8998 (t) cc_final: 0.8768 (m) REVERT: A 470 PHE cc_start: 0.8372 (t80) cc_final: 0.8154 (t80) REVERT: A 471 LYS cc_start: 0.9243 (tppt) cc_final: 0.9009 (tppt) REVERT: A 499 ILE cc_start: 0.8928 (mt) cc_final: 0.8563 (tt) REVERT: A 501 SER cc_start: 0.8123 (m) cc_final: 0.7741 (p) REVERT: A 502 LYS cc_start: 0.8477 (mmtp) cc_final: 0.8086 (mmtp) REVERT: A 507 ASP cc_start: 0.8518 (m-30) cc_final: 0.8272 (m-30) REVERT: A 508 LEU cc_start: 0.8499 (mt) cc_final: 0.8206 (mt) REVERT: A 511 GLU cc_start: 0.8072 (tt0) cc_final: 0.7078 (tt0) REVERT: A 522 THR cc_start: 0.8106 (p) cc_final: 0.7436 (p) REVERT: A 526 LYS cc_start: 0.8844 (mttt) cc_final: 0.7862 (mmtt) REVERT: A 544 SER cc_start: 0.7732 (t) cc_final: 0.7384 (p) REVERT: A 545 ASN cc_start: 0.8459 (m-40) cc_final: 0.7990 (m-40) REVERT: A 546 LYS cc_start: 0.7549 (mmtt) cc_final: 0.6835 (tttm) REVERT: A 551 LYS cc_start: 0.8050 (tptt) cc_final: 0.7765 (tppt) REVERT: A 575 GLU cc_start: 0.7811 (pm20) cc_final: 0.7153 (pm20) REVERT: A 577 ILE cc_start: 0.8550 (mm) cc_final: 0.8296 (mm) REVERT: A 581 LYS cc_start: 0.8896 (tttt) cc_final: 0.8667 (mtpp) REVERT: A 592 PHE cc_start: 0.7746 (m-80) cc_final: 0.7449 (m-10) REVERT: A 629 LYS cc_start: 0.8764 (tptp) cc_final: 0.8522 (tptp) REVERT: A 630 GLU cc_start: 0.8562 (tt0) cc_final: 0.8195 (tt0) REVERT: A 632 LYS cc_start: 0.9081 (mtmt) cc_final: 0.8771 (pttm) REVERT: A 641 ASN cc_start: 0.8985 (m-40) cc_final: 0.8457 (m110) REVERT: A 644 HIS cc_start: 0.8208 (m90) cc_final: 0.7571 (m170) REVERT: A 647 MET cc_start: 0.8038 (tpt) cc_final: 0.7502 (tpt) REVERT: A 648 GLU cc_start: 0.8816 (pt0) cc_final: 0.8412 (tm-30) REVERT: A 651 ASN cc_start: 0.8678 (t0) cc_final: 0.8411 (t0) REVERT: A 653 THR cc_start: 0.8299 (p) cc_final: 0.7978 (p) REVERT: A 657 TYR cc_start: 0.7484 (m-80) cc_final: 0.7136 (m-80) REVERT: A 673 ASP cc_start: 0.7580 (t0) cc_final: 0.7081 (t0) REVERT: A 680 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8223 (mm-40) REVERT: B 26 ASP cc_start: 0.7506 (m-30) cc_final: 0.7270 (m-30) REVERT: B 35 ILE cc_start: 0.8420 (mt) cc_final: 0.7925 (mm) REVERT: B 81 ASP cc_start: 0.8583 (p0) cc_final: 0.8005 (m-30) REVERT: B 83 MET cc_start: 0.8416 (mmm) cc_final: 0.7343 (tmm) REVERT: B 84 GLU cc_start: 0.8465 (tt0) cc_final: 0.8197 (tt0) REVERT: B 87 TRP cc_start: 0.8149 (m-10) cc_final: 0.7576 (m-10) REVERT: B 93 ASN cc_start: 0.8022 (m-40) cc_final: 0.7762 (m-40) REVERT: B 94 GLU cc_start: 0.8022 (tp30) cc_final: 0.7773 (tp30) REVERT: B 100 GLU cc_start: 0.8011 (mp0) cc_final: 0.7748 (mp0) REVERT: B 101 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8111 (mm-30) REVERT: B 114 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8296 (mtmt) REVERT: B 116 ASN cc_start: 0.8283 (t0) cc_final: 0.7879 (t0) REVERT: B 117 ARG cc_start: 0.8143 (ttm110) cc_final: 0.7052 (ttm110) REVERT: B 119 LYS cc_start: 0.8705 (tptt) cc_final: 0.7810 (tptt) REVERT: B 120 MET cc_start: 0.8566 (ttm) cc_final: 0.7999 (ttm) REVERT: B 123 ILE cc_start: 0.8847 (mt) cc_final: 0.8261 (tp) REVERT: B 127 THR cc_start: 0.8674 (m) cc_final: 0.8029 (p) REVERT: B 166 ILE cc_start: 0.8572 (mt) cc_final: 0.8176 (mm) REVERT: B 177 MET cc_start: 0.7232 (mtm) cc_final: 0.6961 (mtt) REVERT: B 180 ASP cc_start: 0.6680 (m-30) cc_final: 0.6107 (t70) REVERT: B 184 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7365 (mmm-85) REVERT: B 185 ASP cc_start: 0.8252 (m-30) cc_final: 0.7810 (m-30) REVERT: B 188 ASP cc_start: 0.7991 (m-30) cc_final: 0.7502 (m-30) REVERT: B 192 LYS cc_start: 0.8632 (tttt) cc_final: 0.8231 (tttt) REVERT: B 194 LEU cc_start: 0.9125 (mt) cc_final: 0.8791 (mm) REVERT: B 196 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7383 (mt-10) REVERT: B 211 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8188 (ttp80) REVERT: B 212 ASP cc_start: 0.8306 (m-30) cc_final: 0.8002 (m-30) REVERT: B 214 LYS cc_start: 0.8839 (ttpt) cc_final: 0.8467 (ttmm) REVERT: B 215 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7128 (mt-10) REVERT: B 253 ASN cc_start: 0.8120 (p0) cc_final: 0.7866 (p0) REVERT: B 254 GLU cc_start: 0.8104 (mp0) cc_final: 0.7892 (mp0) REVERT: B 256 PHE cc_start: 0.7728 (p90) cc_final: 0.7491 (p90) REVERT: B 264 GLN cc_start: 0.7859 (mt0) cc_final: 0.7433 (mp10) REVERT: B 272 SER cc_start: 0.8556 (m) cc_final: 0.8126 (t) REVERT: B 283 ILE cc_start: 0.7994 (mt) cc_final: 0.7775 (mt) REVERT: B 284 MET cc_start: 0.7768 (mmm) cc_final: 0.7358 (mmm) REVERT: B 285 LYS cc_start: 0.8402 (tttp) cc_final: 0.8103 (tttp) REVERT: B 314 MET cc_start: 0.7710 (tpp) cc_final: 0.7380 (tpp) REVERT: B 315 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7928 (tm-30) REVERT: B 358 ILE cc_start: 0.7905 (mt) cc_final: 0.7077 (mm) REVERT: B 362 GLU cc_start: 0.8999 (tt0) cc_final: 0.8641 (tt0) REVERT: C 16 LEU cc_start: 0.7181 (tp) cc_final: 0.6725 (mt) REVERT: C 28 ARG cc_start: 0.8210 (ptt90) cc_final: 0.8010 (ptt90) REVERT: C 50 LYS cc_start: 0.8392 (mttt) cc_final: 0.7982 (mttt) REVERT: C 78 ASN cc_start: 0.7668 (t0) cc_final: 0.7204 (t0) REVERT: C 82 MET cc_start: 0.8061 (mmm) cc_final: 0.7346 (mmm) REVERT: C 83 GLU cc_start: 0.7971 (pt0) cc_final: 0.7430 (pp20) REVERT: C 84 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8333 (ttmm) REVERT: C 99 GLU cc_start: 0.7053 (mp0) cc_final: 0.6685 (mp0) REVERT: C 104 LEU cc_start: 0.8588 (tp) cc_final: 0.8146 (tp) REVERT: C 111 ASN cc_start: 0.8432 (m-40) cc_final: 0.7718 (m-40) REVERT: C 118 LYS cc_start: 0.8320 (tptt) cc_final: 0.7875 (tptt) REVERT: C 119 MET cc_start: 0.8790 (ttm) cc_final: 0.8350 (ttm) REVERT: C 125 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7845 (mt-10) REVERT: C 127 PHE cc_start: 0.8439 (m-10) cc_final: 0.8234 (m-10) REVERT: C 132 MET cc_start: 0.6337 (ppp) cc_final: 0.5532 (ppp) REVERT: C 161 HIS cc_start: 0.7172 (p-80) cc_final: 0.6541 (p-80) REVERT: C 165 ILE cc_start: 0.8622 (mt) cc_final: 0.8291 (tt) REVERT: C 166 TYR cc_start: 0.7975 (t80) cc_final: 0.7725 (t80) REVERT: C 176 MET cc_start: 0.6685 (mtt) cc_final: 0.6403 (mtt) REVERT: C 178 LEU cc_start: 0.8368 (tp) cc_final: 0.8141 (tp) REVERT: C 185 LEU cc_start: 0.8319 (mt) cc_final: 0.8062 (mm) REVERT: C 202 THR cc_start: 0.8363 (m) cc_final: 0.7852 (p) REVERT: C 205 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7147 (mt-10) REVERT: C 208 ILE cc_start: 0.8646 (mp) cc_final: 0.8426 (mm) REVERT: C 214 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7991 (mt-10) REVERT: C 215 LYS cc_start: 0.8684 (mttm) cc_final: 0.8289 (mmmm) REVERT: C 222 ASP cc_start: 0.7564 (p0) cc_final: 0.6027 (p0) REVERT: C 225 ASN cc_start: 0.8701 (m110) cc_final: 0.7872 (m-40) REVERT: C 226 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8168 (mm-30) REVERT: C 256 ARG cc_start: 0.7726 (ttm170) cc_final: 0.7156 (ttm-80) REVERT: C 259 GLU cc_start: 0.7540 (tp30) cc_final: 0.7250 (tm-30) REVERT: C 261 LEU cc_start: 0.8415 (mt) cc_final: 0.8137 (mm) REVERT: C 279 TYR cc_start: 0.8098 (t80) cc_final: 0.7588 (t80) REVERT: C 282 ILE cc_start: 0.8427 (mt) cc_final: 0.7579 (tt) REVERT: C 283 MET cc_start: 0.8019 (mmp) cc_final: 0.7365 (mmp) REVERT: C 284 LYS cc_start: 0.8391 (tppt) cc_final: 0.8006 (tppt) REVERT: C 286 ASP cc_start: 0.8227 (t0) cc_final: 0.8018 (t70) REVERT: C 291 LYS cc_start: 0.8786 (mtpt) cc_final: 0.8403 (mptt) REVERT: C 294 TYR cc_start: 0.7618 (m-80) cc_final: 0.7317 (m-80) REVERT: C 297 ASN cc_start: 0.7749 (m-40) cc_final: 0.7485 (m-40) REVERT: C 299 MET cc_start: 0.7933 (mmm) cc_final: 0.7269 (mmm) REVERT: C 305 MET cc_start: 0.7738 (mmm) cc_final: 0.7439 (mmm) REVERT: C 314 GLN cc_start: 0.8845 (tt0) cc_final: 0.8177 (mm-40) REVERT: C 315 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8777 (ttpp) REVERT: C 316 GLU cc_start: 0.8309 (tp30) cc_final: 0.7545 (tp30) REVERT: C 326 LYS cc_start: 0.8330 (mmtm) cc_final: 0.7921 (mmmt) REVERT: C 328 LYS cc_start: 0.8726 (mttt) cc_final: 0.8374 (mttt) REVERT: C 330 ILE cc_start: 0.8917 (mp) cc_final: 0.8488 (pt) REVERT: C 335 ARG cc_start: 0.7575 (mpp-170) cc_final: 0.6988 (mtm-85) REVERT: C 337 TYR cc_start: 0.6800 (m-10) cc_final: 0.6365 (m-10) REVERT: C 349 LEU cc_start: 0.8761 (tp) cc_final: 0.8484 (tp) REVERT: C 356 TRP cc_start: 0.6970 (m100) cc_final: 0.6361 (m100) REVERT: C 360 GLN cc_start: 0.8938 (pm20) cc_final: 0.8525 (pm20) REVERT: C 361 GLU cc_start: 0.8832 (tt0) cc_final: 0.8306 (tt0) REVERT: D 24 ASP cc_start: 0.7375 (m-30) cc_final: 0.6748 (m-30) REVERT: D 50 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7659 (ttmt) REVERT: D 54 VAL cc_start: 0.8578 (t) cc_final: 0.8226 (m) REVERT: D 59 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7657 (mm-40) REVERT: D 61 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7576 (mtpp) REVERT: D 62 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7596 (mtm180) REVERT: D 76 ILE cc_start: 0.8150 (mt) cc_final: 0.7548 (mt) REVERT: D 78 ASN cc_start: 0.8194 (t0) cc_final: 0.7746 (t0) REVERT: D 79 TRP cc_start: 0.8340 (m100) cc_final: 0.7550 (m100) REVERT: D 100 GLU cc_start: 0.7897 (tp30) cc_final: 0.7185 (tp30) REVERT: D 118 LYS cc_start: 0.8935 (tptt) cc_final: 0.8237 (tptt) REVERT: D 121 GLN cc_start: 0.8872 (pp30) cc_final: 0.8081 (pp30) REVERT: D 122 ILE cc_start: 0.8592 (mt) cc_final: 0.7208 (mt) REVERT: D 126 THR cc_start: 0.8478 (p) cc_final: 0.8200 (t) REVERT: D 137 GLN cc_start: 0.8439 (mt0) cc_final: 0.8209 (mp10) REVERT: D 153 LEU cc_start: 0.8069 (tp) cc_final: 0.7549 (tp) REVERT: D 157 ASP cc_start: 0.6428 (t0) cc_final: 0.6203 (t0) REVERT: D 184 ASP cc_start: 0.8232 (m-30) cc_final: 0.7805 (m-30) REVERT: D 202 THR cc_start: 0.7277 (p) cc_final: 0.6388 (t) REVERT: D 205 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7442 (mt-10) REVERT: D 206 ARG cc_start: 0.8341 (ttm170) cc_final: 0.8132 (mtp180) REVERT: D 208 ILE cc_start: 0.8223 (mm) cc_final: 0.7936 (mm) REVERT: D 210 ARG cc_start: 0.8519 (ttp80) cc_final: 0.7649 (ttp80) REVERT: D 211 ASP cc_start: 0.8048 (m-30) cc_final: 0.6501 (m-30) REVERT: D 213 LYS cc_start: 0.8784 (ttpt) cc_final: 0.8454 (ttpt) REVERT: D 222 ASP cc_start: 0.7878 (t0) cc_final: 0.7520 (t70) REVERT: D 225 ASN cc_start: 0.8475 (m110) cc_final: 0.7992 (m110) REVERT: D 238 LYS cc_start: 0.8502 (mmmt) cc_final: 0.8029 (mmmm) REVERT: D 249 THR cc_start: 0.8238 (m) cc_final: 0.7806 (p) REVERT: D 254 ARG cc_start: 0.7878 (mtm180) cc_final: 0.7670 (mtm180) REVERT: D 262 PHE cc_start: 0.8264 (m-80) cc_final: 0.7765 (m-80) REVERT: D 280 ASN cc_start: 0.8156 (t0) cc_final: 0.7065 (t0) REVERT: D 281 SER cc_start: 0.8427 (p) cc_final: 0.8056 (p) REVERT: D 282 ILE cc_start: 0.8579 (mt) cc_final: 0.8346 (mt) REVERT: D 284 LYS cc_start: 0.8598 (mmpt) cc_final: 0.8327 (mmpt) REVERT: D 292 ASP cc_start: 0.8233 (m-30) cc_final: 0.8002 (m-30) REVERT: D 299 MET cc_start: 0.7536 (mmm) cc_final: 0.7308 (mmm) REVERT: D 300 SER cc_start: 0.7480 (t) cc_final: 0.6987 (p) REVERT: D 313 MET cc_start: 0.8441 (tpt) cc_final: 0.7759 (mmm) REVERT: D 315 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8481 (ttpp) REVERT: D 316 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7315 (mm-30) REVERT: D 317 ILE cc_start: 0.8931 (mm) cc_final: 0.8692 (mm) REVERT: D 340 TRP cc_start: 0.8040 (t60) cc_final: 0.7078 (t60) outliers start: 1 outliers final: 0 residues processed: 752 average time/residue: 0.1393 time to fit residues: 144.6979 Evaluate side-chains 694 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 693 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 82 optimal weight: 0.0670 chunk 121 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 80 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A 641 ASN ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN C 73 HIS C 161 HIS D 280 ASN D 371 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.100833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.082136 restraints weight = 40159.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085504 restraints weight = 22180.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.087814 restraints weight = 14024.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.089392 restraints weight = 9703.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.090590 restraints weight = 7194.553| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15117 Z= 0.135 Angle : 0.695 11.115 20466 Z= 0.348 Chirality : 0.045 0.170 2241 Planarity : 0.005 0.059 2622 Dihedral : 9.430 168.227 2062 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.37 (0.20), residues: 1838 helix: 0.62 (0.18), residues: 838 sheet: -0.13 (0.30), residues: 288 loop : 0.17 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 37 TYR 0.035 0.002 TYR B 295 PHE 0.027 0.002 PHE A 465 TRP 0.056 0.003 TRP A 523 HIS 0.008 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00288 (15117) covalent geometry : angle 0.69480 (20466) hydrogen bonds : bond 0.03908 ( 729) hydrogen bonds : angle 4.79269 ( 2013) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 737 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8110 (p0) cc_final: 0.7155 (t0) REVERT: A 89 LEU cc_start: 0.8857 (mt) cc_final: 0.8521 (pp) REVERT: A 90 ARG cc_start: 0.8391 (ttp-110) cc_final: 0.8097 (ttp-110) REVERT: A 118 ILE cc_start: 0.8416 (mm) cc_final: 0.8094 (pt) REVERT: A 123 ILE cc_start: 0.8382 (mp) cc_final: 0.7429 (mt) REVERT: A 127 TYR cc_start: 0.7935 (m-10) cc_final: 0.7547 (m-80) REVERT: A 140 PHE cc_start: 0.8016 (m-10) cc_final: 0.7761 (m-10) REVERT: A 150 MET cc_start: 0.8234 (ttp) cc_final: 0.7838 (ttp) REVERT: A 155 ARG cc_start: 0.7532 (ttt90) cc_final: 0.7308 (ttt90) REVERT: A 158 SER cc_start: 0.6671 (t) cc_final: 0.6296 (m) REVERT: A 178 ARG cc_start: 0.8656 (ttt-90) cc_final: 0.8197 (mmm-85) REVERT: A 179 TYR cc_start: 0.8007 (t80) cc_final: 0.7715 (t80) REVERT: A 223 TYR cc_start: 0.7952 (t80) cc_final: 0.7263 (t80) REVERT: A 246 LYS cc_start: 0.8840 (mmtm) cc_final: 0.8374 (mmmt) REVERT: A 262 PHE cc_start: 0.8256 (m-80) cc_final: 0.7764 (m-80) REVERT: A 304 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8055 (mm-30) REVERT: A 323 MET cc_start: 0.8154 (mmm) cc_final: 0.7819 (mmm) REVERT: A 328 ILE cc_start: 0.8522 (mt) cc_final: 0.8264 (mm) REVERT: A 361 CYS cc_start: 0.7617 (p) cc_final: 0.7400 (p) REVERT: A 363 LEU cc_start: 0.8343 (mt) cc_final: 0.7883 (pp) REVERT: A 372 CYS cc_start: 0.9023 (t) cc_final: 0.8528 (p) REVERT: A 385 GLU cc_start: 0.7580 (tp30) cc_final: 0.7099 (tm-30) REVERT: A 389 LYS cc_start: 0.8597 (mmtp) cc_final: 0.8225 (tppt) REVERT: A 393 LYS cc_start: 0.8548 (tttt) cc_final: 0.8045 (tppt) REVERT: A 400 ARG cc_start: 0.8070 (ttp-170) cc_final: 0.7511 (ttp80) REVERT: A 401 ASP cc_start: 0.7846 (m-30) cc_final: 0.7477 (m-30) REVERT: A 406 HIS cc_start: 0.8774 (t-170) cc_final: 0.8551 (t70) REVERT: A 410 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8037 (mmmt) REVERT: A 413 ASN cc_start: 0.8587 (m110) cc_final: 0.8287 (m-40) REVERT: A 453 CYS cc_start: 0.8589 (m) cc_final: 0.8271 (p) REVERT: A 459 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7567 (mm-30) REVERT: A 460 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8510 (mmmt) REVERT: A 461 LEU cc_start: 0.8889 (mt) cc_final: 0.8665 (pp) REVERT: A 464 GLN cc_start: 0.8810 (tt0) cc_final: 0.7927 (tm-30) REVERT: A 466 ASN cc_start: 0.8578 (m-40) cc_final: 0.8296 (m-40) REVERT: A 473 GLU cc_start: 0.8539 (tp30) cc_final: 0.8145 (tp30) REVERT: A 476 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8332 (tp30) REVERT: A 499 ILE cc_start: 0.8970 (mt) cc_final: 0.8626 (tt) REVERT: A 501 SER cc_start: 0.8115 (m) cc_final: 0.7834 (p) REVERT: A 502 LYS cc_start: 0.8456 (mmtp) cc_final: 0.8078 (mmtp) REVERT: A 508 LEU cc_start: 0.8441 (mt) cc_final: 0.8200 (mt) REVERT: A 511 GLU cc_start: 0.8011 (tt0) cc_final: 0.7012 (tt0) REVERT: A 526 LYS cc_start: 0.8792 (mttt) cc_final: 0.8366 (mmtm) REVERT: A 544 SER cc_start: 0.7654 (t) cc_final: 0.7352 (p) REVERT: A 545 ASN cc_start: 0.8467 (m-40) cc_final: 0.8109 (m-40) REVERT: A 551 LYS cc_start: 0.8000 (tptt) cc_final: 0.7767 (tppt) REVERT: A 555 ASP cc_start: 0.6869 (t0) cc_final: 0.6444 (t0) REVERT: A 581 LYS cc_start: 0.8928 (tttt) cc_final: 0.8670 (mtpp) REVERT: A 592 PHE cc_start: 0.7724 (m-80) cc_final: 0.7455 (m-10) REVERT: A 629 LYS cc_start: 0.8747 (tptp) cc_final: 0.8447 (tptp) REVERT: A 630 GLU cc_start: 0.8450 (tt0) cc_final: 0.8042 (tt0) REVERT: A 632 LYS cc_start: 0.9051 (mtmt) cc_final: 0.8758 (pttm) REVERT: A 641 ASN cc_start: 0.8915 (m110) cc_final: 0.8388 (m110) REVERT: A 644 HIS cc_start: 0.8210 (m90) cc_final: 0.7527 (m170) REVERT: A 647 MET cc_start: 0.7981 (tpt) cc_final: 0.7483 (tpt) REVERT: A 648 GLU cc_start: 0.8776 (pt0) cc_final: 0.8443 (tm-30) REVERT: A 651 ASN cc_start: 0.8693 (t0) cc_final: 0.8430 (t0) REVERT: A 653 THR cc_start: 0.8273 (p) cc_final: 0.7952 (p) REVERT: A 657 TYR cc_start: 0.7458 (m-80) cc_final: 0.6865 (m-80) REVERT: A 673 ASP cc_start: 0.7490 (t0) cc_final: 0.6916 (t0) REVERT: A 676 ARG cc_start: 0.8298 (tpp-160) cc_final: 0.7750 (tpt90) REVERT: A 680 GLN cc_start: 0.8132 (tp40) cc_final: 0.7531 (tp40) REVERT: B 35 ILE cc_start: 0.8402 (mt) cc_final: 0.7964 (tp) REVERT: B 81 ASP cc_start: 0.8544 (p0) cc_final: 0.7658 (m-30) REVERT: B 83 MET cc_start: 0.8621 (mmm) cc_final: 0.8074 (mmm) REVERT: B 84 GLU cc_start: 0.8405 (tt0) cc_final: 0.8118 (tt0) REVERT: B 85 LYS cc_start: 0.8639 (mttm) cc_final: 0.8168 (mttm) REVERT: B 86 ILE cc_start: 0.8469 (tp) cc_final: 0.8123 (mt) REVERT: B 87 TRP cc_start: 0.8153 (m-10) cc_final: 0.7710 (m-10) REVERT: B 93 ASN cc_start: 0.7954 (m-40) cc_final: 0.7705 (m-40) REVERT: B 94 GLU cc_start: 0.7973 (tp30) cc_final: 0.7679 (tp30) REVERT: B 104 THR cc_start: 0.7557 (p) cc_final: 0.7347 (p) REVERT: B 114 LYS cc_start: 0.8475 (mtmt) cc_final: 0.8080 (mtmt) REVERT: B 116 ASN cc_start: 0.8109 (t0) cc_final: 0.7875 (t0) REVERT: B 117 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7713 (ttm170) REVERT: B 118 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7590 (mt-10) REVERT: B 119 LYS cc_start: 0.8675 (tptt) cc_final: 0.7829 (tptt) REVERT: B 120 MET cc_start: 0.8518 (ttm) cc_final: 0.8012 (ttm) REVERT: B 123 ILE cc_start: 0.8801 (mt) cc_final: 0.8182 (tp) REVERT: B 127 THR cc_start: 0.8654 (m) cc_final: 0.8039 (p) REVERT: B 166 ILE cc_start: 0.8607 (mt) cc_final: 0.8165 (mm) REVERT: B 177 MET cc_start: 0.7190 (mtm) cc_final: 0.6821 (mtt) REVERT: B 180 ASP cc_start: 0.6666 (m-30) cc_final: 0.6015 (t70) REVERT: B 184 ARG cc_start: 0.7909 (tpp80) cc_final: 0.7239 (mmm-85) REVERT: B 185 ASP cc_start: 0.8171 (m-30) cc_final: 0.7793 (m-30) REVERT: B 188 ASP cc_start: 0.7932 (m-30) cc_final: 0.7404 (m-30) REVERT: B 192 LYS cc_start: 0.8426 (tttt) cc_final: 0.8145 (tttt) REVERT: B 194 LEU cc_start: 0.9072 (mt) cc_final: 0.8737 (mm) REVERT: B 196 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7163 (mt-10) REVERT: B 197 ARG cc_start: 0.7889 (mmm160) cc_final: 0.7641 (mmp80) REVERT: B 211 ARG cc_start: 0.8425 (ttp80) cc_final: 0.7889 (ttp80) REVERT: B 212 ASP cc_start: 0.8257 (m-30) cc_final: 0.7944 (m-30) REVERT: B 214 LYS cc_start: 0.8750 (ttpt) cc_final: 0.8410 (ttmm) REVERT: B 215 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6788 (mt-10) REVERT: B 247 GLN cc_start: 0.8068 (tp-100) cc_final: 0.7509 (tm-30) REVERT: B 255 ARG cc_start: 0.8398 (mtp85) cc_final: 0.8141 (mtp85) REVERT: B 257 ARG cc_start: 0.8105 (mtp180) cc_final: 0.7872 (mtp85) REVERT: B 264 GLN cc_start: 0.7812 (mt0) cc_final: 0.7375 (mp10) REVERT: B 272 SER cc_start: 0.8526 (m) cc_final: 0.8079 (t) REVERT: B 281 ASN cc_start: 0.8159 (m-40) cc_final: 0.7952 (m-40) REVERT: B 284 MET cc_start: 0.7772 (mmm) cc_final: 0.7306 (mmm) REVERT: B 285 LYS cc_start: 0.8433 (tttp) cc_final: 0.8048 (tttp) REVERT: B 292 LYS cc_start: 0.7978 (pttm) cc_final: 0.7773 (pttm) REVERT: B 300 MET cc_start: 0.7599 (mmm) cc_final: 0.7354 (mmm) REVERT: B 314 MET cc_start: 0.7647 (tpp) cc_final: 0.7104 (tpp) REVERT: B 355 GLN cc_start: 0.8383 (pm20) cc_final: 0.7912 (pm20) REVERT: B 356 MET cc_start: 0.8515 (mpp) cc_final: 0.7725 (mpp) REVERT: B 357 TRP cc_start: 0.8011 (m100) cc_final: 0.7524 (m100) REVERT: B 358 ILE cc_start: 0.7612 (mt) cc_final: 0.6958 (mm) REVERT: B 362 GLU cc_start: 0.8937 (tt0) cc_final: 0.8612 (tt0) REVERT: C 16 LEU cc_start: 0.7158 (tp) cc_final: 0.6700 (mt) REVERT: C 28 ARG cc_start: 0.8258 (ptt90) cc_final: 0.7792 (ptt90) REVERT: C 50 LYS cc_start: 0.8470 (mttt) cc_final: 0.8045 (mttt) REVERT: C 78 ASN cc_start: 0.7709 (t0) cc_final: 0.7186 (t0) REVERT: C 82 MET cc_start: 0.8053 (mmm) cc_final: 0.7368 (mmm) REVERT: C 83 GLU cc_start: 0.7936 (pt0) cc_final: 0.7423 (pp20) REVERT: C 84 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8290 (ttmm) REVERT: C 95 ARG cc_start: 0.8214 (ptp90) cc_final: 0.7954 (ptp90) REVERT: C 99 GLU cc_start: 0.7021 (mp0) cc_final: 0.6647 (mp0) REVERT: C 104 LEU cc_start: 0.8555 (tp) cc_final: 0.8156 (tp) REVERT: C 113 LYS cc_start: 0.8454 (mttm) cc_final: 0.7770 (mttm) REVERT: C 116 ARG cc_start: 0.8067 (ptp-170) cc_final: 0.7786 (ptm-80) REVERT: C 117 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8212 (mt-10) REVERT: C 118 LYS cc_start: 0.8244 (tptt) cc_final: 0.7786 (tptt) REVERT: C 119 MET cc_start: 0.8771 (ttm) cc_final: 0.8287 (ttm) REVERT: C 125 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7581 (mt-10) REVERT: C 132 MET cc_start: 0.6184 (ppp) cc_final: 0.5451 (ppp) REVERT: C 137 GLN cc_start: 0.8045 (mt0) cc_final: 0.7726 (mp10) REVERT: C 161 HIS cc_start: 0.7272 (p90) cc_final: 0.6678 (p-80) REVERT: C 165 ILE cc_start: 0.8600 (mt) cc_final: 0.8347 (tt) REVERT: C 166 TYR cc_start: 0.7871 (t80) cc_final: 0.7656 (t80) REVERT: C 176 MET cc_start: 0.6551 (mtt) cc_final: 0.6250 (mtt) REVERT: C 178 LEU cc_start: 0.8182 (tp) cc_final: 0.7944 (tp) REVERT: C 190 MET cc_start: 0.7715 (mtm) cc_final: 0.7284 (mtm) REVERT: C 205 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7474 (mt-10) REVERT: C 214 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7715 (mt-10) REVERT: C 215 LYS cc_start: 0.8664 (mttm) cc_final: 0.8257 (mmmm) REVERT: C 222 ASP cc_start: 0.7533 (p0) cc_final: 0.6073 (p0) REVERT: C 225 ASN cc_start: 0.8769 (m110) cc_final: 0.7857 (m-40) REVERT: C 226 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8135 (mm-30) REVERT: C 227 MET cc_start: 0.8631 (ptp) cc_final: 0.8134 (ptp) REVERT: C 252 ASN cc_start: 0.7779 (t0) cc_final: 0.7523 (t0) REVERT: C 256 ARG cc_start: 0.7799 (ttm170) cc_final: 0.7240 (ttm-80) REVERT: C 259 GLU cc_start: 0.7529 (tp30) cc_final: 0.7239 (tm-30) REVERT: C 261 LEU cc_start: 0.8388 (mt) cc_final: 0.8114 (mm) REVERT: C 279 TYR cc_start: 0.7993 (t80) cc_final: 0.7607 (t80) REVERT: C 282 ILE cc_start: 0.8387 (mt) cc_final: 0.7714 (mm) REVERT: C 283 MET cc_start: 0.7988 (mmp) cc_final: 0.7521 (mmp) REVERT: C 284 LYS cc_start: 0.8300 (tppt) cc_final: 0.7892 (tppt) REVERT: C 286 ASP cc_start: 0.8178 (t0) cc_final: 0.7932 (t70) REVERT: C 291 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8379 (mptt) REVERT: C 292 ASP cc_start: 0.8415 (m-30) cc_final: 0.8095 (m-30) REVERT: C 294 TYR cc_start: 0.7602 (m-80) cc_final: 0.7349 (m-80) REVERT: C 297 ASN cc_start: 0.7707 (m-40) cc_final: 0.7458 (m-40) REVERT: C 299 MET cc_start: 0.7861 (mmm) cc_final: 0.7354 (mmm) REVERT: C 305 MET cc_start: 0.7620 (mmm) cc_final: 0.7376 (mmm) REVERT: C 316 GLU cc_start: 0.8312 (tp30) cc_final: 0.7470 (tp30) REVERT: C 325 MET cc_start: 0.7192 (mpp) cc_final: 0.6970 (mpp) REVERT: C 326 LYS cc_start: 0.8301 (mmtm) cc_final: 0.8073 (mmtt) REVERT: C 328 LYS cc_start: 0.8748 (mttt) cc_final: 0.8360 (mttt) REVERT: C 330 ILE cc_start: 0.8944 (mp) cc_final: 0.8433 (pt) REVERT: C 335 ARG cc_start: 0.7454 (mpp-170) cc_final: 0.6510 (mpt180) REVERT: C 341 ILE cc_start: 0.8350 (mm) cc_final: 0.8067 (pt) REVERT: C 349 LEU cc_start: 0.8676 (tp) cc_final: 0.8379 (tp) REVERT: C 356 TRP cc_start: 0.6895 (m100) cc_final: 0.6659 (m100) REVERT: C 360 GLN cc_start: 0.8948 (pm20) cc_final: 0.8501 (pm20) REVERT: C 361 GLU cc_start: 0.8729 (tt0) cc_final: 0.8255 (tt0) REVERT: D 34 ILE cc_start: 0.8968 (mt) cc_final: 0.8677 (mm) REVERT: D 54 VAL cc_start: 0.8564 (t) cc_final: 0.8172 (m) REVERT: D 59 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7537 (mm-40) REVERT: D 61 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7547 (mtpp) REVERT: D 76 ILE cc_start: 0.8149 (mt) cc_final: 0.7592 (mt) REVERT: D 78 ASN cc_start: 0.8240 (t0) cc_final: 0.7783 (t0) REVERT: D 79 TRP cc_start: 0.8283 (m100) cc_final: 0.7581 (m100) REVERT: D 84 LYS cc_start: 0.8700 (ttmm) cc_final: 0.8424 (ttmm) REVERT: D 118 LYS cc_start: 0.8857 (tptt) cc_final: 0.8245 (tptt) REVERT: D 121 GLN cc_start: 0.8747 (pp30) cc_final: 0.7977 (pp30) REVERT: D 122 ILE cc_start: 0.8523 (mt) cc_final: 0.7142 (mt) REVERT: D 126 THR cc_start: 0.8403 (p) cc_final: 0.8087 (t) REVERT: D 137 GLN cc_start: 0.8329 (mt0) cc_final: 0.7942 (mp10) REVERT: D 176 MET cc_start: 0.7194 (mtm) cc_final: 0.6255 (mtm) REVERT: D 183 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7475 (mmm-85) REVERT: D 190 MET cc_start: 0.8055 (mtt) cc_final: 0.7782 (mmt) REVERT: D 202 THR cc_start: 0.7313 (p) cc_final: 0.6515 (t) REVERT: D 205 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7244 (mt-10) REVERT: D 206 ARG cc_start: 0.8401 (ttm170) cc_final: 0.8176 (mtp180) REVERT: D 207 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7228 (mm-30) REVERT: D 208 ILE cc_start: 0.8167 (mm) cc_final: 0.7948 (mm) REVERT: D 210 ARG cc_start: 0.8493 (ttp80) cc_final: 0.7957 (ttp80) REVERT: D 211 ASP cc_start: 0.8052 (m-30) cc_final: 0.6766 (m-30) REVERT: D 238 LYS cc_start: 0.8346 (mmmt) cc_final: 0.7896 (mmmm) REVERT: D 242 LEU cc_start: 0.8061 (mt) cc_final: 0.7675 (mt) REVERT: D 249 THR cc_start: 0.8090 (m) cc_final: 0.7636 (p) REVERT: D 269 MET cc_start: 0.7213 (mmp) cc_final: 0.6997 (mmp) REVERT: D 280 ASN cc_start: 0.8135 (t0) cc_final: 0.7026 (t0) REVERT: D 281 SER cc_start: 0.8410 (p) cc_final: 0.7918 (p) REVERT: D 282 ILE cc_start: 0.8560 (mt) cc_final: 0.8029 (mt) REVERT: D 284 LYS cc_start: 0.8566 (mmpt) cc_final: 0.8218 (mmpt) REVERT: D 289 ILE cc_start: 0.8450 (pt) cc_final: 0.8248 (pt) REVERT: D 291 LYS cc_start: 0.8527 (pttm) cc_final: 0.8300 (mmtt) REVERT: D 292 ASP cc_start: 0.8189 (m-30) cc_final: 0.7875 (m-30) REVERT: D 294 TYR cc_start: 0.6737 (m-80) cc_final: 0.6243 (m-80) REVERT: D 299 MET cc_start: 0.7458 (mmm) cc_final: 0.7255 (mmm) REVERT: D 300 SER cc_start: 0.7509 (t) cc_final: 0.7132 (p) REVERT: D 312 ARG cc_start: 0.8136 (tpt-90) cc_final: 0.7441 (mmm-85) REVERT: D 313 MET cc_start: 0.8372 (tpt) cc_final: 0.7864 (tpt) REVERT: D 315 LYS cc_start: 0.8781 (ttpp) cc_final: 0.8430 (ttpp) REVERT: D 316 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7376 (mm-30) REVERT: D 317 ILE cc_start: 0.8860 (mm) cc_final: 0.8582 (mm) REVERT: D 335 ARG cc_start: 0.7885 (mtm180) cc_final: 0.7502 (mpt180) outliers start: 0 outliers final: 0 residues processed: 737 average time/residue: 0.1423 time to fit residues: 145.0427 Evaluate side-chains 687 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 687 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 138 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 106 optimal weight: 0.1980 chunk 147 optimal weight: 0.2980 chunk 91 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 HIS B 372 HIS C 73 HIS D 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.100366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.081875 restraints weight = 39790.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085210 restraints weight = 22145.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.087474 restraints weight = 14093.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089076 restraints weight = 9802.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090218 restraints weight = 7271.690| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.7251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15117 Z= 0.142 Angle : 0.693 10.426 20466 Z= 0.351 Chirality : 0.045 0.182 2241 Planarity : 0.005 0.050 2622 Dihedral : 9.139 154.849 2062 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 0.43 (0.20), residues: 1838 helix: 0.66 (0.18), residues: 834 sheet: -0.09 (0.30), residues: 290 loop : 0.23 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 63 TYR 0.029 0.002 TYR B 295 PHE 0.026 0.001 PHE A 564 TRP 0.062 0.003 TRP A 523 HIS 0.010 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00301 (15117) covalent geometry : angle 0.69257 (20466) hydrogen bonds : bond 0.03962 ( 729) hydrogen bonds : angle 4.80750 ( 2013) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 732 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8105 (p0) cc_final: 0.7151 (t0) REVERT: A 88 ASN cc_start: 0.8813 (t0) cc_final: 0.8596 (m-40) REVERT: A 89 LEU cc_start: 0.8890 (mt) cc_final: 0.8480 (pp) REVERT: A 90 ARG cc_start: 0.8467 (ttp-110) cc_final: 0.8147 (ttp-110) REVERT: A 116 LEU cc_start: 0.8337 (tp) cc_final: 0.8131 (tp) REVERT: A 118 ILE cc_start: 0.8393 (mm) cc_final: 0.8161 (pt) REVERT: A 123 ILE cc_start: 0.8427 (mp) cc_final: 0.7702 (mt) REVERT: A 127 TYR cc_start: 0.7959 (m-10) cc_final: 0.7556 (m-80) REVERT: A 140 PHE cc_start: 0.8062 (m-10) cc_final: 0.7776 (m-10) REVERT: A 148 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8491 (mmtm) REVERT: A 150 MET cc_start: 0.8184 (ttp) cc_final: 0.7802 (ttp) REVERT: A 155 ARG cc_start: 0.7622 (ttt90) cc_final: 0.7372 (ttt90) REVERT: A 158 SER cc_start: 0.6711 (t) cc_final: 0.6217 (m) REVERT: A 178 ARG cc_start: 0.8615 (ttt-90) cc_final: 0.8139 (mmm-85) REVERT: A 179 TYR cc_start: 0.8003 (t80) cc_final: 0.7663 (t80) REVERT: A 228 PHE cc_start: 0.7739 (m-80) cc_final: 0.7514 (m-80) REVERT: A 243 LEU cc_start: 0.7983 (mt) cc_final: 0.7781 (mt) REVERT: A 246 LYS cc_start: 0.8863 (mmtm) cc_final: 0.8329 (mmmt) REVERT: A 251 PHE cc_start: 0.7128 (t80) cc_final: 0.6914 (t80) REVERT: A 262 PHE cc_start: 0.8261 (m-80) cc_final: 0.7825 (m-80) REVERT: A 264 GLN cc_start: 0.8334 (mt0) cc_final: 0.7576 (mt0) REVERT: A 285 PHE cc_start: 0.7939 (m-80) cc_final: 0.7715 (m-80) REVERT: A 303 LYS cc_start: 0.8687 (mmtm) cc_final: 0.8198 (mmtm) REVERT: A 312 CYS cc_start: 0.8716 (m) cc_final: 0.8511 (m) REVERT: A 323 MET cc_start: 0.8157 (mmm) cc_final: 0.7783 (mmm) REVERT: A 328 ILE cc_start: 0.8511 (mt) cc_final: 0.8265 (mm) REVERT: A 363 LEU cc_start: 0.8331 (mt) cc_final: 0.8083 (mt) REVERT: A 369 GLU cc_start: 0.8356 (mp0) cc_final: 0.8071 (pm20) REVERT: A 372 CYS cc_start: 0.9025 (t) cc_final: 0.8558 (p) REVERT: A 385 GLU cc_start: 0.7541 (tp30) cc_final: 0.7097 (tm-30) REVERT: A 389 LYS cc_start: 0.8609 (mmtp) cc_final: 0.8092 (tppt) REVERT: A 393 LYS cc_start: 0.8544 (tttt) cc_final: 0.8039 (tppt) REVERT: A 406 HIS cc_start: 0.8772 (t-170) cc_final: 0.8550 (t70) REVERT: A 410 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8021 (mmmt) REVERT: A 413 ASN cc_start: 0.8572 (m110) cc_final: 0.8249 (m-40) REVERT: A 436 LEU cc_start: 0.8076 (tp) cc_final: 0.7874 (tp) REVERT: A 438 ILE cc_start: 0.7933 (tp) cc_final: 0.7480 (tp) REVERT: A 453 CYS cc_start: 0.8690 (m) cc_final: 0.8371 (p) REVERT: A 458 ASN cc_start: 0.8489 (m110) cc_final: 0.8281 (m-40) REVERT: A 459 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7518 (mm-30) REVERT: A 460 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8474 (mmmt) REVERT: A 461 LEU cc_start: 0.8893 (mt) cc_final: 0.8663 (pp) REVERT: A 464 GLN cc_start: 0.8781 (tt0) cc_final: 0.7932 (tm-30) REVERT: A 466 ASN cc_start: 0.8623 (m-40) cc_final: 0.8299 (m-40) REVERT: A 476 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8421 (tp30) REVERT: A 478 MET cc_start: 0.8161 (ttt) cc_final: 0.7941 (ttt) REVERT: A 498 LEU cc_start: 0.8873 (tp) cc_final: 0.8604 (tp) REVERT: A 499 ILE cc_start: 0.8977 (mt) cc_final: 0.8644 (tt) REVERT: A 502 LYS cc_start: 0.8468 (mmtp) cc_final: 0.8097 (mmtp) REVERT: A 508 LEU cc_start: 0.8449 (mt) cc_final: 0.7963 (mt) REVERT: A 509 LEU cc_start: 0.8219 (tp) cc_final: 0.7990 (tp) REVERT: A 526 LYS cc_start: 0.8760 (mttt) cc_final: 0.8386 (mmtm) REVERT: A 544 SER cc_start: 0.7766 (t) cc_final: 0.7466 (p) REVERT: A 545 ASN cc_start: 0.8476 (m-40) cc_final: 0.7974 (m-40) REVERT: A 546 LYS cc_start: 0.7741 (mmtt) cc_final: 0.6955 (tttm) REVERT: A 551 LYS cc_start: 0.7999 (tptt) cc_final: 0.7774 (tppt) REVERT: A 555 ASP cc_start: 0.6923 (t0) cc_final: 0.6498 (t0) REVERT: A 575 GLU cc_start: 0.7883 (pm20) cc_final: 0.7584 (pm20) REVERT: A 578 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8472 (mtmm) REVERT: A 581 LYS cc_start: 0.8909 (tttt) cc_final: 0.8695 (mtpp) REVERT: A 592 PHE cc_start: 0.7720 (m-80) cc_final: 0.7427 (m-10) REVERT: A 629 LYS cc_start: 0.8728 (tptp) cc_final: 0.8479 (tptp) REVERT: A 630 GLU cc_start: 0.8411 (tt0) cc_final: 0.7958 (tt0) REVERT: A 632 LYS cc_start: 0.9059 (mtmt) cc_final: 0.8770 (pttm) REVERT: A 641 ASN cc_start: 0.8872 (m110) cc_final: 0.8337 (m110) REVERT: A 644 HIS cc_start: 0.8194 (m90) cc_final: 0.7514 (m170) REVERT: A 647 MET cc_start: 0.7952 (tpt) cc_final: 0.7441 (tpt) REVERT: A 648 GLU cc_start: 0.8757 (pt0) cc_final: 0.8425 (tm-30) REVERT: A 650 LEU cc_start: 0.8765 (mt) cc_final: 0.8550 (mt) REVERT: A 651 ASN cc_start: 0.8698 (t0) cc_final: 0.8409 (t0) REVERT: A 653 THR cc_start: 0.8272 (p) cc_final: 0.7957 (p) REVERT: A 657 TYR cc_start: 0.7405 (m-80) cc_final: 0.6859 (m-80) REVERT: A 673 ASP cc_start: 0.7478 (t0) cc_final: 0.7021 (t0) REVERT: B 26 ASP cc_start: 0.7517 (m-30) cc_final: 0.7306 (m-30) REVERT: B 35 ILE cc_start: 0.8365 (mt) cc_final: 0.7911 (mm) REVERT: B 81 ASP cc_start: 0.8094 (p0) cc_final: 0.7582 (m-30) REVERT: B 83 MET cc_start: 0.8584 (mmm) cc_final: 0.7976 (mmm) REVERT: B 84 GLU cc_start: 0.8430 (tt0) cc_final: 0.8166 (tt0) REVERT: B 85 LYS cc_start: 0.8605 (mttm) cc_final: 0.8042 (mttm) REVERT: B 86 ILE cc_start: 0.8404 (tp) cc_final: 0.8133 (mt) REVERT: B 87 TRP cc_start: 0.8116 (m-10) cc_final: 0.7648 (m-10) REVERT: B 93 ASN cc_start: 0.7969 (m-40) cc_final: 0.7720 (m-40) REVERT: B 94 GLU cc_start: 0.7996 (tp30) cc_final: 0.7666 (tp30) REVERT: B 100 GLU cc_start: 0.7936 (tp30) cc_final: 0.7705 (tp30) REVERT: B 101 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7997 (mm-30) REVERT: B 114 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8266 (mtmt) REVERT: B 117 ARG cc_start: 0.8097 (ttm110) cc_final: 0.7703 (ttm170) REVERT: B 119 LYS cc_start: 0.8649 (tptt) cc_final: 0.7807 (tptt) REVERT: B 120 MET cc_start: 0.8517 (ttm) cc_final: 0.8043 (ttm) REVERT: B 123 ILE cc_start: 0.8835 (mt) cc_final: 0.8218 (tp) REVERT: B 127 THR cc_start: 0.8694 (m) cc_final: 0.8055 (p) REVERT: B 166 ILE cc_start: 0.8638 (mt) cc_final: 0.8196 (mm) REVERT: B 180 ASP cc_start: 0.6705 (m-30) cc_final: 0.6050 (t70) REVERT: B 184 ARG cc_start: 0.7813 (tpp80) cc_final: 0.7306 (mmm-85) REVERT: B 185 ASP cc_start: 0.8236 (m-30) cc_final: 0.7838 (m-30) REVERT: B 188 ASP cc_start: 0.7966 (m-30) cc_final: 0.7442 (m-30) REVERT: B 192 LYS cc_start: 0.8427 (tttt) cc_final: 0.8137 (tttt) REVERT: B 194 LEU cc_start: 0.9074 (mt) cc_final: 0.8787 (tp) REVERT: B 196 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7144 (mt-10) REVERT: B 197 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7640 (mmp80) REVERT: B 199 TYR cc_start: 0.6883 (m-10) cc_final: 0.6432 (m-10) REVERT: B 211 ARG cc_start: 0.8411 (ttp80) cc_final: 0.8116 (ttp80) REVERT: B 212 ASP cc_start: 0.8253 (m-30) cc_final: 0.8003 (m-30) REVERT: B 214 LYS cc_start: 0.8721 (ttpt) cc_final: 0.8500 (ttpt) REVERT: B 215 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7026 (mt-10) REVERT: B 247 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7535 (tm-30) REVERT: B 255 ARG cc_start: 0.8451 (mtp85) cc_final: 0.8163 (mtp85) REVERT: B 257 ARG cc_start: 0.8120 (mtp180) cc_final: 0.7662 (mtp180) REVERT: B 264 GLN cc_start: 0.7806 (mt0) cc_final: 0.7423 (mp10) REVERT: B 272 SER cc_start: 0.8517 (m) cc_final: 0.8089 (t) REVERT: B 277 GLU cc_start: 0.8097 (mt-10) cc_final: 0.6922 (mt-10) REVERT: B 281 ASN cc_start: 0.8091 (m-40) cc_final: 0.7840 (m-40) REVERT: B 284 MET cc_start: 0.7690 (mmm) cc_final: 0.7280 (mmm) REVERT: B 285 LYS cc_start: 0.8458 (tttp) cc_final: 0.8075 (tttp) REVERT: B 292 LYS cc_start: 0.7986 (pttm) cc_final: 0.7736 (pttm) REVERT: B 295 TYR cc_start: 0.6900 (m-80) cc_final: 0.6356 (m-80) REVERT: B 300 MET cc_start: 0.7628 (mmm) cc_final: 0.7385 (mmm) REVERT: B 314 MET cc_start: 0.7622 (tpp) cc_final: 0.7088 (tpp) REVERT: B 355 GLN cc_start: 0.8403 (pm20) cc_final: 0.7953 (pm20) REVERT: B 356 MET cc_start: 0.8506 (mpp) cc_final: 0.7954 (mpp) REVERT: B 358 ILE cc_start: 0.7652 (mt) cc_final: 0.7036 (mm) REVERT: B 362 GLU cc_start: 0.8944 (tt0) cc_final: 0.8581 (tt0) REVERT: C 16 LEU cc_start: 0.7184 (tp) cc_final: 0.6715 (mt) REVERT: C 37 ARG cc_start: 0.7289 (mmm-85) cc_final: 0.6674 (mmm-85) REVERT: C 47 MET cc_start: 0.6179 (ptt) cc_final: 0.5918 (ptt) REVERT: C 50 LYS cc_start: 0.8494 (mttt) cc_final: 0.8111 (mttt) REVERT: C 61 LYS cc_start: 0.8418 (mttm) cc_final: 0.8021 (mmtp) REVERT: C 78 ASN cc_start: 0.7714 (t0) cc_final: 0.7172 (t0) REVERT: C 82 MET cc_start: 0.8024 (mmm) cc_final: 0.7374 (mmm) REVERT: C 83 GLU cc_start: 0.7950 (pt0) cc_final: 0.7417 (pp20) REVERT: C 84 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8313 (ttmm) REVERT: C 99 GLU cc_start: 0.7117 (mp0) cc_final: 0.6738 (mp0) REVERT: C 104 LEU cc_start: 0.8566 (tp) cc_final: 0.8193 (tp) REVERT: C 111 ASN cc_start: 0.8134 (m-40) cc_final: 0.7659 (m-40) REVERT: C 113 LYS cc_start: 0.8442 (mttm) cc_final: 0.7982 (mttm) REVERT: C 116 ARG cc_start: 0.8027 (ptp-170) cc_final: 0.7732 (ptm-80) REVERT: C 118 LYS cc_start: 0.8286 (tptt) cc_final: 0.7807 (tptt) REVERT: C 119 MET cc_start: 0.8765 (ttm) cc_final: 0.8259 (ttm) REVERT: C 125 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7614 (mt-10) REVERT: C 132 MET cc_start: 0.6154 (ppp) cc_final: 0.5427 (ppp) REVERT: C 137 GLN cc_start: 0.8052 (mt0) cc_final: 0.7691 (mp10) REVERT: C 161 HIS cc_start: 0.7171 (p90) cc_final: 0.6554 (p-80) REVERT: C 165 ILE cc_start: 0.8581 (mt) cc_final: 0.8339 (tt) REVERT: C 166 TYR cc_start: 0.7869 (t80) cc_final: 0.7660 (t80) REVERT: C 176 MET cc_start: 0.6631 (mtt) cc_final: 0.6348 (mtt) REVERT: C 178 LEU cc_start: 0.8224 (tp) cc_final: 0.7951 (tp) REVERT: C 190 MET cc_start: 0.7735 (mtm) cc_final: 0.7348 (mtm) REVERT: C 202 THR cc_start: 0.8394 (m) cc_final: 0.7861 (p) REVERT: C 205 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7046 (mt-10) REVERT: C 208 ILE cc_start: 0.8583 (mp) cc_final: 0.8358 (mp) REVERT: C 211 ASP cc_start: 0.8220 (m-30) cc_final: 0.7959 (m-30) REVERT: C 214 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7906 (mt-10) REVERT: C 215 LYS cc_start: 0.8667 (mttm) cc_final: 0.8276 (mmmm) REVERT: C 222 ASP cc_start: 0.7487 (p0) cc_final: 0.6095 (p0) REVERT: C 225 ASN cc_start: 0.8749 (m110) cc_final: 0.7904 (m-40) REVERT: C 226 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8153 (mm-30) REVERT: C 227 MET cc_start: 0.8627 (ptp) cc_final: 0.8124 (ptp) REVERT: C 238 LYS cc_start: 0.7653 (mmtt) cc_final: 0.7430 (mmtt) REVERT: C 252 ASN cc_start: 0.7843 (t0) cc_final: 0.7556 (t0) REVERT: C 256 ARG cc_start: 0.7807 (ttm170) cc_final: 0.7216 (ttm-80) REVERT: C 261 LEU cc_start: 0.8347 (mt) cc_final: 0.8111 (mm) REVERT: C 276 GLU cc_start: 0.7638 (pm20) cc_final: 0.7329 (pm20) REVERT: C 279 TYR cc_start: 0.7930 (t80) cc_final: 0.7569 (t80) REVERT: C 282 ILE cc_start: 0.8391 (mt) cc_final: 0.7754 (mm) REVERT: C 283 MET cc_start: 0.8020 (mmp) cc_final: 0.7581 (mmp) REVERT: C 284 LYS cc_start: 0.8313 (tppt) cc_final: 0.7780 (tppt) REVERT: C 286 ASP cc_start: 0.8173 (t0) cc_final: 0.7642 (t70) REVERT: C 288 ASP cc_start: 0.7998 (m-30) cc_final: 0.7650 (p0) REVERT: C 289 ILE cc_start: 0.7645 (pt) cc_final: 0.7293 (pt) REVERT: C 291 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8386 (mptt) REVERT: C 294 TYR cc_start: 0.7650 (m-80) cc_final: 0.7404 (m-80) REVERT: C 297 ASN cc_start: 0.7726 (m-40) cc_final: 0.7438 (m-40) REVERT: C 299 MET cc_start: 0.7888 (mmm) cc_final: 0.7381 (mmm) REVERT: C 305 MET cc_start: 0.7609 (mmm) cc_final: 0.7349 (mmm) REVERT: C 314 GLN cc_start: 0.8845 (tt0) cc_final: 0.8577 (tt0) REVERT: C 316 GLU cc_start: 0.8310 (tp30) cc_final: 0.7502 (tp30) REVERT: C 326 LYS cc_start: 0.8310 (mmtm) cc_final: 0.7930 (mmmt) REVERT: C 328 LYS cc_start: 0.8730 (mttt) cc_final: 0.8342 (mttt) REVERT: C 330 ILE cc_start: 0.8952 (mp) cc_final: 0.8423 (pt) REVERT: C 335 ARG cc_start: 0.7434 (mpp-170) cc_final: 0.6422 (mpt180) REVERT: C 349 LEU cc_start: 0.8654 (tp) cc_final: 0.8352 (tp) REVERT: C 360 GLN cc_start: 0.8980 (pm20) cc_final: 0.8548 (pm20) REVERT: C 361 GLU cc_start: 0.8701 (tt0) cc_final: 0.8199 (tt0) REVERT: D 54 VAL cc_start: 0.8479 (t) cc_final: 0.8128 (m) REVERT: D 59 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7643 (mm-40) REVERT: D 61 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7535 (mtpp) REVERT: D 76 ILE cc_start: 0.8135 (mt) cc_final: 0.7533 (mt) REVERT: D 78 ASN cc_start: 0.8264 (t0) cc_final: 0.7805 (t0) REVERT: D 79 TRP cc_start: 0.8353 (m100) cc_final: 0.7686 (m100) REVERT: D 82 MET cc_start: 0.7918 (mmm) cc_final: 0.7132 (tmm) REVERT: D 84 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8400 (ttmm) REVERT: D 118 LYS cc_start: 0.8855 (tptt) cc_final: 0.8241 (tptt) REVERT: D 121 GLN cc_start: 0.8776 (pp30) cc_final: 0.7931 (pp30) REVERT: D 122 ILE cc_start: 0.8514 (mt) cc_final: 0.7195 (mt) REVERT: D 125 GLU cc_start: 0.7887 (tp30) cc_final: 0.7245 (tp30) REVERT: D 126 THR cc_start: 0.8414 (p) cc_final: 0.8163 (p) REVERT: D 137 GLN cc_start: 0.8329 (mt0) cc_final: 0.7948 (mp10) REVERT: D 153 LEU cc_start: 0.8103 (tp) cc_final: 0.7504 (tp) REVERT: D 176 MET cc_start: 0.7170 (mtm) cc_final: 0.6209 (mtm) REVERT: D 183 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7418 (mmm-85) REVERT: D 190 MET cc_start: 0.8074 (mtt) cc_final: 0.7773 (mmt) REVERT: D 202 THR cc_start: 0.7279 (p) cc_final: 0.6468 (t) REVERT: D 205 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7251 (mt-10) REVERT: D 207 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7311 (mm-30) REVERT: D 210 ARG cc_start: 0.8517 (ttp80) cc_final: 0.8065 (ttp80) REVERT: D 211 ASP cc_start: 0.8044 (m-30) cc_final: 0.7187 (m-30) REVERT: D 225 ASN cc_start: 0.8306 (m110) cc_final: 0.8106 (m-40) REVERT: D 238 LYS cc_start: 0.8350 (mmmt) cc_final: 0.8010 (mmtm) REVERT: D 246 GLN cc_start: 0.6938 (pt0) cc_final: 0.6584 (pt0) REVERT: D 249 THR cc_start: 0.8107 (m) cc_final: 0.7651 (p) REVERT: D 280 ASN cc_start: 0.8148 (t0) cc_final: 0.7092 (t0) REVERT: D 281 SER cc_start: 0.8419 (p) cc_final: 0.7879 (p) REVERT: D 284 LYS cc_start: 0.8574 (mmpt) cc_final: 0.8246 (mmpt) REVERT: D 289 ILE cc_start: 0.8400 (pt) cc_final: 0.8089 (pt) REVERT: D 292 ASP cc_start: 0.8232 (m-30) cc_final: 0.7966 (m-30) REVERT: D 293 LEU cc_start: 0.8376 (mt) cc_final: 0.8155 (mm) REVERT: D 300 SER cc_start: 0.7440 (t) cc_final: 0.7103 (p) REVERT: D 312 ARG cc_start: 0.8130 (tpt-90) cc_final: 0.7268 (mmm-85) REVERT: D 313 MET cc_start: 0.8383 (tpt) cc_final: 0.7920 (tpt) REVERT: D 315 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8463 (ttpp) REVERT: D 316 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7456 (mm-30) REVERT: D 335 ARG cc_start: 0.7823 (mtm180) cc_final: 0.7499 (mpt180) REVERT: D 340 TRP cc_start: 0.8049 (t60) cc_final: 0.7704 (t60) REVERT: D 356 TRP cc_start: 0.7308 (m100) cc_final: 0.7074 (m100) outliers start: 0 outliers final: 0 residues processed: 732 average time/residue: 0.1401 time to fit residues: 141.9629 Evaluate side-chains 696 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 696 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 124 optimal weight: 0.4980 chunk 170 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 149 optimal weight: 0.0270 chunk 160 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN C 73 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS D 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.100123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.081618 restraints weight = 39738.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.084957 restraints weight = 22046.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087214 restraints weight = 13966.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.088791 restraints weight = 9698.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089915 restraints weight = 7220.816| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.7372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15117 Z= 0.144 Angle : 0.693 10.152 20466 Z= 0.350 Chirality : 0.045 0.175 2241 Planarity : 0.005 0.051 2622 Dihedral : 8.759 134.711 2062 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.37 (0.20), residues: 1838 helix: 0.61 (0.18), residues: 840 sheet: -0.12 (0.30), residues: 290 loop : 0.19 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 92 TYR 0.027 0.002 TYR D 166 PHE 0.025 0.002 PHE A 564 TRP 0.059 0.003 TRP A 523 HIS 0.008 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00306 (15117) covalent geometry : angle 0.69333 (20466) hydrogen bonds : bond 0.03905 ( 729) hydrogen bonds : angle 4.76033 ( 2013) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3285.73 seconds wall clock time: 57 minutes 21.28 seconds (3441.28 seconds total)