Starting phenix.real_space_refine on Tue Dec 31 05:46:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rbf_19030/12_2024/8rbf_19030.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rbf_19030/12_2024/8rbf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rbf_19030/12_2024/8rbf_19030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rbf_19030/12_2024/8rbf_19030.map" model { file = "/net/cci-nas-00/data/ceres_data/8rbf_19030/12_2024/8rbf_19030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rbf_19030/12_2024/8rbf_19030.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 9.23, per 1000 atoms: 0.62 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: 4.06 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.92 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: 5.64 Time building geometry restraints manager: 4.60 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 376 or resid 401 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: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.450 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.440 ------------------------------------------------------------------------------- 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= 0.856 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (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 TRP 0.019 0.003 TRP C 356 HIS 0.008 0.001 HIS A 631 PHE 0.034 0.003 PHE B 22 TYR 0.025 0.002 TYR A 100 ARG 0.007 0.001 ARG B 291 *********************** 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 : 2.167 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: 0.7542 (mtpt) REVERT: A 29 LYS cc_start: 0.7739 (ptmt) cc_final: 0.7396 (ttpp) REVERT: A 32 LYS cc_start: 0.8644 (mttp) cc_final: 0.8325 (mttp) REVERT: A 110 ILE cc_start: 0.7444 (mp) cc_final: 0.7208 (mp) REVERT: A 132 MET cc_start: 0.3384 (ppp) cc_final: 0.3164 (ppp) REVERT: A 140 PHE cc_start: 0.8328 (m-10) cc_final: 0.7779 (m-10) REVERT: A 149 GLN cc_start: 0.8344 (mt0) cc_final: 0.7753 (mt0) REVERT: A 150 MET cc_start: 0.7645 (ttp) cc_final: 0.7288 (ttp) REVERT: A 169 LYS cc_start: 0.7972 (ptpp) cc_final: 0.7770 (ptpp) REVERT: A 194 GLU cc_start: 0.7724 (tt0) cc_final: 0.7436 (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: 0.7131 (ttpt) REVERT: A 223 TYR cc_start: 0.7894 (t80) cc_final: 0.6603 (t80) REVERT: A 228 PHE cc_start: 0.7537 (m-80) cc_final: 0.7150 (m-80) REVERT: A 230 LYS cc_start: 0.8875 (mttt) cc_final: 0.8559 (mmtm) REVERT: A 246 LYS cc_start: 0.8345 (mmtt) cc_final: 0.8107 (mmtt) REVERT: A 249 VAL cc_start: 0.8559 (t) cc_final: 0.8270 (t) REVERT: A 259 TYR cc_start: 0.7097 (m-80) cc_final: 0.6154 (m-10) REVERT: A 262 PHE cc_start: 0.7984 (m-80) cc_final: 0.7355 (m-80) REVERT: A 277 LEU cc_start: 0.8717 (mp) cc_final: 0.8287 (tp) REVERT: A 310 GLN cc_start: 0.8986 (mt0) cc_final: 0.8448 (mt0) REVERT: A 315 LEU cc_start: 0.7602 (mt) cc_final: 0.7305 (mt) REVERT: A 328 ILE cc_start: 0.8374 (mt) cc_final: 0.8143 (mm) REVERT: A 354 HIS cc_start: 0.7441 (t70) cc_final: 0.6731 (t70) REVERT: A 356 PRO cc_start: 0.8579 (Cg_exo) cc_final: 0.8333 (Cg_endo) REVERT: A 364 MET cc_start: 0.6997 (mmt) cc_final: 0.5998 (mmt) REVERT: A 370 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 385 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6790 (mt-10) REVERT: A 387 TYR cc_start: 0.7251 (m-80) cc_final: 0.6813 (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: 0.7805 (t80) REVERT: A 413 ASN cc_start: 0.8659 (m-40) cc_final: 0.8176 (m-40) REVERT: A 414 TRP cc_start: 0.7682 (t60) cc_final: 0.7445 (t60) REVERT: A 416 VAL cc_start: 0.8508 (t) cc_final: 0.8173 (p) REVERT: A 427 VAL cc_start: 0.8163 (t) cc_final: 0.7939 (p) REVERT: A 438 ILE cc_start: 0.7423 (tt) cc_final: 0.6737 (pt) REVERT: A 451 GLN cc_start: 0.8319 (mp10) cc_final: 0.7471 (mp-120) REVERT: A 452 PHE cc_start: 0.8374 (t80) cc_final: 0.7727 (t80) REVERT: A 453 CYS cc_start: 0.8684 (m) cc_final: 0.8376 (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: 0.6883 (tp40) REVERT: A 464 GLN cc_start: 0.8594 (tt0) cc_final: 0.8310 (tt0) REVERT: A 472 LEU cc_start: 0.8518 (tp) cc_final: 0.8282 (pp) REVERT: A 475 GLU cc_start: 0.8766 (tp30) cc_final: 0.8528 (tp30) REVERT: A 480 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6898 (mm-30) REVERT: A 496 ILE cc_start: 0.8085 (mt) cc_final: 0.7769 (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: 0.7441 (tp) REVERT: A 520 ASP cc_start: 0.6441 (m-30) cc_final: 0.6070 (m-30) REVERT: A 522 THR cc_start: 0.7529 (m) cc_final: 0.7303 (p) REVERT: A 525 GLN cc_start: 0.8558 (tp40) cc_final: 0.7587 (tp-100) REVERT: A 527 LEU cc_start: 0.8582 (mt) cc_final: 0.8333 (mt) REVERT: A 537 LEU cc_start: 0.7541 (mt) cc_final: 0.7326 (tp) REVERT: A 540 LYS cc_start: 0.7724 (tttm) cc_final: 0.6981 (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: 0.6716 (t70) REVERT: A 558 GLU cc_start: 0.7288 (tt0) cc_final: 0.7031 (tm-30) REVERT: A 559 TYR cc_start: 0.7166 (m-80) cc_final: 0.6460 (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: 0.8265 (mm) REVERT: A 578 LYS cc_start: 0.8780 (mmtp) cc_final: 0.8352 (mmtp) REVERT: A 632 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8798 (mtmt) REVERT: A 641 ASN cc_start: 0.8515 (m-40) cc_final: 0.8140 (m110) REVERT: A 644 HIS cc_start: 0.7551 (m170) cc_final: 0.7251 (m170) REVERT: A 646 LEU cc_start: 0.8594 (tp) cc_final: 0.8348 (tt) REVERT: A 657 TYR cc_start: 0.7615 (m-80) cc_final: 0.7092 (m-80) REVERT: A 667 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8443 (mtpt) REVERT: A 675 LYS cc_start: 0.8044 (mmtp) cc_final: 0.7605 (mmtp) REVERT: A 732 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7210 (tm-30) REVERT: B 7 THR cc_start: 0.8820 (m) cc_final: 0.8468 (p) REVERT: B 9 LEU cc_start: 0.7974 (mt) cc_final: 0.7707 (mt) REVERT: B 32 PHE cc_start: 0.7446 (p90) cc_final: 0.7241 (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: 0.8168 (t) REVERT: B 63 ARG cc_start: 0.7793 (mtm180) cc_final: 0.6655 (ppt170) REVERT: B 77 ILE cc_start: 0.8027 (mt) cc_final: 0.7733 (tt) REVERT: B 81 ASP cc_start: 0.7936 (p0) cc_final: 0.7182 (m-30) REVERT: B 83 MET cc_start: 0.8423 (mmm) cc_final: 0.7366 (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: 0.7480 (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: 0.7764 (mm-30) REVERT: B 101 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8011 (mm-30) REVERT: B 102 HIS cc_start: 0.8313 (m-70) cc_final: 0.7645 (m90) REVERT: B 105 LEU cc_start: 0.8636 (tt) cc_final: 0.8384 (tp) REVERT: B 106 LEU cc_start: 0.7963 (mt) cc_final: 0.7618 (mp) REVERT: B 111 LEU cc_start: 0.8067 (mt) cc_final: 0.7831 (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: 0.8090 (ttm170) REVERT: B 118 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7505 (mt-10) REVERT: B 119 LYS cc_start: 0.8545 (tptt) cc_final: 0.7720 (mmmt) REVERT: B 120 MET cc_start: 0.8713 (ttm) cc_final: 0.7616 (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: 0.6797 (t0) REVERT: B 135 VAL cc_start: 0.8664 (t) cc_final: 0.7872 (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: 0.6668 (mtm) REVERT: B 181 LEU cc_start: 0.7852 (tp) cc_final: 0.7494 (mp) REVERT: B 184 ARG cc_start: 0.7452 (tpp80) cc_final: 0.6970 (mtp85) REVERT: B 186 LEU cc_start: 0.8493 (mt) cc_final: 0.8196 (mm) REVERT: B 187 THR cc_start: 0.8494 (m) cc_final: 0.8093 (p) REVERT: B 188 ASP cc_start: 0.7742 (m-30) cc_final: 0.7279 (m-30) REVERT: B 190 LEU cc_start: 0.8514 (tp) cc_final: 0.7681 (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: 0.6338 (p) REVERT: B 209 ILE cc_start: 0.8659 (mm) cc_final: 0.8111 (mm) REVERT: B 210 VAL cc_start: 0.8876 (t) cc_final: 0.8671 (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: 0.7479 (m-30) REVERT: B 213 ILE cc_start: 0.8657 (mt) cc_final: 0.8360 (mt) REVERT: B 215 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6138 (mt-10) REVERT: B 216 LYS cc_start: 0.8102 (mttt) cc_final: 0.7768 (mttt) REVERT: B 241 TYR cc_start: 0.8285 (t80) cc_final: 0.7957 (t80) REVERT: B 242 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7514 (tm-30) REVERT: B 247 GLN cc_start: 0.7026 (mp10) cc_final: 0.6401 (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: 0.8000 (mt) REVERT: B 272 SER cc_start: 0.7938 (m) cc_final: 0.7530 (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: 0.7483 (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: 0.7251 (m-30) REVERT: B 295 TYR cc_start: 0.6750 (m-80) cc_final: 0.6468 (m-80) REVERT: B 300 MET cc_start: 0.7744 (mmm) cc_final: 0.7021 (mmp) REVERT: B 313 ARG cc_start: 0.8140 (tpt-90) cc_final: 0.7862 (tpt170) REVERT: B 314 MET cc_start: 0.7712 (tpp) cc_final: 0.7158 (tpp) REVERT: B 341 TRP cc_start: 0.7961 (t60) cc_final: 0.7627 (t60) REVERT: B 347 LEU cc_start: 0.7662 (tp) cc_final: 0.7430 (tp) REVERT: B 357 TRP cc_start: 0.7875 (m100) cc_final: 0.7566 (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: 0.7572 (mt) REVERT: C 50 LYS cc_start: 0.7707 (mttt) cc_final: 0.7434 (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: 0.7851 (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: 0.7025 (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: 0.5947 (Cg_endo) REVERT: C 110 LEU cc_start: 0.8009 (mt) cc_final: 0.7699 (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: 0.7977 (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: 0.7429 (tpp) REVERT: C 137 GLN cc_start: 0.7787 (mt0) cc_final: 0.7300 (mp10) REVERT: C 148 THR cc_start: 0.7746 (p) cc_final: 0.7499 (p) REVERT: C 151 ILE cc_start: 0.8681 (tt) cc_final: 0.8447 (tt) REVERT: C 165 ILE cc_start: 0.8393 (mt) cc_final: 0.8189 (mm) REVERT: C 166 TYR cc_start: 0.7958 (t80) cc_final: 0.7259 (t80) REVERT: C 175 ILE cc_start: 0.7542 (pt) cc_final: 0.6769 (mt) REVERT: C 176 MET cc_start: 0.6131 (mtt) cc_final: 0.5633 (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: 0.7370 (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: 0.8323 (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: 0.7149 (tp30) REVERT: C 261 LEU cc_start: 0.8144 (mt) cc_final: 0.7779 (mp) REVERT: C 271 SER cc_start: 0.8689 (m) cc_final: 0.8217 (t) REVERT: C 277 THR cc_start: 0.7014 (p) cc_final: 0.6490 (p) REVERT: C 281 SER cc_start: 0.8345 (t) cc_final: 0.7667 (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: 0.7009 (mmm) REVERT: C 305 MET cc_start: 0.7590 (mmm) cc_final: 0.6905 (mmt) REVERT: C 314 GLN cc_start: 0.8908 (tt0) cc_final: 0.8677 (tt0) REVERT: C 324 THR cc_start: 0.8547 (p) cc_final: 0.8182 (p) REVERT: C 328 LYS cc_start: 0.8424 (mttt) cc_final: 0.8020 (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: 0.6687 (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: 0.7229 (p) REVERT: D 24 ASP cc_start: 0.6226 (m-30) cc_final: 0.5909 (m-30) REVERT: D 34 ILE cc_start: 0.8678 (mt) cc_final: 0.8322 (mm) REVERT: D 47 MET cc_start: 0.7080 (ttm) cc_final: 0.6868 (ttm) REVERT: D 54 VAL cc_start: 0.8303 (t) cc_final: 0.7983 (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: 0.6903 (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: 0.8188 (tttt) REVERT: D 86 TRP cc_start: 0.7658 (m-10) cc_final: 0.7261 (m-10) REVERT: D 87 HIS cc_start: 0.8366 (t-90) cc_final: 0.8145 (t-90) REVERT: D 92 ASN cc_start: 0.7033 (m-40) cc_final: 0.6780 (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: 0.7334 (tp30) REVERT: D 116 ARG cc_start: 0.8272 (ttm110) cc_final: 0.7916 (ttm110) REVERT: D 118 LYS cc_start: 0.8937 (tptt) cc_final: 0.8159 (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: 0.7753 (mmp) REVERT: D 133 TYR cc_start: 0.7828 (t80) cc_final: 0.7032 (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: 0.7154 (pp) REVERT: D 159 VAL cc_start: 0.7585 (p) cc_final: 0.6989 (m) REVERT: D 166 TYR cc_start: 0.8012 (t80) cc_final: 0.7730 (t80) REVERT: D 176 MET cc_start: 0.6381 (mtp) cc_final: 0.5550 (mtp) REVERT: D 184 ASP cc_start: 0.8188 (m-30) cc_final: 0.7886 (m-30) REVERT: D 190 MET cc_start: 0.8005 (mtm) cc_final: 0.7769 (mtt) REVERT: D 206 ARG cc_start: 0.8194 (ttm170) cc_final: 0.7813 (ttm-80) REVERT: D 211 ASP cc_start: 0.7894 (m-30) cc_final: 0.7469 (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: 0.7089 (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: 0.7292 (p-80) REVERT: D 280 ASN cc_start: 0.7280 (t0) cc_final: 0.6924 (t0) REVERT: D 281 SER cc_start: 0.8216 (p) cc_final: 0.7891 (m) REVERT: D 282 ILE cc_start: 0.8202 (mt) cc_final: 0.7865 (mt) REVERT: D 294 TYR cc_start: 0.7031 (m-80) cc_final: 0.6702 (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: 0.7769 (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: 0.7682 (tttt) REVERT: D 361 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7659 (mt-10) outliers start: 3 outliers final: 2 residues processed: 805 average time/residue: 0.3398 time to fit residues: 373.2054 Evaluate side-chains 752 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 750 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 77 optimal weight: 0.0370 chunk 47 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 372 HIS C 101 HIS C 111 ASN C 162 ASN C 353 GLN D 73 HIS D 92 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15117 Z= 0.214 Angle : 0.675 12.208 20466 Z= 0.346 Chirality : 0.045 0.185 2241 Planarity : 0.005 0.043 2622 Dihedral : 11.404 157.493 2062 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 1838 helix: 0.51 (0.17), residues: 843 sheet: -0.48 (0.29), residues: 297 loop : 0.02 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 356 HIS 0.008 0.001 HIS A 418 PHE 0.019 0.002 PHE B 128 TYR 0.029 0.002 TYR A 477 ARG 0.007 0.001 ARG A 700 *********************** 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 810 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 810 time to evaluate : 1.706 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: A 32 LYS cc_start: 0.8745 (mttp) cc_final: 0.8330 (mttp) REVERT: A 88 ASN cc_start: 0.8796 (m110) cc_final: 0.8402 (m-40) REVERT: A 132 MET cc_start: 0.3367 (ppp) cc_final: 0.2959 (ppp) REVERT: A 140 PHE cc_start: 0.8345 (m-10) cc_final: 0.7902 (m-10) REVERT: A 149 GLN cc_start: 0.8513 (mt0) cc_final: 0.7982 (mt0) REVERT: A 150 MET cc_start: 0.7980 (ttp) cc_final: 0.7423 (ttp) REVERT: A 159 ILE cc_start: 0.8083 (mp) cc_final: 0.7815 (tp) REVERT: A 174 LYS cc_start: 0.8499 (pttp) cc_final: 0.7768 (ttpp) REVERT: A 178 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.8503 (mmm-85) REVERT: A 210 LYS cc_start: 0.7052 (tmtt) cc_final: 0.6326 (tptp) REVERT: A 219 ARG cc_start: 0.6912 (mmp-170) cc_final: 0.6463 (mmm-85) REVERT: A 223 TYR cc_start: 0.8044 (t80) cc_final: 0.7601 (t80) REVERT: A 225 GLU cc_start: 0.6982 (mp0) cc_final: 0.4717 (pm20) REVERT: A 228 PHE cc_start: 0.7796 (m-80) cc_final: 0.7425 (m-80) REVERT: A 240 ARG cc_start: 0.7003 (mtt180) cc_final: 0.6477 (mtt180) REVERT: A 259 TYR cc_start: 0.6999 (m-80) cc_final: 0.6486 (m-10) REVERT: A 285 PHE cc_start: 0.8022 (m-80) cc_final: 0.7481 (m-80) REVERT: A 312 CYS cc_start: 0.8689 (m) cc_final: 0.8374 (m) REVERT: A 321 TYR cc_start: 0.8250 (m-10) cc_final: 0.8030 (m-80) REVERT: A 323 MET cc_start: 0.8233 (mmp) cc_final: 0.8008 (mmm) REVERT: A 325 ILE cc_start: 0.8541 (mm) cc_final: 0.8217 (mm) REVERT: A 327 ARG cc_start: 0.8022 (ttt180) cc_final: 0.7408 (ptm-80) REVERT: A 328 ILE cc_start: 0.8507 (mt) cc_final: 0.8273 (mt) REVERT: A 354 HIS cc_start: 0.7509 (t70) cc_final: 0.6957 (t-170) REVERT: A 359 ILE cc_start: 0.8145 (mm) cc_final: 0.7938 (mt) REVERT: A 362 ASP cc_start: 0.8714 (m-30) cc_final: 0.8425 (m-30) REVERT: A 369 GLU cc_start: 0.8173 (mp0) cc_final: 0.7728 (mp0) REVERT: A 371 MET cc_start: 0.8304 (mmm) cc_final: 0.8095 (mmm) REVERT: A 372 CYS cc_start: 0.8965 (t) cc_final: 0.8314 (p) REVERT: A 389 LYS cc_start: 0.8659 (mmtp) cc_final: 0.8333 (tppt) REVERT: A 405 LYS cc_start: 0.8944 (mtmt) cc_final: 0.8235 (mtmt) REVERT: A 408 TYR cc_start: 0.8442 (t80) cc_final: 0.8035 (t80) REVERT: A 414 TRP cc_start: 0.8146 (t60) cc_final: 0.7544 (t60) REVERT: A 427 VAL cc_start: 0.8369 (t) cc_final: 0.8152 (p) REVERT: A 433 ILE cc_start: 0.7740 (mt) cc_final: 0.7165 (mm) REVERT: A 450 GLU cc_start: 0.8347 (mp0) cc_final: 0.8092 (mp0) REVERT: A 452 PHE cc_start: 0.8602 (t80) cc_final: 0.8068 (t80) REVERT: A 453 CYS cc_start: 0.8781 (m) cc_final: 0.8464 (p) REVERT: A 455 ASN cc_start: 0.8939 (m-40) cc_final: 0.7840 (m110) REVERT: A 456 TYR cc_start: 0.8183 (t80) cc_final: 0.7729 (t80) REVERT: A 458 ASN cc_start: 0.8627 (m-40) cc_final: 0.8347 (m110) REVERT: A 459 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7839 (mm-30) REVERT: A 460 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8352 (mmmt) REVERT: A 461 LEU cc_start: 0.8912 (mt) cc_final: 0.8673 (tp) REVERT: A 466 ASN cc_start: 0.8655 (m-40) cc_final: 0.8222 (m-40) REVERT: A 467 MET cc_start: 0.8411 (tmm) cc_final: 0.8208 (tmm) REVERT: A 469 VAL cc_start: 0.8823 (t) cc_final: 0.8600 (m) REVERT: A 472 LEU cc_start: 0.8659 (tp) cc_final: 0.8350 (tp) REVERT: A 475 GLU cc_start: 0.8714 (tp30) cc_final: 0.8228 (tp30) REVERT: A 499 ILE cc_start: 0.8746 (mt) cc_final: 0.8400 (mm) REVERT: A 500 GLU cc_start: 0.7995 (pt0) cc_final: 0.6934 (pt0) REVERT: A 508 LEU cc_start: 0.8326 (mt) cc_final: 0.8068 (mt) REVERT: A 509 LEU cc_start: 0.8066 (tp) cc_final: 0.7829 (tp) REVERT: A 511 GLU cc_start: 0.8262 (tt0) cc_final: 0.7292 (tt0) REVERT: A 517 LYS cc_start: 0.5709 (mtpp) cc_final: 0.5458 (mtpp) REVERT: A 526 LYS cc_start: 0.8870 (mttt) cc_final: 0.8543 (mmtt) REVERT: A 527 LEU cc_start: 0.8757 (mt) cc_final: 0.8545 (mt) REVERT: A 532 LEU cc_start: 0.7449 (tp) cc_final: 0.7183 (mt) REVERT: A 533 ASN cc_start: 0.8001 (t0) cc_final: 0.7733 (t0) REVERT: A 540 LYS cc_start: 0.7693 (tmtt) cc_final: 0.7336 (tttm) REVERT: A 555 ASP cc_start: 0.7139 (t0) cc_final: 0.6791 (t0) REVERT: A 557 VAL cc_start: 0.7282 (t) cc_final: 0.6247 (t) REVERT: A 558 GLU cc_start: 0.7431 (tt0) cc_final: 0.7179 (tm-30) REVERT: A 559 TYR cc_start: 0.7561 (m-80) cc_final: 0.6992 (m-80) REVERT: A 567 LYS cc_start: 0.8105 (mttt) cc_final: 0.7393 (mtmm) REVERT: A 578 LYS cc_start: 0.8817 (mmtp) cc_final: 0.8435 (mmtp) REVERT: A 581 LYS cc_start: 0.8845 (tttt) cc_final: 0.8632 (mtpp) REVERT: A 585 PHE cc_start: 0.6791 (t80) cc_final: 0.6211 (t80) REVERT: A 632 LYS cc_start: 0.9128 (mtmt) cc_final: 0.8758 (mtmt) REVERT: A 641 ASN cc_start: 0.8816 (m-40) cc_final: 0.8325 (m110) REVERT: A 644 HIS cc_start: 0.7668 (m170) cc_final: 0.7376 (m170) REVERT: A 647 MET cc_start: 0.8084 (tpt) cc_final: 0.7521 (tpt) REVERT: A 654 THR cc_start: 0.7737 (m) cc_final: 0.7509 (m) REVERT: A 675 LYS cc_start: 0.8506 (mmtp) cc_final: 0.8109 (mptt) REVERT: A 700 ARG cc_start: 0.7031 (ttp80) cc_final: 0.6812 (ttp80) REVERT: A 705 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8122 (tm-30) REVERT: B 7 THR cc_start: 0.8745 (m) cc_final: 0.8525 (m) REVERT: B 9 LEU cc_start: 0.8122 (mt) cc_final: 0.7848 (mt) REVERT: B 18 VAL cc_start: 0.7973 (t) cc_final: 0.7754 (p) REVERT: B 32 PHE cc_start: 0.7426 (p90) cc_final: 0.6971 (p90) REVERT: B 35 ILE cc_start: 0.8439 (mt) cc_final: 0.8122 (mm) REVERT: B 51 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7659 (mtpp) REVERT: B 81 ASP cc_start: 0.8355 (p0) cc_final: 0.6777 (m-30) REVERT: B 83 MET cc_start: 0.8531 (mmm) cc_final: 0.7420 (mmm) REVERT: B 84 GLU cc_start: 0.8361 (tt0) cc_final: 0.8051 (tt0) REVERT: B 85 LYS cc_start: 0.8872 (mttm) cc_final: 0.8546 (mttm) REVERT: B 87 TRP cc_start: 0.7960 (m-10) cc_final: 0.7628 (m-90) REVERT: B 88 HIS cc_start: 0.8193 (t-90) cc_final: 0.7930 (t-170) REVERT: B 93 ASN cc_start: 0.7823 (m-40) cc_final: 0.7567 (m-40) REVERT: B 101 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8182 (mm-30) REVERT: B 102 HIS cc_start: 0.8345 (m-70) cc_final: 0.7828 (m90) REVERT: B 108 GLU cc_start: 0.7165 (mt-10) cc_final: 0.5290 (mt-10) REVERT: B 117 ARG cc_start: 0.8461 (ttm110) cc_final: 0.7514 (ttm110) REVERT: B 119 LYS cc_start: 0.8564 (tptt) cc_final: 0.7839 (mmmt) REVERT: B 120 MET cc_start: 0.8681 (ttm) cc_final: 0.7982 (ttm) REVERT: B 123 ILE cc_start: 0.8811 (mt) cc_final: 0.8320 (tp) REVERT: B 128 PHE cc_start: 0.7902 (m-10) cc_final: 0.7513 (m-10) REVERT: B 134 TYR cc_start: 0.8205 (t80) cc_final: 0.7870 (t80) REVERT: B 144 TYR cc_start: 0.7606 (m-80) cc_final: 0.7350 (m-10) REVERT: B 180 ASP cc_start: 0.6768 (m-30) cc_final: 0.6290 (t70) REVERT: B 181 LEU cc_start: 0.8055 (tp) cc_final: 0.7806 (mm) REVERT: B 184 ARG cc_start: 0.7654 (tpp80) cc_final: 0.7246 (mmm-85) REVERT: B 185 ASP cc_start: 0.8446 (m-30) cc_final: 0.8148 (m-30) REVERT: B 186 LEU cc_start: 0.8584 (mt) cc_final: 0.8291 (mm) REVERT: B 187 THR cc_start: 0.8557 (m) cc_final: 0.8165 (p) REVERT: B 188 ASP cc_start: 0.7944 (m-30) cc_final: 0.7357 (m-30) REVERT: B 190 LEU cc_start: 0.8500 (tp) cc_final: 0.7832 (tp) REVERT: B 194 LEU cc_start: 0.8669 (mt) cc_final: 0.8182 (mt) REVERT: B 208 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7651 (mm-30) REVERT: B 209 ILE cc_start: 0.8765 (mm) cc_final: 0.8390 (mm) REVERT: B 211 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7707 (ttp80) REVERT: B 212 ASP cc_start: 0.8335 (m-30) cc_final: 0.7595 (m-30) REVERT: B 213 ILE cc_start: 0.8824 (mt) cc_final: 0.8498 (mt) REVERT: B 215 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6840 (mt-10) REVERT: B 241 TYR cc_start: 0.8385 (t80) cc_final: 0.8140 (t80) REVERT: B 243 LEU cc_start: 0.7933 (mt) cc_final: 0.7540 (mt) REVERT: B 247 GLN cc_start: 0.7571 (mm110) cc_final: 0.6979 (tp-100) REVERT: B 254 GLU cc_start: 0.8228 (mp0) cc_final: 0.7821 (mp0) REVERT: B 257 ARG cc_start: 0.7956 (mtp180) cc_final: 0.7732 (mtp85) REVERT: B 263 PHE cc_start: 0.8598 (m-10) cc_final: 0.8377 (m-80) REVERT: B 272 SER cc_start: 0.8016 (m) cc_final: 0.7712 (t) REVERT: B 283 ILE cc_start: 0.7597 (mt) cc_final: 0.7358 (tt) REVERT: B 295 TYR cc_start: 0.6858 (m-80) cc_final: 0.6553 (m-80) REVERT: B 300 MET cc_start: 0.7749 (mmm) cc_final: 0.7142 (mmp) REVERT: B 314 MET cc_start: 0.7701 (tpp) cc_final: 0.7271 (tpp) REVERT: B 350 LEU cc_start: 0.8165 (mp) cc_final: 0.7848 (mp) REVERT: B 362 GLU cc_start: 0.8981 (tt0) cc_final: 0.8622 (tt0) REVERT: C 9 VAL cc_start: 0.7763 (t) cc_final: 0.7532 (p) REVERT: C 12 ASN cc_start: 0.7578 (m110) cc_final: 0.6769 (m110) REVERT: C 16 LEU cc_start: 0.6830 (tp) cc_final: 0.6480 (tp) REVERT: C 17 VAL cc_start: 0.7757 (m) cc_final: 0.7549 (p) REVERT: C 31 PHE cc_start: 0.8395 (p90) cc_final: 0.8179 (p90) REVERT: C 34 ILE cc_start: 0.7986 (mt) cc_final: 0.7734 (mt) REVERT: C 50 LYS cc_start: 0.7967 (mttt) cc_final: 0.7544 (mttt) REVERT: C 67 LEU cc_start: 0.7859 (mt) cc_final: 0.7611 (mt) REVERT: C 78 ASN cc_start: 0.7266 (t0) cc_final: 0.6543 (t0) REVERT: C 81 ASP cc_start: 0.7895 (m-30) cc_final: 0.7598 (m-30) REVERT: C 82 MET cc_start: 0.8157 (mmm) cc_final: 0.7609 (mmm) REVERT: C 85 ILE cc_start: 0.8666 (pt) cc_final: 0.8462 (pt) REVERT: C 87 HIS cc_start: 0.8653 (t-90) cc_final: 0.8167 (t-90) REVERT: C 92 ASN cc_start: 0.8048 (m-40) cc_final: 0.7749 (m-40) REVERT: C 105 LEU cc_start: 0.7957 (mt) cc_final: 0.7356 (mt) REVERT: C 111 ASN cc_start: 0.7925 (m110) cc_final: 0.7442 (m-40) REVERT: C 113 LYS cc_start: 0.7992 (mttp) cc_final: 0.7786 (mttp) REVERT: C 115 ASN cc_start: 0.7780 (t0) cc_final: 0.7414 (t0) REVERT: C 116 ARG cc_start: 0.8388 (ttm110) cc_final: 0.7739 (ttm170) REVERT: C 118 LYS cc_start: 0.8319 (tptt) cc_final: 0.8024 (tptt) REVERT: C 119 MET cc_start: 0.8597 (ttm) cc_final: 0.8322 (ttm) REVERT: C 123 MET cc_start: 0.8101 (tpp) cc_final: 0.7573 (tpp) REVERT: C 125 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7497 (mt-10) REVERT: C 128 ASN cc_start: 0.8527 (m-40) cc_final: 0.8266 (m-40) REVERT: C 137 GLN cc_start: 0.7752 (mt0) cc_final: 0.7381 (mp10) REVERT: C 139 VAL cc_start: 0.8602 (m) cc_final: 0.8389 (p) REVERT: C 148 THR cc_start: 0.7943 (p) cc_final: 0.7710 (p) REVERT: C 152 VAL cc_start: 0.8286 (t) cc_final: 0.7918 (p) REVERT: C 162 ASN cc_start: 0.7921 (m-40) cc_final: 0.7693 (m-40) REVERT: C 166 TYR cc_start: 0.8001 (t80) cc_final: 0.7665 (t80) REVERT: C 175 ILE cc_start: 0.7668 (pt) cc_final: 0.6913 (mt) REVERT: C 176 MET cc_start: 0.6433 (mtt) cc_final: 0.6080 (mtt) REVERT: C 205 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7323 (mt-10) REVERT: C 207 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7645 (mm-30) REVERT: C 208 ILE cc_start: 0.8484 (mp) cc_final: 0.8138 (mp) REVERT: C 209 VAL cc_start: 0.8657 (t) cc_final: 0.8404 (t) REVERT: C 210 ARG cc_start: 0.8458 (ttp-110) cc_final: 0.7749 (ttp-110) REVERT: C 212 ILE cc_start: 0.8852 (mt) cc_final: 0.8608 (mt) REVERT: C 213 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8187 (ttpp) REVERT: C 215 LYS cc_start: 0.8851 (mttm) cc_final: 0.8523 (mtpp) REVERT: C 222 ASP cc_start: 0.7132 (t0) cc_final: 0.6676 (t0) REVERT: C 225 ASN cc_start: 0.8755 (m110) cc_final: 0.8506 (m-40) REVERT: C 238 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7814 (mmtt) REVERT: C 269 MET cc_start: 0.7180 (mtm) cc_final: 0.6904 (mtm) REVERT: C 271 SER cc_start: 0.8682 (m) cc_final: 0.8226 (t) REVERT: C 278 THR cc_start: 0.7977 (m) cc_final: 0.7263 (p) REVERT: C 283 MET cc_start: 0.7729 (mmm) cc_final: 0.7481 (mmm) REVERT: C 291 LYS cc_start: 0.8730 (mtpt) cc_final: 0.8262 (mptt) REVERT: C 297 ASN cc_start: 0.8193 (m-40) cc_final: 0.7783 (m-40) REVERT: C 299 MET cc_start: 0.8065 (mmm) cc_final: 0.7631 (mmm) REVERT: C 305 MET cc_start: 0.7368 (mmm) cc_final: 0.7063 (mmt) REVERT: C 326 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7445 (mmtt) REVERT: C 328 LYS cc_start: 0.8456 (mttt) cc_final: 0.7954 (mttt) REVERT: C 334 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7509 (tp30) REVERT: C 337 TYR cc_start: 0.6913 (m-10) cc_final: 0.6496 (m-10) REVERT: C 356 TRP cc_start: 0.6079 (m100) cc_final: 0.5471 (m100) REVERT: C 371 HIS cc_start: 0.7797 (m-70) cc_final: 0.6808 (m-70) REVERT: D 24 ASP cc_start: 0.6460 (m-30) cc_final: 0.6011 (m-30) REVERT: D 41 GLN cc_start: 0.7170 (tp40) cc_final: 0.6854 (tp40) REVERT: D 44 MET cc_start: 0.6362 (mmm) cc_final: 0.6069 (mmm) REVERT: D 47 MET cc_start: 0.6830 (ttm) cc_final: 0.6529 (ttm) REVERT: D 54 VAL cc_start: 0.8247 (t) cc_final: 0.7808 (m) REVERT: D 64 ILE cc_start: 0.8480 (mm) cc_final: 0.8182 (mm) REVERT: D 76 ILE cc_start: 0.8068 (mt) cc_final: 0.7258 (mt) REVERT: D 78 ASN cc_start: 0.8170 (t0) cc_final: 0.7826 (t0) REVERT: D 79 TRP cc_start: 0.7696 (m100) cc_final: 0.6981 (m100) REVERT: D 84 LYS cc_start: 0.8620 (tttt) cc_final: 0.8314 (tptt) REVERT: D 92 ASN cc_start: 0.7246 (m110) cc_final: 0.7001 (m110) REVERT: D 95 ARG cc_start: 0.8508 (ptp90) cc_final: 0.8175 (ptp90) REVERT: D 99 GLU cc_start: 0.7811 (mp0) cc_final: 0.7565 (mp0) REVERT: D 100 GLU cc_start: 0.7925 (tp30) cc_final: 0.7328 (tp30) REVERT: D 107 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6209 (mt-10) REVERT: D 116 ARG cc_start: 0.8364 (ttm110) cc_final: 0.7891 (ttm110) REVERT: D 119 MET cc_start: 0.8593 (ttt) cc_final: 0.8385 (ttt) REVERT: D 123 MET cc_start: 0.8264 (mmp) cc_final: 0.8040 (mmp) REVERT: D 133 TYR cc_start: 0.8004 (t80) cc_final: 0.7247 (t80) REVERT: D 134 VAL cc_start: 0.8225 (t) cc_final: 0.7824 (p) REVERT: D 153 LEU cc_start: 0.8113 (tp) cc_final: 0.7426 (tt) REVERT: D 157 ASP cc_start: 0.6237 (t0) cc_final: 0.6023 (t0) REVERT: D 176 MET cc_start: 0.6604 (mtp) cc_final: 0.5867 (mtp) REVERT: D 183 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7292 (ttm-80) REVERT: D 184 ASP cc_start: 0.8217 (m-30) cc_final: 0.7987 (m-30) REVERT: D 188 TYR cc_start: 0.7497 (t80) cc_final: 0.7191 (t80) REVERT: D 190 MET cc_start: 0.7864 (mtm) cc_final: 0.7554 (mtt) REVERT: D 192 ILE cc_start: 0.7833 (mm) cc_final: 0.7067 (mm) REVERT: D 195 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6584 (mt-10) REVERT: D 205 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7189 (mt-10) REVERT: D 206 ARG cc_start: 0.8308 (ttm170) cc_final: 0.8043 (ttm-80) REVERT: D 207 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7183 (mm-30) REVERT: D 210 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7928 (ttp80) REVERT: D 211 ASP cc_start: 0.8052 (m-30) cc_final: 0.7173 (m-30) REVERT: D 223 PHE cc_start: 0.7384 (t80) cc_final: 0.7157 (t80) REVERT: D 238 LYS cc_start: 0.7823 (mmmt) cc_final: 0.7407 (mmmm) REVERT: D 253 GLU cc_start: 0.7468 (mp0) cc_final: 0.7092 (mp0) REVERT: D 255 PHE cc_start: 0.8129 (p90) cc_final: 0.7854 (p90) REVERT: D 256 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7000 (mtp180) REVERT: D 279 TYR cc_start: 0.7892 (t80) cc_final: 0.7588 (t80) REVERT: D 280 ASN cc_start: 0.7661 (t0) cc_final: 0.6999 (t0) REVERT: D 294 TYR cc_start: 0.7212 (m-80) cc_final: 0.6680 (m-80) REVERT: D 298 VAL cc_start: 0.8133 (t) cc_final: 0.7793 (m) REVERT: D 299 MET cc_start: 0.7625 (mmm) cc_final: 0.7395 (mmm) REVERT: D 313 MET cc_start: 0.8633 (tpt) cc_final: 0.7903 (tpt) REVERT: D 315 LYS cc_start: 0.8874 (ttpp) cc_final: 0.8242 (ttpp) REVERT: D 316 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7116 (mm-30) REVERT: D 320 LEU cc_start: 0.8791 (mt) cc_final: 0.8357 (mt) REVERT: D 325 MET cc_start: 0.6881 (ttm) cc_final: 0.6393 (ttm) REVERT: D 361 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7937 (mt-10) outliers start: 0 outliers final: 0 residues processed: 810 average time/residue: 0.3555 time to fit residues: 391.5282 Evaluate side-chains 741 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 741 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 180 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 680 GLN B 13 ASN B 50 GLN B 298 ASN B 372 HIS ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 296 ASN D 111 ASN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15117 Z= 0.235 Angle : 0.670 11.331 20466 Z= 0.344 Chirality : 0.044 0.167 2241 Planarity : 0.005 0.042 2622 Dihedral : 10.633 165.252 2062 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1838 helix: 0.94 (0.18), residues: 828 sheet: -0.20 (0.30), residues: 295 loop : 0.23 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 701 HIS 0.012 0.002 HIS A 418 PHE 0.015 0.002 PHE C 255 TYR 0.021 0.002 TYR A 477 ARG 0.019 0.001 ARG A 709 *********************** 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 763 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 763 time to evaluate : 1.759 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 88 ASN cc_start: 0.8735 (m110) cc_final: 0.8515 (m-40) REVERT: A 103 CYS cc_start: 0.7409 (m) cc_final: 0.6852 (m) REVERT: A 132 MET cc_start: 0.3236 (ppp) cc_final: 0.2767 (ppp) REVERT: A 140 PHE cc_start: 0.8379 (m-10) cc_final: 0.7976 (m-10) REVERT: A 144 GLU cc_start: 0.8298 (tp30) cc_final: 0.7535 (tp30) REVERT: A 150 MET cc_start: 0.8055 (ttp) cc_final: 0.7730 (ttp) REVERT: A 159 ILE cc_start: 0.8054 (mp) cc_final: 0.7722 (tp) REVERT: A 203 MET cc_start: 0.8668 (ptp) cc_final: 0.8375 (ptp) REVERT: A 225 GLU cc_start: 0.6894 (mp0) cc_final: 0.6086 (pm20) REVERT: A 228 PHE cc_start: 0.7810 (m-80) cc_final: 0.7194 (m-10) REVERT: A 246 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8156 (mmtm) REVERT: A 248 ARG cc_start: 0.7776 (tpp-160) cc_final: 0.7559 (mmp-170) REVERT: A 251 PHE cc_start: 0.7133 (t80) cc_final: 0.6375 (t80) REVERT: A 274 PHE cc_start: 0.8284 (m-10) cc_final: 0.8050 (m-80) REVERT: A 285 PHE cc_start: 0.8179 (m-80) cc_final: 0.7778 (m-80) REVERT: A 307 HIS cc_start: 0.8518 (m90) cc_final: 0.8293 (m170) REVERT: A 309 ARG cc_start: 0.8279 (ttp80) cc_final: 0.8063 (tmm-80) REVERT: A 319 GLU cc_start: 0.7365 (tp30) cc_final: 0.6810 (tp30) REVERT: A 323 MET cc_start: 0.8273 (mmp) cc_final: 0.7693 (mmp) REVERT: A 325 ILE cc_start: 0.8460 (mm) cc_final: 0.8237 (mm) REVERT: A 328 ILE cc_start: 0.8560 (mt) cc_final: 0.8313 (mm) REVERT: A 342 SER cc_start: 0.8370 (t) cc_final: 0.7975 (t) REVERT: A 354 HIS cc_start: 0.7827 (t70) cc_final: 0.7151 (t-90) REVERT: A 359 ILE cc_start: 0.8191 (mm) cc_final: 0.7980 (mt) REVERT: A 363 LEU cc_start: 0.8218 (mt) cc_final: 0.7452 (mt) REVERT: A 364 MET cc_start: 0.7380 (mmt) cc_final: 0.6499 (mmt) REVERT: A 367 ASP cc_start: 0.8127 (t0) cc_final: 0.7291 (t70) REVERT: A 371 MET cc_start: 0.8219 (mmm) cc_final: 0.7708 (mmm) REVERT: A 372 CYS cc_start: 0.8933 (t) cc_final: 0.8408 (p) REVERT: A 374 TRP cc_start: 0.8771 (m100) cc_final: 0.8519 (m100) REVERT: A 385 GLU cc_start: 0.7627 (tp30) cc_final: 0.7000 (tm-30) REVERT: A 393 LYS cc_start: 0.8411 (tttt) cc_final: 0.8124 (mmmt) REVERT: A 395 GLN cc_start: 0.8309 (mm110) cc_final: 0.7520 (mt0) REVERT: A 408 TYR cc_start: 0.8462 (t80) cc_final: 0.8234 (t80) REVERT: A 410 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8061 (mtpt) REVERT: A 413 ASN cc_start: 0.8647 (m-40) cc_final: 0.8408 (m-40) REVERT: A 414 TRP cc_start: 0.7881 (t60) cc_final: 0.7637 (t60) REVERT: A 433 ILE cc_start: 0.7764 (mt) cc_final: 0.7405 (mm) REVERT: A 441 PHE cc_start: 0.6207 (m-80) cc_final: 0.5986 (m-80) REVERT: A 453 CYS cc_start: 0.8657 (m) cc_final: 0.8381 (p) REVERT: A 455 ASN cc_start: 0.8891 (m-40) cc_final: 0.7913 (m110) REVERT: A 459 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7747 (mm-30) REVERT: A 460 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8477 (mmmt) REVERT: A 461 LEU cc_start: 0.8971 (mt) cc_final: 0.8766 (pp) REVERT: A 464 GLN cc_start: 0.8950 (tt0) cc_final: 0.8727 (tt0) REVERT: A 466 ASN cc_start: 0.8652 (m-40) cc_final: 0.8263 (m-40) REVERT: A 468 HIS cc_start: 0.8583 (t-90) cc_final: 0.8195 (t-90) REVERT: A 469 VAL cc_start: 0.9041 (t) cc_final: 0.8501 (m) REVERT: A 499 ILE cc_start: 0.8810 (mt) cc_final: 0.8445 (tp) REVERT: A 502 LYS cc_start: 0.8461 (mmtp) cc_final: 0.8014 (mmtp) REVERT: A 508 LEU cc_start: 0.8346 (mt) cc_final: 0.8125 (mt) REVERT: A 511 GLU cc_start: 0.8105 (tt0) cc_final: 0.7421 (tt0) REVERT: A 515 MET cc_start: 0.6582 (tpt) cc_final: 0.6358 (tpt) REVERT: A 526 LYS cc_start: 0.8882 (mttt) cc_final: 0.8491 (mmtt) REVERT: A 532 LEU cc_start: 0.7642 (tp) cc_final: 0.7386 (mt) REVERT: A 533 ASN cc_start: 0.8037 (t0) cc_final: 0.7701 (t0) REVERT: A 551 LYS cc_start: 0.8237 (tttt) cc_final: 0.7960 (tppt) REVERT: A 552 HIS cc_start: 0.7072 (m-70) cc_final: 0.6399 (m-70) REVERT: A 557 VAL cc_start: 0.7654 (t) cc_final: 0.6814 (t) REVERT: A 558 GLU cc_start: 0.7522 (tt0) cc_final: 0.7178 (tm-30) REVERT: A 559 TYR cc_start: 0.7804 (m-80) cc_final: 0.7442 (m-80) REVERT: A 566 GLU cc_start: 0.7732 (mp0) cc_final: 0.7528 (pm20) REVERT: A 574 GLU cc_start: 0.7811 (pp20) cc_final: 0.7598 (pm20) REVERT: A 581 LYS cc_start: 0.8961 (tttt) cc_final: 0.8703 (mtpp) REVERT: A 588 LEU cc_start: 0.9014 (mt) cc_final: 0.8808 (mt) REVERT: A 630 GLU cc_start: 0.8401 (tt0) cc_final: 0.7873 (tt0) REVERT: A 632 LYS cc_start: 0.9114 (mtmt) cc_final: 0.8781 (pttm) REVERT: A 641 ASN cc_start: 0.8881 (m-40) cc_final: 0.8510 (m110) REVERT: A 644 HIS cc_start: 0.8002 (m170) cc_final: 0.7732 (m90) REVERT: A 647 MET cc_start: 0.8189 (tpt) cc_final: 0.7681 (tpt) REVERT: A 648 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8091 (tm-30) REVERT: A 675 LYS cc_start: 0.8535 (mmtp) cc_final: 0.8171 (mptt) REVERT: A 682 ARG cc_start: 0.6863 (tpm170) cc_final: 0.6604 (tpm170) REVERT: B 7 THR cc_start: 0.8660 (m) cc_final: 0.8440 (m) REVERT: B 9 LEU cc_start: 0.8287 (mt) cc_final: 0.8078 (mt) REVERT: B 35 ILE cc_start: 0.8574 (mt) cc_final: 0.8162 (mm) REVERT: B 77 ILE cc_start: 0.8422 (mt) cc_final: 0.8051 (tt) REVERT: B 81 ASP cc_start: 0.8527 (p0) cc_final: 0.7386 (m-30) REVERT: B 83 MET cc_start: 0.8583 (mmm) cc_final: 0.7704 (mmm) REVERT: B 85 LYS cc_start: 0.8827 (mttm) cc_final: 0.8410 (mttm) REVERT: B 87 TRP cc_start: 0.8121 (m-10) cc_final: 0.7673 (m-90) REVERT: B 88 HIS cc_start: 0.8257 (t-90) cc_final: 0.7830 (t70) REVERT: B 92 TYR cc_start: 0.7818 (m-80) cc_final: 0.7597 (m-80) REVERT: B 93 ASN cc_start: 0.7899 (m-40) cc_final: 0.7658 (m-40) REVERT: B 101 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8193 (mm-30) REVERT: B 102 HIS cc_start: 0.8399 (m-70) cc_final: 0.7770 (m90) REVERT: B 108 GLU cc_start: 0.7088 (mt-10) cc_final: 0.5564 (mt-10) REVERT: B 114 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8121 (mtmt) REVERT: B 116 ASN cc_start: 0.8477 (t0) cc_final: 0.8109 (t0) REVERT: B 117 ARG cc_start: 0.8365 (ttm110) cc_final: 0.7333 (ttm110) REVERT: B 119 LYS cc_start: 0.8607 (tptt) cc_final: 0.7884 (mmmt) REVERT: B 120 MET cc_start: 0.8700 (ttm) cc_final: 0.8070 (ttm) REVERT: B 123 ILE cc_start: 0.8855 (mt) cc_final: 0.8278 (tp) REVERT: B 127 THR cc_start: 0.8726 (m) cc_final: 0.7714 (t) REVERT: B 155 ASP cc_start: 0.7384 (t0) cc_final: 0.6922 (t0) REVERT: B 177 MET cc_start: 0.7371 (mtt) cc_final: 0.6873 (mtm) REVERT: B 180 ASP cc_start: 0.6925 (m-30) cc_final: 0.6280 (t70) REVERT: B 181 LEU cc_start: 0.8030 (tp) cc_final: 0.7801 (mm) REVERT: B 184 ARG cc_start: 0.7831 (tpp80) cc_final: 0.7135 (mtp85) REVERT: B 185 ASP cc_start: 0.8424 (m-30) cc_final: 0.8076 (m-30) REVERT: B 186 LEU cc_start: 0.8757 (mt) cc_final: 0.8447 (mm) REVERT: B 188 ASP cc_start: 0.7998 (m-30) cc_final: 0.7571 (m-30) REVERT: B 194 LEU cc_start: 0.8906 (mt) cc_final: 0.8679 (tp) REVERT: B 197 ARG cc_start: 0.8085 (mmp-170) cc_final: 0.7831 (mmp-170) REVERT: B 199 TYR cc_start: 0.7556 (m-80) cc_final: 0.6815 (m-80) REVERT: B 208 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7804 (mm-30) REVERT: B 209 ILE cc_start: 0.8774 (mm) cc_final: 0.8553 (mm) REVERT: B 211 ARG cc_start: 0.8464 (ttp80) cc_final: 0.7890 (ttp80) REVERT: B 212 ASP cc_start: 0.8343 (m-30) cc_final: 0.8115 (m-30) REVERT: B 214 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8516 (ttpt) REVERT: B 215 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7051 (mt-10) REVERT: B 223 ASP cc_start: 0.8212 (t0) cc_final: 0.7902 (t70) REVERT: B 225 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8126 (pp20) REVERT: B 243 LEU cc_start: 0.7987 (mt) cc_final: 0.7522 (mt) REVERT: B 247 GLN cc_start: 0.7661 (mm110) cc_final: 0.6703 (mp10) REVERT: B 254 GLU cc_start: 0.8063 (mp0) cc_final: 0.7720 (mp0) REVERT: B 263 PHE cc_start: 0.8606 (m-10) cc_final: 0.8007 (m-80) REVERT: B 264 GLN cc_start: 0.8010 (mt0) cc_final: 0.7506 (mp10) REVERT: B 272 SER cc_start: 0.8215 (m) cc_final: 0.7788 (t) REVERT: B 283 ILE cc_start: 0.7867 (mt) cc_final: 0.7598 (tt) REVERT: B 285 LYS cc_start: 0.8330 (tttp) cc_final: 0.7952 (tttp) REVERT: B 287 ASP cc_start: 0.7568 (m-30) cc_final: 0.7362 (m-30) REVERT: B 292 LYS cc_start: 0.7825 (pttm) cc_final: 0.7618 (pttm) REVERT: B 295 TYR cc_start: 0.6931 (m-80) cc_final: 0.6612 (m-80) REVERT: B 300 MET cc_start: 0.7693 (mmm) cc_final: 0.7210 (mmp) REVERT: B 314 MET cc_start: 0.7749 (tpp) cc_final: 0.7276 (tpp) REVERT: B 331 ILE cc_start: 0.8493 (mt) cc_final: 0.8282 (mm) REVERT: B 347 LEU cc_start: 0.8148 (tp) cc_final: 0.7914 (tp) REVERT: B 354 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7813 (mm110) REVERT: B 362 GLU cc_start: 0.9072 (tt0) cc_final: 0.8869 (tt0) REVERT: C 16 LEU cc_start: 0.6842 (tp) cc_final: 0.6606 (tp) REVERT: C 27 PRO cc_start: 0.8614 (Cg_endo) cc_final: 0.8368 (Cg_exo) REVERT: C 28 ARG cc_start: 0.8380 (ptm160) cc_final: 0.7655 (ptt90) REVERT: C 34 ILE cc_start: 0.8109 (mt) cc_final: 0.7762 (tp) REVERT: C 50 LYS cc_start: 0.8070 (mttt) cc_final: 0.7602 (mttt) REVERT: C 62 ARG cc_start: 0.5192 (ppt170) cc_final: 0.4758 (ppt170) REVERT: C 78 ASN cc_start: 0.7425 (t0) cc_final: 0.6087 (t0) REVERT: C 81 ASP cc_start: 0.7851 (m-30) cc_final: 0.7097 (m-30) REVERT: C 82 MET cc_start: 0.8058 (mmm) cc_final: 0.7275 (mmm) REVERT: C 86 TRP cc_start: 0.8067 (m-10) cc_final: 0.7475 (m-10) REVERT: C 92 ASN cc_start: 0.7994 (m-40) cc_final: 0.7759 (m-40) REVERT: C 111 ASN cc_start: 0.7979 (m-40) cc_final: 0.7502 (m-40) REVERT: C 113 LYS cc_start: 0.8302 (mttp) cc_final: 0.7633 (mttp) REVERT: C 117 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7539 (mp0) REVERT: C 119 MET cc_start: 0.8726 (ttm) cc_final: 0.8254 (ttm) REVERT: C 123 MET cc_start: 0.8266 (tpp) cc_final: 0.7432 (tpp) REVERT: C 137 GLN cc_start: 0.7864 (mt0) cc_final: 0.7575 (mp10) REVERT: C 152 VAL cc_start: 0.8394 (t) cc_final: 0.8077 (p) REVERT: C 162 ASN cc_start: 0.7787 (m-40) cc_final: 0.7526 (m-40) REVERT: C 165 ILE cc_start: 0.8642 (mt) cc_final: 0.8229 (tt) REVERT: C 166 TYR cc_start: 0.7987 (t80) cc_final: 0.7778 (t80) REVERT: C 176 MET cc_start: 0.6595 (mtt) cc_final: 0.6341 (mtt) REVERT: C 192 ILE cc_start: 0.7822 (pt) cc_final: 0.7314 (pt) REVERT: C 198 TYR cc_start: 0.7487 (m-80) cc_final: 0.7208 (m-80) REVERT: C 205 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7623 (mt-10) REVERT: C 207 GLU cc_start: 0.8028 (mm-30) cc_final: 0.6352 (tp30) REVERT: C 208 ILE cc_start: 0.8482 (mp) cc_final: 0.8269 (mm) REVERT: C 210 ARG cc_start: 0.8329 (ptm-80) cc_final: 0.7051 (ttp-170) REVERT: C 211 ASP cc_start: 0.8434 (m-30) cc_final: 0.7941 (m-30) REVERT: C 213 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8233 (ttpp) REVERT: C 214 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7245 (mt-10) REVERT: C 215 LYS cc_start: 0.8773 (mttm) cc_final: 0.8429 (mmmm) REVERT: C 222 ASP cc_start: 0.7275 (t0) cc_final: 0.6967 (t0) REVERT: C 237 GLU cc_start: 0.8000 (tp30) cc_final: 0.7790 (tp30) REVERT: C 238 LYS cc_start: 0.8134 (mmtm) cc_final: 0.7686 (mmtt) REVERT: C 252 ASN cc_start: 0.7276 (t0) cc_final: 0.6147 (t0) REVERT: C 256 ARG cc_start: 0.7874 (ttm170) cc_final: 0.6974 (ttm-80) REVERT: C 259 GLU cc_start: 0.7682 (tp30) cc_final: 0.7459 (tp30) REVERT: C 278 THR cc_start: 0.7912 (m) cc_final: 0.7673 (p) REVERT: C 284 LYS cc_start: 0.8140 (tppt) cc_final: 0.7692 (tptt) REVERT: C 291 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8241 (mptt) REVERT: C 299 MET cc_start: 0.8107 (mmm) cc_final: 0.7419 (mmm) REVERT: C 305 MET cc_start: 0.7445 (mmm) cc_final: 0.6971 (mmt) REVERT: C 306 TYR cc_start: 0.7764 (m-80) cc_final: 0.7499 (m-10) REVERT: C 325 MET cc_start: 0.7469 (mpp) cc_final: 0.7131 (mpp) REVERT: C 328 LYS cc_start: 0.8556 (mttt) cc_final: 0.8216 (mttt) REVERT: C 356 TRP cc_start: 0.6227 (m100) cc_final: 0.5695 (m100) REVERT: C 361 GLU cc_start: 0.8732 (tt0) cc_final: 0.7880 (tt0) REVERT: C 371 HIS cc_start: 0.8066 (m-70) cc_final: 0.6704 (m-70) REVERT: C 372 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7888 (mtt180) REVERT: D 24 ASP cc_start: 0.6661 (m-30) cc_final: 0.6015 (m-30) REVERT: D 47 MET cc_start: 0.6972 (ttm) cc_final: 0.6623 (ttm) REVERT: D 50 LYS cc_start: 0.7851 (ttmt) cc_final: 0.7581 (ttmt) REVERT: D 54 VAL cc_start: 0.8426 (t) cc_final: 0.7906 (m) REVERT: D 76 ILE cc_start: 0.7979 (mt) cc_final: 0.7334 (mt) REVERT: D 78 ASN cc_start: 0.8196 (t0) cc_final: 0.7901 (t0) REVERT: D 79 TRP cc_start: 0.7913 (m100) cc_final: 0.7342 (m100) REVERT: D 84 LYS cc_start: 0.8680 (tttt) cc_final: 0.8421 (tptt) REVERT: D 99 GLU cc_start: 0.7760 (mp0) cc_final: 0.7514 (mp0) REVERT: D 100 GLU cc_start: 0.7964 (tp30) cc_final: 0.7266 (tp30) REVERT: D 107 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6556 (mt-10) REVERT: D 116 ARG cc_start: 0.8343 (ttm110) cc_final: 0.7939 (ttm110) REVERT: D 133 TYR cc_start: 0.8145 (t80) cc_final: 0.7636 (t80) REVERT: D 151 ILE cc_start: 0.8343 (tt) cc_final: 0.8142 (tt) REVERT: D 153 LEU cc_start: 0.8010 (tp) cc_final: 0.7672 (tt) REVERT: D 154 ASP cc_start: 0.6994 (t0) cc_final: 0.6653 (t0) REVERT: D 157 ASP cc_start: 0.6140 (t0) cc_final: 0.5925 (t0) REVERT: D 161 HIS cc_start: 0.7395 (p90) cc_final: 0.7073 (p-80) REVERT: D 176 MET cc_start: 0.6599 (mtp) cc_final: 0.5905 (mtp) REVERT: D 183 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7725 (ttm170) REVERT: D 184 ASP cc_start: 0.8202 (m-30) cc_final: 0.7868 (m-30) REVERT: D 188 TYR cc_start: 0.7706 (t80) cc_final: 0.7467 (t80) REVERT: D 192 ILE cc_start: 0.7962 (mm) cc_final: 0.7364 (mm) REVERT: D 195 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6433 (mt-10) REVERT: D 202 THR cc_start: 0.7832 (p) cc_final: 0.6832 (t) REVERT: D 205 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7412 (mt-10) REVERT: D 206 ARG cc_start: 0.8324 (ttm170) cc_final: 0.7954 (ttm-80) REVERT: D 207 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7376 (mm-30) REVERT: D 210 ARG cc_start: 0.8477 (ttp80) cc_final: 0.8173 (ttp80) REVERT: D 211 ASP cc_start: 0.8089 (m-30) cc_final: 0.7309 (m-30) REVERT: D 238 LYS cc_start: 0.8126 (mmmt) cc_final: 0.7714 (mmmm) REVERT: D 252 ASN cc_start: 0.7210 (t0) cc_final: 0.6681 (t0) REVERT: D 256 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7531 (mtp-110) REVERT: D 267 ILE cc_start: 0.7573 (pt) cc_final: 0.7182 (pt) REVERT: D 280 ASN cc_start: 0.7787 (t0) cc_final: 0.6667 (t0) REVERT: D 281 SER cc_start: 0.8468 (p) cc_final: 0.7753 (p) REVERT: D 282 ILE cc_start: 0.8495 (mt) cc_final: 0.8260 (mt) REVERT: D 284 LYS cc_start: 0.8479 (mmpt) cc_final: 0.8147 (mmpt) REVERT: D 294 TYR cc_start: 0.7433 (m-80) cc_final: 0.7018 (m-80) REVERT: D 298 VAL cc_start: 0.8236 (t) cc_final: 0.7880 (m) REVERT: D 303 THR cc_start: 0.8275 (t) cc_final: 0.7235 (p) REVERT: D 306 TYR cc_start: 0.7288 (m-80) cc_final: 0.6727 (m-10) REVERT: D 312 ARG cc_start: 0.8144 (tpt-90) cc_final: 0.6992 (tpt-90) REVERT: D 313 MET cc_start: 0.8590 (tpt) cc_final: 0.7055 (tpt) REVERT: D 315 LYS cc_start: 0.8900 (ttpp) cc_final: 0.8417 (ttpp) REVERT: D 316 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7434 (mm-30) REVERT: D 317 ILE cc_start: 0.8902 (mm) cc_final: 0.7985 (mm) REVERT: D 320 LEU cc_start: 0.8861 (mt) cc_final: 0.8439 (mt) REVERT: D 325 MET cc_start: 0.7014 (ttm) cc_final: 0.6648 (ttm) REVERT: D 329 ILE cc_start: 0.7934 (mt) cc_final: 0.7278 (mt) REVERT: D 361 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8209 (mt-10) outliers start: 0 outliers final: 0 residues processed: 763 average time/residue: 0.3402 time to fit residues: 354.2120 Evaluate side-chains 715 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 715 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 18 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 129 ASN B 162 HIS B 372 HIS C 115 ASN C 161 HIS D 73 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15117 Z= 0.190 Angle : 0.644 10.979 20466 Z= 0.322 Chirality : 0.044 0.214 2241 Planarity : 0.004 0.046 2622 Dihedral : 10.358 163.198 2062 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 1838 helix: 0.99 (0.18), residues: 832 sheet: -0.06 (0.30), residues: 296 loop : 0.27 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 414 HIS 0.008 0.001 HIS A 418 PHE 0.021 0.001 PHE A 452 TYR 0.031 0.002 TYR C 337 ARG 0.005 0.001 ARG D 37 *********************** 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 758 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 758 time to evaluate : 1.747 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: A 88 ASN cc_start: 0.8706 (m110) cc_final: 0.8372 (m110) REVERT: A 90 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.8001 (ttp80) REVERT: A 132 MET cc_start: 0.3131 (ppp) cc_final: 0.2719 (ppp) REVERT: A 140 PHE cc_start: 0.8244 (m-10) cc_final: 0.7652 (m-10) REVERT: A 144 GLU cc_start: 0.8214 (tp30) cc_final: 0.7146 (tp30) REVERT: A 145 GLU cc_start: 0.8723 (tt0) cc_final: 0.8350 (tt0) REVERT: A 148 LYS cc_start: 0.8592 (ptpp) cc_final: 0.7537 (pttt) REVERT: A 150 MET cc_start: 0.8216 (ttp) cc_final: 0.7908 (ttp) REVERT: A 159 ILE cc_start: 0.8092 (mp) cc_final: 0.7779 (tp) REVERT: A 225 GLU cc_start: 0.7608 (mp0) cc_final: 0.7225 (mp0) REVERT: A 228 PHE cc_start: 0.7722 (m-80) cc_final: 0.7311 (m-10) REVERT: A 245 GLU cc_start: 0.7251 (tp30) cc_final: 0.6786 (tp30) REVERT: A 248 ARG cc_start: 0.7849 (tpp-160) cc_final: 0.7494 (mmp-170) REVERT: A 262 PHE cc_start: 0.8341 (m-80) cc_final: 0.7931 (m-80) REVERT: A 273 GLU cc_start: 0.8934 (mp0) cc_final: 0.8005 (mp0) REVERT: A 274 PHE cc_start: 0.8199 (m-10) cc_final: 0.7879 (m-80) REVERT: A 285 PHE cc_start: 0.8180 (m-80) cc_final: 0.7840 (m-80) REVERT: A 304 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8028 (mm-30) REVERT: A 309 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7971 (tmm-80) REVERT: A 319 GLU cc_start: 0.7381 (tp30) cc_final: 0.6896 (tp30) REVERT: A 323 MET cc_start: 0.8315 (mmp) cc_final: 0.7493 (mmp) REVERT: A 328 ILE cc_start: 0.8554 (mt) cc_final: 0.8300 (mm) REVERT: A 342 SER cc_start: 0.8454 (t) cc_final: 0.7927 (t) REVERT: A 354 HIS cc_start: 0.7873 (t70) cc_final: 0.7191 (t-170) REVERT: A 359 ILE cc_start: 0.8211 (mm) cc_final: 0.8008 (mt) REVERT: A 363 LEU cc_start: 0.8249 (mt) cc_final: 0.7551 (mt) REVERT: A 364 MET cc_start: 0.7345 (mmt) cc_final: 0.6420 (mmt) REVERT: A 372 CYS cc_start: 0.8916 (t) cc_final: 0.8407 (p) REVERT: A 374 TRP cc_start: 0.8748 (m100) cc_final: 0.8432 (m100) REVERT: A 385 GLU cc_start: 0.7540 (tp30) cc_final: 0.6863 (tm-30) REVERT: A 389 LYS cc_start: 0.8796 (tptt) cc_final: 0.8374 (tppt) REVERT: A 393 LYS cc_start: 0.8483 (tttt) cc_final: 0.8209 (mmmt) REVERT: A 410 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8076 (mttt) REVERT: A 413 ASN cc_start: 0.8638 (m-40) cc_final: 0.8423 (m-40) REVERT: A 453 CYS cc_start: 0.8666 (m) cc_final: 0.8383 (p) REVERT: A 455 ASN cc_start: 0.8788 (m-40) cc_final: 0.7561 (m-40) REVERT: A 459 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7659 (mm-30) REVERT: A 460 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8490 (mmmt) REVERT: A 461 LEU cc_start: 0.8941 (mt) cc_final: 0.8694 (pp) REVERT: A 464 GLN cc_start: 0.8871 (tt0) cc_final: 0.7742 (tm-30) REVERT: A 465 PHE cc_start: 0.8596 (t80) cc_final: 0.8362 (t80) REVERT: A 466 ASN cc_start: 0.8636 (m-40) cc_final: 0.8301 (m-40) REVERT: A 468 HIS cc_start: 0.8341 (t-90) cc_final: 0.8056 (t-90) REVERT: A 469 VAL cc_start: 0.8857 (t) cc_final: 0.8637 (m) REVERT: A 493 GLN cc_start: 0.8521 (tt0) cc_final: 0.8184 (tp-100) REVERT: A 499 ILE cc_start: 0.8911 (mt) cc_final: 0.8349 (tp) REVERT: A 502 LYS cc_start: 0.8464 (mmtp) cc_final: 0.7986 (mmtp) REVERT: A 508 LEU cc_start: 0.8323 (mt) cc_final: 0.8098 (mt) REVERT: A 511 GLU cc_start: 0.8211 (tt0) cc_final: 0.7318 (tt0) REVERT: A 522 THR cc_start: 0.7792 (p) cc_final: 0.7473 (p) REVERT: A 526 LYS cc_start: 0.8836 (mttt) cc_final: 0.8006 (mmtt) REVERT: A 532 LEU cc_start: 0.7712 (tp) cc_final: 0.7477 (mt) REVERT: A 533 ASN cc_start: 0.8051 (t0) cc_final: 0.7709 (t0) REVERT: A 545 ASN cc_start: 0.8383 (m-40) cc_final: 0.8101 (m-40) REVERT: A 557 VAL cc_start: 0.7682 (t) cc_final: 0.7233 (t) REVERT: A 558 GLU cc_start: 0.7561 (tt0) cc_final: 0.7304 (tm-30) REVERT: A 559 TYR cc_start: 0.7864 (m-80) cc_final: 0.7143 (m-80) REVERT: A 566 GLU cc_start: 0.7840 (mp0) cc_final: 0.7417 (pm20) REVERT: A 567 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7922 (mmtp) REVERT: A 574 GLU cc_start: 0.7668 (pp20) cc_final: 0.7437 (pm20) REVERT: A 578 LYS cc_start: 0.8812 (mtpp) cc_final: 0.8599 (mtpp) REVERT: A 581 LYS cc_start: 0.8942 (tttt) cc_final: 0.8718 (mtpp) REVERT: A 588 LEU cc_start: 0.9025 (mt) cc_final: 0.8799 (mt) REVERT: A 592 PHE cc_start: 0.7859 (m-80) cc_final: 0.7250 (m-80) REVERT: A 632 LYS cc_start: 0.9060 (mtmt) cc_final: 0.8741 (pttm) REVERT: A 635 VAL cc_start: 0.8763 (t) cc_final: 0.8483 (p) REVERT: A 641 ASN cc_start: 0.8883 (m-40) cc_final: 0.8539 (m110) REVERT: A 644 HIS cc_start: 0.8033 (m170) cc_final: 0.7723 (m90) REVERT: A 647 MET cc_start: 0.8149 (tpt) cc_final: 0.7659 (tpt) REVERT: A 648 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 657 TYR cc_start: 0.7511 (m-80) cc_final: 0.6865 (m-80) REVERT: A 673 ASP cc_start: 0.7447 (t0) cc_final: 0.7119 (t0) REVERT: A 675 LYS cc_start: 0.8534 (mmtp) cc_final: 0.7984 (mptt) REVERT: A 679 GLN cc_start: 0.8430 (pt0) cc_final: 0.8155 (pt0) REVERT: A 681 LEU cc_start: 0.7949 (mm) cc_final: 0.7706 (mm) REVERT: A 682 ARG cc_start: 0.6795 (tpm170) cc_final: 0.6557 (tpm170) REVERT: A 705 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8252 (tt0) REVERT: B 9 LEU cc_start: 0.8274 (mt) cc_final: 0.8068 (mt) REVERT: B 17 LEU cc_start: 0.7226 (tp) cc_final: 0.6743 (mt) REVERT: B 35 ILE cc_start: 0.8493 (mt) cc_final: 0.8122 (mm) REVERT: B 55 VAL cc_start: 0.8338 (t) cc_final: 0.8087 (m) REVERT: B 69 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7554 (mtpt) REVERT: B 81 ASP cc_start: 0.8557 (p0) cc_final: 0.7341 (m-30) REVERT: B 83 MET cc_start: 0.8585 (mmm) cc_final: 0.7947 (mmm) REVERT: B 84 GLU cc_start: 0.8482 (tt0) cc_final: 0.8177 (tt0) REVERT: B 85 LYS cc_start: 0.8829 (mttm) cc_final: 0.8385 (mttm) REVERT: B 87 TRP cc_start: 0.8038 (m-10) cc_final: 0.7724 (m-10) REVERT: B 93 ASN cc_start: 0.7906 (m-40) cc_final: 0.7687 (m-40) REVERT: B 101 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8132 (mm-30) REVERT: B 102 HIS cc_start: 0.8453 (m-70) cc_final: 0.7814 (m90) REVERT: B 108 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6307 (mt-10) REVERT: B 114 LYS cc_start: 0.8447 (mtmt) cc_final: 0.8179 (mtmt) REVERT: B 116 ASN cc_start: 0.8306 (t0) cc_final: 0.8006 (t0) REVERT: B 117 ARG cc_start: 0.8340 (ttm110) cc_final: 0.8024 (ttm170) REVERT: B 119 LYS cc_start: 0.8623 (tptt) cc_final: 0.7863 (mmmt) REVERT: B 120 MET cc_start: 0.8679 (ttm) cc_final: 0.8104 (ttm) REVERT: B 123 ILE cc_start: 0.8882 (mt) cc_final: 0.8227 (tp) REVERT: B 127 THR cc_start: 0.8684 (m) cc_final: 0.7791 (t) REVERT: B 128 PHE cc_start: 0.8368 (m-10) cc_final: 0.7783 (m-10) REVERT: B 129 ASN cc_start: 0.7870 (t0) cc_final: 0.7599 (t0) REVERT: B 144 TYR cc_start: 0.7618 (m-80) cc_final: 0.7231 (m-80) REVERT: B 177 MET cc_start: 0.7288 (mtt) cc_final: 0.6859 (mtm) REVERT: B 180 ASP cc_start: 0.6984 (m-30) cc_final: 0.6261 (t70) REVERT: B 184 ARG cc_start: 0.7841 (tpp80) cc_final: 0.7120 (mtp85) REVERT: B 185 ASP cc_start: 0.8346 (m-30) cc_final: 0.7975 (m-30) REVERT: B 188 ASP cc_start: 0.8015 (m-30) cc_final: 0.7489 (m-30) REVERT: B 194 LEU cc_start: 0.8975 (mt) cc_final: 0.8675 (tp) REVERT: B 197 ARG cc_start: 0.8134 (mmp-170) cc_final: 0.7864 (mmp-170) REVERT: B 199 TYR cc_start: 0.7561 (m-80) cc_final: 0.6704 (m-80) REVERT: B 208 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7789 (mm-30) REVERT: B 211 ARG cc_start: 0.8486 (ttp80) cc_final: 0.7782 (ttp80) REVERT: B 212 ASP cc_start: 0.8415 (m-30) cc_final: 0.7895 (m-30) REVERT: B 214 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8496 (ttpt) REVERT: B 215 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6990 (mt-10) REVERT: B 243 LEU cc_start: 0.7907 (mt) cc_final: 0.7552 (mt) REVERT: B 247 GLN cc_start: 0.7806 (mm110) cc_final: 0.7337 (tp-100) REVERT: B 248 VAL cc_start: 0.8599 (t) cc_final: 0.8287 (p) REVERT: B 254 GLU cc_start: 0.8070 (mp0) cc_final: 0.7693 (mp0) REVERT: B 257 ARG cc_start: 0.8045 (mtp180) cc_final: 0.7409 (mtp180) REVERT: B 263 PHE cc_start: 0.8546 (m-10) cc_final: 0.8303 (m-80) REVERT: B 264 GLN cc_start: 0.8073 (mt0) cc_final: 0.7458 (mp10) REVERT: B 272 SER cc_start: 0.8233 (m) cc_final: 0.7806 (t) REVERT: B 283 ILE cc_start: 0.7890 (mt) cc_final: 0.7625 (tt) REVERT: B 285 LYS cc_start: 0.8383 (tttp) cc_final: 0.8074 (tttp) REVERT: B 287 ASP cc_start: 0.7619 (m-30) cc_final: 0.7400 (m-30) REVERT: B 292 LYS cc_start: 0.7871 (pttm) cc_final: 0.7592 (pttm) REVERT: B 293 ASP cc_start: 0.7779 (m-30) cc_final: 0.7561 (m-30) REVERT: B 295 TYR cc_start: 0.6957 (m-80) cc_final: 0.6562 (m-80) REVERT: B 300 MET cc_start: 0.7687 (mmm) cc_final: 0.7196 (mmp) REVERT: B 314 MET cc_start: 0.7743 (tpp) cc_final: 0.7231 (tpp) REVERT: B 315 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 355 GLN cc_start: 0.8296 (pm20) cc_final: 0.8001 (pm20) REVERT: B 356 MET cc_start: 0.8569 (mpp) cc_final: 0.7837 (mpp) REVERT: B 362 GLU cc_start: 0.9036 (tt0) cc_final: 0.8800 (tt0) REVERT: C 8 LEU cc_start: 0.8007 (mt) cc_final: 0.7780 (mt) REVERT: C 17 VAL cc_start: 0.7725 (m) cc_final: 0.7511 (t) REVERT: C 28 ARG cc_start: 0.8350 (ptm160) cc_final: 0.7852 (ptm160) REVERT: C 50 LYS cc_start: 0.8103 (mttt) cc_final: 0.7628 (mttt) REVERT: C 62 ARG cc_start: 0.5205 (ppt170) cc_final: 0.4577 (ppt170) REVERT: C 78 ASN cc_start: 0.7438 (t0) cc_final: 0.6272 (t0) REVERT: C 81 ASP cc_start: 0.7855 (m-30) cc_final: 0.7223 (m-30) REVERT: C 82 MET cc_start: 0.8117 (mmm) cc_final: 0.7322 (mmm) REVERT: C 86 TRP cc_start: 0.8045 (m-10) cc_final: 0.7216 (m-10) REVERT: C 90 PHE cc_start: 0.8059 (m-10) cc_final: 0.7680 (m-80) REVERT: C 92 ASN cc_start: 0.7992 (m-40) cc_final: 0.7673 (m-40) REVERT: C 105 LEU cc_start: 0.8064 (mm) cc_final: 0.7655 (mm) REVERT: C 111 ASN cc_start: 0.8046 (m-40) cc_final: 0.7535 (m-40) REVERT: C 113 LYS cc_start: 0.8298 (mttp) cc_final: 0.7989 (mttp) REVERT: C 115 ASN cc_start: 0.7863 (t0) cc_final: 0.7637 (t0) REVERT: C 119 MET cc_start: 0.8701 (ttm) cc_final: 0.8235 (ttm) REVERT: C 121 GLN cc_start: 0.8505 (tt0) cc_final: 0.7752 (tt0) REVERT: C 125 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7343 (mt-10) REVERT: C 128 ASN cc_start: 0.8466 (m110) cc_final: 0.7683 (m110) REVERT: C 139 VAL cc_start: 0.8595 (m) cc_final: 0.8381 (p) REVERT: C 152 VAL cc_start: 0.8408 (t) cc_final: 0.8052 (p) REVERT: C 153 LEU cc_start: 0.7480 (pp) cc_final: 0.7213 (pt) REVERT: C 162 ASN cc_start: 0.7788 (m-40) cc_final: 0.7499 (m-40) REVERT: C 176 MET cc_start: 0.6571 (mtt) cc_final: 0.6225 (mtt) REVERT: C 178 LEU cc_start: 0.8101 (tp) cc_final: 0.7896 (tp) REVERT: C 185 LEU cc_start: 0.8471 (mp) cc_final: 0.8255 (mm) REVERT: C 190 MET cc_start: 0.7902 (mtm) cc_final: 0.7646 (mtm) REVERT: C 192 ILE cc_start: 0.7847 (pt) cc_final: 0.7191 (pt) REVERT: C 195 GLU cc_start: 0.7240 (mt-10) cc_final: 0.7021 (mt-10) REVERT: C 198 TYR cc_start: 0.7579 (m-80) cc_final: 0.7371 (m-80) REVERT: C 205 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7433 (mt-10) REVERT: C 207 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7605 (mm-30) REVERT: C 208 ILE cc_start: 0.8461 (mp) cc_final: 0.8250 (mp) REVERT: C 210 ARG cc_start: 0.8362 (ptm-80) cc_final: 0.7728 (tmm-80) REVERT: C 213 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8214 (ttpp) REVERT: C 214 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7473 (mt-10) REVERT: C 215 LYS cc_start: 0.8726 (mttm) cc_final: 0.8349 (mmmm) REVERT: C 222 ASP cc_start: 0.7277 (t0) cc_final: 0.7037 (t0) REVERT: C 237 GLU cc_start: 0.8011 (tp30) cc_final: 0.7789 (tp30) REVERT: C 238 LYS cc_start: 0.8142 (mmtm) cc_final: 0.7857 (mmtt) REVERT: C 256 ARG cc_start: 0.7766 (ttm170) cc_final: 0.7045 (ttm-80) REVERT: C 261 LEU cc_start: 0.8291 (mt) cc_final: 0.8018 (mm) REVERT: C 278 THR cc_start: 0.7850 (m) cc_final: 0.7622 (p) REVERT: C 279 TYR cc_start: 0.7996 (t80) cc_final: 0.7663 (t80) REVERT: C 283 MET cc_start: 0.7570 (mmm) cc_final: 0.7203 (mpp) REVERT: C 284 LYS cc_start: 0.8083 (tppt) cc_final: 0.7829 (tppt) REVERT: C 291 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8335 (mptt) REVERT: C 294 TYR cc_start: 0.7804 (m-80) cc_final: 0.7511 (m-80) REVERT: C 299 MET cc_start: 0.8065 (mmm) cc_final: 0.7381 (mmm) REVERT: C 305 MET cc_start: 0.7786 (mmm) cc_final: 0.7149 (mmt) REVERT: C 306 TYR cc_start: 0.7820 (m-80) cc_final: 0.7505 (m-10) REVERT: C 316 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8356 (mm-30) REVERT: C 325 MET cc_start: 0.7465 (mpp) cc_final: 0.7098 (mpp) REVERT: C 328 LYS cc_start: 0.8733 (mttt) cc_final: 0.8288 (mttt) REVERT: C 330 ILE cc_start: 0.8766 (mp) cc_final: 0.8494 (mm) REVERT: C 336 LYS cc_start: 0.8030 (ptmm) cc_final: 0.7159 (ptmm) REVERT: C 356 TRP cc_start: 0.6311 (m100) cc_final: 0.5706 (m100) REVERT: C 361 GLU cc_start: 0.8738 (tt0) cc_final: 0.7975 (tt0) REVERT: D 24 ASP cc_start: 0.6738 (m-30) cc_final: 0.6166 (m-30) REVERT: D 43 VAL cc_start: 0.7860 (t) cc_final: 0.7548 (p) REVERT: D 47 MET cc_start: 0.6912 (ttm) cc_final: 0.6447 (ttm) REVERT: D 50 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7593 (ttmt) REVERT: D 54 VAL cc_start: 0.8433 (t) cc_final: 0.7941 (m) REVERT: D 62 ARG cc_start: 0.8237 (mtm-85) cc_final: 0.7905 (mtm-85) REVERT: D 76 ILE cc_start: 0.8132 (mt) cc_final: 0.7573 (mt) REVERT: D 78 ASN cc_start: 0.8148 (t0) cc_final: 0.7796 (t0) REVERT: D 79 TRP cc_start: 0.8044 (m100) cc_final: 0.7568 (m100) REVERT: D 82 MET cc_start: 0.8093 (mmm) cc_final: 0.7826 (mmm) REVERT: D 84 LYS cc_start: 0.8685 (tttt) cc_final: 0.8400 (tptt) REVERT: D 86 TRP cc_start: 0.7864 (m-10) cc_final: 0.7521 (m-90) REVERT: D 99 GLU cc_start: 0.7763 (mp0) cc_final: 0.7552 (mp0) REVERT: D 100 GLU cc_start: 0.7949 (tp30) cc_final: 0.7226 (tp30) REVERT: D 107 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6707 (mt-10) REVERT: D 118 LYS cc_start: 0.8788 (tptt) cc_final: 0.8188 (tptt) REVERT: D 122 ILE cc_start: 0.8635 (mt) cc_final: 0.7972 (mt) REVERT: D 133 TYR cc_start: 0.8169 (t80) cc_final: 0.7891 (t80) REVERT: D 153 LEU cc_start: 0.7862 (tp) cc_final: 0.7652 (tp) REVERT: D 154 ASP cc_start: 0.6945 (t0) cc_final: 0.6522 (t0) REVERT: D 157 ASP cc_start: 0.6277 (t0) cc_final: 0.6024 (t0) REVERT: D 176 MET cc_start: 0.6578 (mtp) cc_final: 0.5897 (mtp) REVERT: D 183 ARG cc_start: 0.7857 (ttm170) cc_final: 0.7558 (ttp80) REVERT: D 184 ASP cc_start: 0.8212 (m-30) cc_final: 0.7893 (m-30) REVERT: D 205 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7307 (mt-10) REVERT: D 206 ARG cc_start: 0.8351 (ttm170) cc_final: 0.8066 (ttm-80) REVERT: D 207 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7384 (mm-30) REVERT: D 210 ARG cc_start: 0.8453 (ttp80) cc_final: 0.7830 (ttp80) REVERT: D 211 ASP cc_start: 0.8036 (m-30) cc_final: 0.7263 (m-30) REVERT: D 213 LYS cc_start: 0.8635 (ttpt) cc_final: 0.8235 (ttpt) REVERT: D 224 GLU cc_start: 0.7669 (pp20) cc_final: 0.7390 (pp20) REVERT: D 238 LYS cc_start: 0.8208 (mmmt) cc_final: 0.7679 (mmmm) REVERT: D 254 ARG cc_start: 0.7319 (mtp180) cc_final: 0.7103 (ttp-170) REVERT: D 269 MET cc_start: 0.7210 (mtt) cc_final: 0.6902 (mtt) REVERT: D 280 ASN cc_start: 0.7779 (t0) cc_final: 0.6592 (t0) REVERT: D 281 SER cc_start: 0.8443 (p) cc_final: 0.7819 (p) REVERT: D 282 ILE cc_start: 0.8426 (mt) cc_final: 0.8221 (mt) REVERT: D 284 LYS cc_start: 0.8437 (mmpt) cc_final: 0.8169 (mmpt) REVERT: D 294 TYR cc_start: 0.7363 (m-80) cc_final: 0.6875 (m-80) REVERT: D 300 SER cc_start: 0.7330 (t) cc_final: 0.6760 (p) REVERT: D 303 THR cc_start: 0.8367 (t) cc_final: 0.7618 (p) REVERT: D 306 TYR cc_start: 0.7335 (m-80) cc_final: 0.6917 (m-10) REVERT: D 313 MET cc_start: 0.8524 (tpt) cc_final: 0.7976 (tpt) REVERT: D 315 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8596 (ttpp) REVERT: D 316 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7338 (mm-30) REVERT: D 317 ILE cc_start: 0.8923 (mm) cc_final: 0.8659 (mm) REVERT: D 320 LEU cc_start: 0.8811 (mt) cc_final: 0.8502 (mt) REVERT: D 325 MET cc_start: 0.7104 (ttm) cc_final: 0.6717 (ttm) REVERT: D 361 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8207 (mt-10) outliers start: 0 outliers final: 0 residues processed: 758 average time/residue: 0.3433 time to fit residues: 353.9658 Evaluate side-chains 718 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 718 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.6008 > 50: distance: 41 - 73: 23.441 distance: 44 - 70: 7.915 distance: 60 - 64: 6.480 distance: 65 - 66: 19.274 distance: 65 - 68: 18.213 distance: 66 - 67: 10.212 distance: 66 - 70: 20.008 distance: 68 - 69: 8.141 distance: 70 - 71: 21.025 distance: 71 - 72: 12.708 distance: 71 - 74: 6.418 distance: 72 - 73: 10.015 distance: 72 - 75: 6.310 distance: 75 - 76: 17.063 distance: 75 - 180: 26.298 distance: 76 - 77: 22.023 distance: 76 - 79: 24.127 distance: 77 - 78: 8.646 distance: 77 - 84: 9.638 distance: 78 - 177: 23.453 distance: 79 - 80: 15.238 distance: 80 - 81: 17.504 distance: 81 - 82: 13.889 distance: 81 - 83: 24.510 distance: 84 - 85: 16.157 distance: 85 - 86: 4.428 distance: 85 - 88: 13.981 distance: 86 - 87: 17.706 distance: 86 - 92: 16.702 distance: 88 - 89: 7.012 distance: 89 - 90: 11.321 distance: 89 - 91: 8.820 distance: 92 - 93: 22.502 distance: 93 - 94: 12.251 distance: 93 - 96: 20.038 distance: 94 - 95: 35.350 distance: 94 - 100: 16.436 distance: 96 - 97: 10.093 distance: 97 - 98: 4.958 distance: 97 - 99: 20.076 distance: 100 - 101: 25.509 distance: 101 - 102: 8.696 distance: 101 - 104: 17.398 distance: 102 - 109: 3.430 distance: 104 - 105: 11.543 distance: 105 - 106: 13.883 distance: 106 - 107: 18.536 distance: 107 - 108: 14.360 distance: 109 - 110: 24.207 distance: 110 - 111: 30.237 distance: 110 - 113: 9.479 distance: 111 - 112: 12.665 distance: 111 - 117: 18.152 distance: 113 - 114: 7.610 distance: 114 - 115: 15.338 distance: 114 - 116: 14.306 distance: 117 - 118: 21.758 distance: 118 - 119: 15.502 distance: 118 - 121: 14.189 distance: 119 - 120: 25.706 distance: 119 - 129: 18.184 distance: 121 - 122: 15.594 distance: 122 - 123: 8.825 distance: 122 - 124: 14.859 distance: 123 - 125: 3.196 distance: 124 - 126: 8.299 distance: 125 - 127: 13.949 distance: 126 - 127: 12.333 distance: 127 - 128: 11.362 distance: 129 - 130: 6.395 distance: 130 - 131: 16.845 distance: 131 - 132: 23.302 distance: 131 - 138: 9.716 distance: 133 - 134: 16.990 distance: 134 - 135: 27.873 distance: 135 - 136: 14.394 distance: 136 - 137: 15.756 distance: 138 - 139: 22.088 distance: 138 - 144: 49.360 distance: 139 - 140: 25.350 distance: 139 - 142: 54.958 distance: 140 - 141: 36.813 distance: 140 - 145: 26.369 distance: 142 - 143: 39.160