Starting phenix.real_space_refine on Sat Aug 23 22:10:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r9v_19013/08_2025/8r9v_19013.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r9v_19013/08_2025/8r9v_19013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r9v_19013/08_2025/8r9v_19013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r9v_19013/08_2025/8r9v_19013.map" model { file = "/net/cci-nas-00/data/ceres_data/8r9v_19013/08_2025/8r9v_19013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r9v_19013/08_2025/8r9v_19013.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 9 5.49 5 Mg 4 5.21 5 S 98 5.16 5 C 9407 2.51 5 N 2516 2.21 5 O 2817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14851 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 6000 Classifications: {'peptide': 740} Link IDs: {'PTRANS': 26, 'TRANS': 713} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 2.50, per 1000 atoms: 0.17 Number of scatterers: 14851 At special positions: 0 Unit cell: (110.21, 169.06, 140.17, 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 98 16.00 P 9 15.00 Mg 4 11.99 O 2817 8.00 N 2516 7.00 C 9407 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 Atom "HETATM14792 O5' ADP B 401 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 502.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3472 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 25 sheets defined 49.5% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 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 184 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 189 through 206 removed outlier: 3.946A pdb=" N GLU A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 251 removed outlier: 4.132A pdb=" N VAL A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.224A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.650A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 Processing helix chain 'A' and resid 318 through 336 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 423 Processing helix chain 'A' and resid 448 through 469 Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 493 through 501 removed outlier: 4.789A 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: 3.714A pdb=" N LEU A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 570 Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.779A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 593 removed outlier: 3.981A pdb=" N GLU A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 652 Processing helix chain 'A' and resid 673 through 685 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 703 through 710 Processing helix chain 'A' and resid 711 through 714 Processing helix chain 'A' and resid 722 through 735 removed outlier: 3.813A pdb=" N LYS A 733 " --> pdb=" O ASN A 729 " (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 774 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 113 through 129 removed outlier: 3.511A pdb=" N ARG B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 182 through 198 Processing helix chain 'B' and resid 203 through 218 removed outlier: 3.871A pdb=" N ILE B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 235 Processing helix chain 'B' and resid 253 through 261 removed outlier: 3.812A pdb=" N CYS B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) 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 268 Processing helix chain 'B' and resid 274 through 286 Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.565A pdb=" N LYS B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 360 through 367 Processing helix chain 'B' and resid 370 through 375 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.568A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.715A 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 308 through 321 Processing helix chain 'C' and resid 338 through 349 removed outlier: 3.702A pdb=" N LEU C 349 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 353 Processing helix chain 'C' and resid 359 through 366 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 127 Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.610A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.510A pdb=" N LEU D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.763A 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 273 through 285 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.185A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.129A 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 removed outlier: 3.502A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 349 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 47 through 51 removed outlier: 3.945A 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: 6.615A pdb=" N LEU A 107 " --> pdb=" O ARG A 659 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE A 661 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA A 109 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER A 158 " --> pdb=" O HIS A 656 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL A 658 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE A 160 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N CYS A 660 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER A 162 " --> pdb=" O CYS A 660 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 161 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 435 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY A 221 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR A 241 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR A 223 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N MET A 239 " --> pdb=" O TYR A 223 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLU A 225 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA A 237 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY A 227 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 343 Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 379 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 699 through 702 Processing sheet with id=AA8, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.536A pdb=" N LEU B 9 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N THR B 107 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 7.989A 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 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 170 through 171 Processing sheet with id=AB3, first strand: chain 'B' and resid 170 through 171 removed outlier: 6.436A pdb=" N ILE B 152 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N SER B 301 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 154 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN B 298 " --> pdb=" O ILE B 331 " (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 32 removed outlier: 6.861A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (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 169 through 170 Processing sheet with id=AB9, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.468A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) 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 32 removed outlier: 6.920A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 54 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 removed outlier: 6.480A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 238 through 241 730 hydrogen bonds defined for protein. 2007 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2896 1.33 - 1.45: 3589 1.45 - 1.58: 8515 1.58 - 1.70: 12 1.70 - 1.82: 165 Bond restraints: 15177 Sorted by residual: bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C4 ADP A 903 " pdb=" C5 ADP A 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" O1 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.565 1.465 0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 15172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 16900 2.24 - 4.48: 3393 4.48 - 6.73: 213 6.73 - 8.97: 20 8.97 - 11.21: 21 Bond angle restraints: 20547 Sorted by residual: angle pdb=" C ALA A 217 " pdb=" N SER A 218 " pdb=" CA SER A 218 " ideal model delta sigma weight residual 122.26 133.02 -10.76 1.60e+00 3.91e-01 4.53e+01 angle pdb=" CA GLN C 263 " pdb=" C GLN C 263 " pdb=" N PRO C 264 " ideal model delta sigma weight residual 117.73 123.65 -5.92 1.04e+00 9.25e-01 3.24e+01 angle pdb=" N PRO A 655 " pdb=" CA PRO A 655 " pdb=" C PRO A 655 " ideal model delta sigma weight residual 111.68 120.90 -9.22 1.67e+00 3.59e-01 3.05e+01 angle pdb=" O PRO B 333 " pdb=" C PRO B 333 " pdb=" N PRO B 334 " ideal model delta sigma weight residual 121.15 118.68 2.47 4.70e-01 4.53e+00 2.75e+01 angle pdb=" CA GLU A 164 " pdb=" C GLU A 164 " pdb=" N SER A 165 " ideal model delta sigma weight residual 115.36 122.48 -7.12 1.37e+00 5.33e-01 2.70e+01 ... (remaining 20542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.15: 8897 33.15 - 66.29: 210 66.29 - 99.44: 33 99.44 - 132.59: 2 132.59 - 165.74: 6 Dihedral angle restraints: 9148 sinusoidal: 3743 harmonic: 5405 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 134.26 165.74 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual 300.00 137.90 162.10 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 92.73 -152.73 1 2.00e+01 2.50e-03 4.53e+01 ... (remaining 9145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1215 0.074 - 0.149: 756 0.149 - 0.223: 230 0.223 - 0.297: 45 0.297 - 0.371: 5 Chirality restraints: 2251 Sorted by residual: chirality pdb=" CA GLU D 334 " pdb=" N GLU D 334 " pdb=" C GLU D 334 " pdb=" CB GLU D 334 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA VAL A 686 " pdb=" N VAL A 686 " pdb=" C VAL A 686 " pdb=" CB VAL A 686 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ILE A 15 " pdb=" N ILE A 15 " pdb=" C ILE A 15 " pdb=" CB ILE A 15 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 2248 not shown) Planarity restraints: 2631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 232 " -0.138 2.00e-02 2.50e+03 7.66e-02 1.17e+02 pdb=" CG TYR A 232 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 232 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR A 232 " 0.066 2.00e-02 2.50e+03 pdb=" CE1 TYR A 232 " 0.054 2.00e-02 2.50e+03 pdb=" CE2 TYR A 232 " 0.042 2.00e-02 2.50e+03 pdb=" CZ TYR A 232 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 232 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 127 " -0.146 2.00e-02 2.50e+03 7.58e-02 1.15e+02 pdb=" CG TYR A 127 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR A 127 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 TYR A 127 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR A 127 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 127 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 127 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 127 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 523 " 0.089 2.00e-02 2.50e+03 5.90e-02 8.69e+01 pdb=" CG TRP A 523 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 523 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 523 " -0.068 2.00e-02 2.50e+03 pdb=" NE1 TRP A 523 " -0.052 2.00e-02 2.50e+03 pdb=" CE2 TRP A 523 " -0.033 2.00e-02 2.50e+03 pdb=" CE3 TRP A 523 " -0.088 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 523 " 0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 523 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 523 " 0.078 2.00e-02 2.50e+03 ... (remaining 2628 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 12 2.04 - 2.75: 981 2.75 - 3.47: 21406 3.47 - 4.18: 36994 4.18 - 4.90: 62632 Nonbonded interactions: 122025 Sorted by model distance: nonbonded pdb=" NH1 ARG C 37 " pdb=" O ASP C 51 " model vdw 1.324 3.120 nonbonded pdb=" CD1 ILE A 110 " pdb=" CD1 ILE A 661 " model vdw 1.501 3.880 nonbonded pdb=" O CYS A 561 " pdb=" CD2 PHE A 564 " model vdw 1.585 3.340 nonbonded pdb=" CA PRO B 39 " pdb=" CD2 LEU B 66 " model vdw 1.687 3.890 nonbonded pdb=" OE1 GLU A 204 " pdb=" ND2 ASN A 208 " model vdw 1.741 3.120 ... (remaining 122020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 6 through 402) selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.030 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 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 0.349 15178 Z= 0.939 Angle : 1.693 11.212 20547 Z= 1.171 Chirality : 0.098 0.371 2251 Planarity : 0.008 0.105 2631 Dihedral : 14.893 165.735 5676 Min Nonbonded Distance : 1.324 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.33 % Favored : 95.34 % Rotamer: Outliers : 0.25 % Allowed : 3.58 % Favored : 96.17 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.18), residues: 1847 helix: -1.35 (0.15), residues: 820 sheet: -2.37 (0.29), residues: 241 loop : -0.67 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 219 TYR 0.146 0.005 TYR A 127 PHE 0.073 0.005 PHE A 220 TRP 0.089 0.006 TRP A 523 HIS 0.014 0.001 HIS A 644 Details of bonding type rmsd covalent geometry : bond 0.01304 (15177) covalent geometry : angle 1.69321 (20547) hydrogen bonds : bond 0.18865 ( 724) hydrogen bonds : angle 8.19087 ( 2007) Misc. bond : bond 0.34913 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 814 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8427 (mp0) REVERT: A 48 LEU cc_start: 0.7789 (tp) cc_final: 0.7513 (tt) REVERT: A 87 HIS cc_start: 0.8654 (t-90) cc_final: 0.7959 (t-90) REVERT: A 94 ILE cc_start: 0.8384 (mt) cc_final: 0.7578 (tt) REVERT: A 95 ASP cc_start: 0.7884 (t0) cc_final: 0.7602 (t0) REVERT: A 97 LYS cc_start: 0.7913 (mptt) cc_final: 0.6993 (mttp) REVERT: A 103 CYS cc_start: 0.7442 (m) cc_final: 0.7164 (t) REVERT: A 113 TYR cc_start: 0.6363 (m-80) cc_final: 0.5823 (m-80) REVERT: A 121 GLU cc_start: 0.8685 (tp30) cc_final: 0.8328 (tp30) REVERT: A 138 HIS cc_start: 0.6432 (m90) cc_final: 0.5980 (m90) REVERT: A 144 GLU cc_start: 0.8406 (tp30) cc_final: 0.8201 (tt0) REVERT: A 145 GLU cc_start: 0.8879 (tp30) cc_final: 0.8669 (tm-30) REVERT: A 150 MET cc_start: 0.7823 (ttp) cc_final: 0.7307 (ttp) REVERT: A 179 TYR cc_start: 0.8620 (t80) cc_final: 0.8246 (t80) REVERT: A 222 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8283 (tptp) REVERT: A 223 TYR cc_start: 0.7676 (t80) cc_final: 0.7143 (t80) REVERT: A 225 GLU cc_start: 0.7593 (mt-10) cc_final: 0.6999 (mp0) REVERT: A 228 PHE cc_start: 0.6764 (m-80) cc_final: 0.6069 (m-80) REVERT: A 242 TYR cc_start: 0.6942 (m-80) cc_final: 0.6349 (m-80) REVERT: A 248 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7218 (tpp80) REVERT: A 259 TYR cc_start: 0.7908 (m-80) cc_final: 0.6736 (m-80) REVERT: A 260 HIS cc_start: 0.7939 (m90) cc_final: 0.7262 (m-70) REVERT: A 262 PHE cc_start: 0.8793 (m-80) cc_final: 0.8054 (m-80) REVERT: A 304 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7900 (mm-30) REVERT: A 305 MET cc_start: 0.8451 (tpt) cc_final: 0.8162 (tpt) REVERT: A 312 CYS cc_start: 0.8415 (m) cc_final: 0.8116 (m) REVERT: A 315 LEU cc_start: 0.6682 (mt) cc_final: 0.6387 (mt) REVERT: A 364 MET cc_start: 0.7779 (mtt) cc_final: 0.7539 (mtt) REVERT: A 370 GLU cc_start: 0.8647 (tt0) cc_final: 0.8208 (tt0) REVERT: A 408 TYR cc_start: 0.8851 (t80) cc_final: 0.8012 (t80) REVERT: A 448 SER cc_start: 0.8243 (m) cc_final: 0.7614 (p) REVERT: A 450 GLU cc_start: 0.8800 (pm20) cc_final: 0.8485 (pp20) REVERT: A 451 GLN cc_start: 0.8868 (mp10) cc_final: 0.7993 (mt0) REVERT: A 453 CYS cc_start: 0.8635 (m) cc_final: 0.8409 (m) REVERT: A 458 ASN cc_start: 0.9042 (m-40) cc_final: 0.8653 (m110) REVERT: A 460 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8116 (mmmt) REVERT: A 468 HIS cc_start: 0.7877 (t-90) cc_final: 0.7372 (t-90) REVERT: A 472 LEU cc_start: 0.8319 (mt) cc_final: 0.7902 (tp) REVERT: A 496 ILE cc_start: 0.7984 (mt) cc_final: 0.7453 (mt) REVERT: A 505 ILE cc_start: 0.8760 (mt) cc_final: 0.7978 (tt) REVERT: A 509 LEU cc_start: 0.8852 (tp) cc_final: 0.8512 (mt) REVERT: A 511 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7707 (mm-30) REVERT: A 512 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7955 (tt0) REVERT: A 520 ASP cc_start: 0.8392 (m-30) cc_final: 0.7571 (t0) REVERT: A 526 LYS cc_start: 0.9059 (tttt) cc_final: 0.8622 (mmtm) REVERT: A 528 TYR cc_start: 0.7906 (m-10) cc_final: 0.7533 (m-80) REVERT: A 534 LYS cc_start: 0.8488 (tptt) cc_final: 0.7993 (tptt) REVERT: A 535 CYS cc_start: 0.6907 (p) cc_final: 0.6438 (p) REVERT: A 543 MET cc_start: 0.5850 (mmt) cc_final: 0.5553 (mmt) REVERT: A 556 LYS cc_start: 0.8541 (mttt) cc_final: 0.8091 (mttm) REVERT: A 558 GLU cc_start: 0.7902 (tt0) cc_final: 0.7391 (tm-30) REVERT: A 559 TYR cc_start: 0.7650 (m-80) cc_final: 0.6654 (m-80) REVERT: A 575 GLU cc_start: 0.6891 (mp0) cc_final: 0.5651 (pt0) REVERT: A 633 LYS cc_start: 0.6851 (mtmm) cc_final: 0.6615 (mtmm) REVERT: A 637 HIS cc_start: 0.8056 (t-90) cc_final: 0.7804 (t-90) REVERT: A 638 GLN cc_start: 0.9129 (tt0) cc_final: 0.8290 (mt0) REVERT: A 640 ARG cc_start: 0.8396 (ptp-170) cc_final: 0.7990 (ptm160) REVERT: A 641 ASN cc_start: 0.8848 (m110) cc_final: 0.8507 (m110) REVERT: A 643 LEU cc_start: 0.8900 (tp) cc_final: 0.8051 (tp) REVERT: A 644 HIS cc_start: 0.7762 (m-70) cc_final: 0.7538 (m-70) REVERT: A 646 LEU cc_start: 0.8827 (tp) cc_final: 0.8307 (tt) REVERT: A 647 MET cc_start: 0.8154 (mmm) cc_final: 0.7313 (mmm) REVERT: A 650 LEU cc_start: 0.8238 (mm) cc_final: 0.8027 (mm) REVERT: A 657 TYR cc_start: 0.6858 (m-80) cc_final: 0.6387 (m-80) REVERT: A 750 PHE cc_start: 0.8241 (m-80) cc_final: 0.7910 (m-80) REVERT: A 757 TYR cc_start: 0.8667 (t80) cc_final: 0.8280 (t80) REVERT: B 17 LEU cc_start: 0.5987 (mt) cc_final: 0.5683 (mt) REVERT: B 34 SER cc_start: 0.7813 (p) cc_final: 0.7501 (p) REVERT: B 54 TYR cc_start: 0.7656 (m-80) cc_final: 0.6484 (m-80) REVERT: B 62 LYS cc_start: 0.8441 (mttm) cc_final: 0.7810 (mttm) REVERT: B 63 ARG cc_start: 0.7668 (mtm180) cc_final: 0.6822 (ppt170) REVERT: B 73 GLU cc_start: 0.7820 (tt0) cc_final: 0.7342 (tm-30) REVERT: B 83 MET cc_start: 0.8324 (tpp) cc_final: 0.7662 (tpp) REVERT: B 84 GLU cc_start: 0.8680 (tt0) cc_final: 0.8329 (tm-30) REVERT: B 101 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8193 (tm-30) REVERT: B 102 HIS cc_start: 0.7942 (m90) cc_final: 0.6858 (m90) REVERT: B 117 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7654 (mtp180) REVERT: B 119 LYS cc_start: 0.8448 (tppt) cc_final: 0.7098 (mmmt) REVERT: B 121 THR cc_start: 0.8646 (p) cc_final: 0.8398 (p) REVERT: B 122 GLN cc_start: 0.8467 (tt0) cc_final: 0.7924 (tm-30) REVERT: B 123 ILE cc_start: 0.8730 (mt) cc_final: 0.7819 (mt) REVERT: B 124 MET cc_start: 0.8404 (tpp) cc_final: 0.7258 (tpp) REVERT: B 125 PHE cc_start: 0.7943 (m-10) cc_final: 0.7670 (m-10) REVERT: B 126 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7273 (mt-10) REVERT: B 128 PHE cc_start: 0.7560 (m-80) cc_final: 0.6759 (m-10) REVERT: B 130 VAL cc_start: 0.8413 (t) cc_final: 0.7786 (p) REVERT: B 133 MET cc_start: 0.7391 (ttp) cc_final: 0.6771 (ttp) REVERT: B 155 ASP cc_start: 0.6818 (t0) cc_final: 0.5867 (p0) REVERT: B 163 ASN cc_start: 0.8333 (t0) cc_final: 0.7737 (t0) REVERT: B 168 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7214 (mm-30) REVERT: B 179 LEU cc_start: 0.6623 (tp) cc_final: 0.6289 (tp) REVERT: B 194 LEU cc_start: 0.8676 (mt) cc_final: 0.8372 (mt) REVERT: B 206 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7737 (mt-10) REVERT: B 212 ASP cc_start: 0.8911 (m-30) cc_final: 0.8060 (m-30) REVERT: B 214 LYS cc_start: 0.9159 (ttpt) cc_final: 0.8937 (ttpt) REVERT: B 216 LYS cc_start: 0.8746 (mttt) cc_final: 0.8468 (mmmm) REVERT: B 223 ASP cc_start: 0.7599 (t70) cc_final: 0.7247 (m-30) REVERT: B 256 PHE cc_start: 0.7957 (p90) cc_final: 0.7574 (p90) REVERT: B 257 ARG cc_start: 0.7454 (mtp180) cc_final: 0.7060 (ttp80) REVERT: B 260 GLU cc_start: 0.8287 (tp30) cc_final: 0.7978 (tm-30) REVERT: B 263 PHE cc_start: 0.8379 (m-80) cc_final: 0.7089 (m-80) REVERT: B 264 GLN cc_start: 0.7829 (mt0) cc_final: 0.6879 (mm-40) REVERT: B 267 PHE cc_start: 0.7321 (m-10) cc_final: 0.6534 (m-10) REVERT: B 272 SER cc_start: 0.8093 (m) cc_final: 0.7205 (p) REVERT: B 281 ASN cc_start: 0.8383 (m-40) cc_final: 0.7544 (m110) REVERT: B 291 ARG cc_start: 0.7871 (mtt180) cc_final: 0.7654 (mtt180) REVERT: B 293 ASP cc_start: 0.8847 (m-30) cc_final: 0.8641 (m-30) REVERT: B 306 MET cc_start: 0.7111 (mmm) cc_final: 0.6719 (mmm) REVERT: B 313 ARG cc_start: 0.8488 (tpt-90) cc_final: 0.7394 (tpp-160) REVERT: B 314 MET cc_start: 0.8587 (tpt) cc_final: 0.7760 (mmm) REVERT: B 315 GLN cc_start: 0.8221 (mt0) cc_final: 0.7702 (mm-40) REVERT: B 318 ILE cc_start: 0.8216 (mm) cc_final: 0.8014 (mt) REVERT: B 326 MET cc_start: 0.7222 (mmp) cc_final: 0.6890 (mmm) REVERT: B 330 ILE cc_start: 0.6067 (mm) cc_final: 0.5647 (mm) REVERT: B 335 GLU cc_start: 0.7804 (mp0) cc_final: 0.7460 (mp0) REVERT: B 353 PHE cc_start: 0.7563 (t80) cc_final: 0.7314 (t80) REVERT: B 358 ILE cc_start: 0.7504 (mp) cc_final: 0.7250 (mm) REVERT: B 372 HIS cc_start: 0.6878 (m-70) cc_final: 0.6594 (m-70) REVERT: C 53 TYR cc_start: 0.6965 (m-80) cc_final: 0.5946 (m-80) REVERT: C 57 GLU cc_start: 0.8013 (pt0) cc_final: 0.7304 (pt0) REVERT: C 64 ILE cc_start: 0.7911 (mt) cc_final: 0.7522 (mt) REVERT: C 82 MET cc_start: 0.7951 (tpp) cc_final: 0.6641 (tpp) REVERT: C 84 LYS cc_start: 0.9166 (ttmm) cc_final: 0.8938 (ttmm) REVERT: C 87 HIS cc_start: 0.7794 (t70) cc_final: 0.7311 (t70) REVERT: C 90 PHE cc_start: 0.7694 (m-10) cc_final: 0.7356 (m-80) REVERT: C 91 TYR cc_start: 0.7630 (m-80) cc_final: 0.7399 (m-80) REVERT: C 99 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6293 (mp0) REVERT: C 100 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7880 (tp30) REVERT: C 115 ASN cc_start: 0.8080 (t0) cc_final: 0.7699 (t0) REVERT: C 118 LYS cc_start: 0.8297 (tptt) cc_final: 0.7440 (tptt) REVERT: C 123 MET cc_start: 0.8283 (tpp) cc_final: 0.7120 (tpp) REVERT: C 127 PHE cc_start: 0.8273 (m-80) cc_final: 0.7689 (m-80) REVERT: C 136 ILE cc_start: 0.8385 (mm) cc_final: 0.7919 (tp) REVERT: C 139 VAL cc_start: 0.8838 (m) cc_final: 0.8273 (m) REVERT: C 152 VAL cc_start: 0.8126 (p) cc_final: 0.7907 (m) REVERT: C 157 ASP cc_start: 0.6574 (t0) cc_final: 0.6218 (t0) REVERT: C 161 HIS cc_start: 0.6639 (p90) cc_final: 0.6193 (p90) REVERT: C 167 GLU cc_start: 0.8520 (mm-30) cc_final: 0.7974 (mm-30) REVERT: C 169 TYR cc_start: 0.7234 (m-80) cc_final: 0.7018 (t80) REVERT: C 176 MET cc_start: 0.6122 (mtt) cc_final: 0.5084 (mtt) REVERT: C 186 THR cc_start: 0.8936 (m) cc_final: 0.8420 (p) REVERT: C 187 ASP cc_start: 0.8988 (m-30) cc_final: 0.8648 (m-30) REVERT: C 190 MET cc_start: 0.8659 (mtm) cc_final: 0.8119 (mtm) REVERT: C 198 TYR cc_start: 0.5412 (m-10) cc_final: 0.5058 (m-80) REVERT: C 205 GLU cc_start: 0.7813 (mt-10) cc_final: 0.6968 (mt-10) REVERT: C 207 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7282 (tp30) REVERT: C 218 TYR cc_start: 0.5565 (p90) cc_final: 0.4491 (p90) REVERT: C 256 ARG cc_start: 0.7738 (mtp180) cc_final: 0.6767 (mtp180) REVERT: C 280 ASN cc_start: 0.8829 (m-40) cc_final: 0.8039 (m-40) REVERT: C 282 ILE cc_start: 0.8599 (mt) cc_final: 0.8392 (mt) REVERT: C 283 MET cc_start: 0.8309 (mmm) cc_final: 0.7961 (mmm) REVERT: C 284 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8074 (mtpt) REVERT: C 286 ASP cc_start: 0.8287 (t0) cc_final: 0.7954 (p0) REVERT: C 287 ILE cc_start: 0.8242 (tt) cc_final: 0.7889 (tp) REVERT: C 289 ILE cc_start: 0.8014 (pt) cc_final: 0.7036 (mm) REVERT: C 290 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6214 (mtt90) REVERT: C 292 ASP cc_start: 0.8275 (m-30) cc_final: 0.7810 (p0) REVERT: C 294 TYR cc_start: 0.7987 (m-80) cc_final: 0.7321 (m-80) REVERT: C 299 MET cc_start: 0.7984 (mmm) cc_final: 0.7185 (mmm) REVERT: C 303 THR cc_start: 0.8715 (m) cc_final: 0.8434 (p) REVERT: C 305 MET cc_start: 0.6117 (mmm) cc_final: 0.5632 (mmp) REVERT: C 306 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6992 (t80) REVERT: C 313 MET cc_start: 0.8469 (tpp) cc_final: 0.6906 (tpp) REVERT: C 314 GLN cc_start: 0.8570 (tt0) cc_final: 0.8010 (tt0) REVERT: C 315 LYS cc_start: 0.8781 (tttp) cc_final: 0.8440 (tttp) REVERT: C 317 ILE cc_start: 0.8942 (mm) cc_final: 0.8065 (mm) REVERT: C 328 LYS cc_start: 0.8133 (mttm) cc_final: 0.7897 (mttm) REVERT: D 8 LEU cc_start: 0.7749 (mt) cc_final: 0.7512 (mt) REVERT: D 9 VAL cc_start: 0.7495 (m) cc_final: 0.7139 (p) REVERT: D 11 ASP cc_start: 0.7274 (t70) cc_final: 0.6978 (t0) REVERT: D 16 LEU cc_start: 0.8653 (tp) cc_final: 0.8444 (tp) REVERT: D 34 ILE cc_start: 0.8062 (mt) cc_final: 0.7517 (tp) REVERT: D 51 ASP cc_start: 0.6178 (p0) cc_final: 0.5232 (p0) REVERT: D 52 SER cc_start: 0.6757 (t) cc_final: 0.6348 (m) REVERT: D 57 GLU cc_start: 0.8200 (tt0) cc_final: 0.7205 (tt0) REVERT: D 61 LYS cc_start: 0.8142 (mttm) cc_final: 0.7686 (mttt) REVERT: D 62 ARG cc_start: 0.6965 (mtm180) cc_final: 0.6667 (mtt90) REVERT: D 66 THR cc_start: 0.7084 (t) cc_final: 0.6034 (p) REVERT: D 68 LYS cc_start: 0.7365 (mmtt) cc_final: 0.7040 (mmtt) REVERT: D 87 HIS cc_start: 0.8541 (t-90) cc_final: 0.8331 (t-90) REVERT: D 101 HIS cc_start: 0.6985 (m-70) cc_final: 0.6734 (m90) REVERT: D 115 ASN cc_start: 0.8594 (t0) cc_final: 0.8367 (t0) REVERT: D 118 LYS cc_start: 0.8934 (tptt) cc_final: 0.8241 (tppt) REVERT: D 119 MET cc_start: 0.8412 (ttm) cc_final: 0.8045 (ttm) REVERT: D 137 GLN cc_start: 0.7902 (mt0) cc_final: 0.7561 (mt0) REVERT: D 139 VAL cc_start: 0.8693 (m) cc_final: 0.7585 (p) REVERT: D 143 TYR cc_start: 0.6909 (m-10) cc_final: 0.6316 (m-80) REVERT: D 166 TYR cc_start: 0.7802 (t80) cc_final: 0.7583 (t80) REVERT: D 167 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7837 (mt-10) REVERT: D 175 ILE cc_start: 0.7477 (pt) cc_final: 0.6087 (mm) REVERT: D 176 MET cc_start: 0.6798 (mmm) cc_final: 0.6535 (mmm) REVERT: D 186 THR cc_start: 0.8914 (m) cc_final: 0.8597 (p) REVERT: D 187 ASP cc_start: 0.8526 (m-30) cc_final: 0.8279 (m-30) REVERT: D 190 MET cc_start: 0.8305 (mtm) cc_final: 0.8076 (mtm) REVERT: D 205 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8140 (mt-10) REVERT: D 206 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7789 (ttm-80) REVERT: D 207 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7455 (tp30) REVERT: D 209 VAL cc_start: 0.8690 (t) cc_final: 0.8432 (t) REVERT: D 212 ILE cc_start: 0.8823 (mt) cc_final: 0.8379 (mt) REVERT: D 215 LYS cc_start: 0.8608 (mttt) cc_final: 0.8350 (ptpp) REVERT: D 216 LEU cc_start: 0.7508 (mt) cc_final: 0.7253 (mt) REVERT: D 252 ASN cc_start: 0.8080 (t0) cc_final: 0.7152 (t0) REVERT: D 284 LYS cc_start: 0.8635 (mttm) cc_final: 0.8327 (tptp) REVERT: D 288 ASP cc_start: 0.8585 (m-30) cc_final: 0.8355 (p0) REVERT: D 290 ARG cc_start: 0.7238 (mtt180) cc_final: 0.6216 (mtm-85) REVERT: D 294 TYR cc_start: 0.8096 (m-80) cc_final: 0.7553 (m-80) REVERT: D 299 MET cc_start: 0.8154 (mmm) cc_final: 0.7434 (mmm) REVERT: D 303 THR cc_start: 0.7377 (m) cc_final: 0.7030 (p) REVERT: D 314 GLN cc_start: 0.8844 (tt0) cc_final: 0.8631 (tm-30) REVERT: D 329 ILE cc_start: 0.8002 (mm) cc_final: 0.7002 (mm) outliers start: 4 outliers final: 2 residues processed: 816 average time/residue: 0.1108 time to fit residues: 126.9860 Evaluate side-chains 731 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 728 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS A 420 ASN A 430 HIS A 525 GLN A 552 HIS A 576 GLN A 742 GLN B 79 ASN ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 173 HIS C 263 GLN C 280 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.121271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.093570 restraints weight = 41769.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.097487 restraints weight = 26084.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.100289 restraints weight = 18140.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.102370 restraints weight = 13514.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.103900 restraints weight = 10603.634| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15178 Z= 0.158 Angle : 0.686 8.788 20547 Z= 0.353 Chirality : 0.044 0.195 2251 Planarity : 0.005 0.064 2631 Dihedral : 10.101 166.900 2071 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.19), residues: 1847 helix: 0.58 (0.17), residues: 832 sheet: -1.49 (0.28), residues: 288 loop : -0.11 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 40 TYR 0.027 0.002 TYR A 439 PHE 0.026 0.002 PHE D 124 TRP 0.011 0.001 TRP B 357 HIS 0.010 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00322 (15177) covalent geometry : angle 0.68615 (20547) hydrogen bonds : bond 0.04374 ( 724) hydrogen bonds : angle 5.50112 ( 2007) Misc. bond : bond 0.00081 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 769 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7426 (mm-30) REVERT: A 87 HIS cc_start: 0.8495 (t-90) cc_final: 0.8228 (t-90) REVERT: A 89 LEU cc_start: 0.8418 (mt) cc_final: 0.8053 (pp) REVERT: A 94 ILE cc_start: 0.8335 (mt) cc_final: 0.7718 (tp) REVERT: A 99 ILE cc_start: 0.8167 (pt) cc_final: 0.7822 (pt) REVERT: A 110 ILE cc_start: 0.7878 (mp) cc_final: 0.7358 (tp) REVERT: A 121 GLU cc_start: 0.8477 (tp30) cc_final: 0.8148 (tp30) REVERT: A 122 ASP cc_start: 0.9217 (m-30) cc_final: 0.8881 (p0) REVERT: A 144 GLU cc_start: 0.8654 (tp30) cc_final: 0.8391 (tm-30) REVERT: A 150 MET cc_start: 0.7687 (ttp) cc_final: 0.7188 (ttp) REVERT: A 174 LYS cc_start: 0.8529 (ttpp) cc_final: 0.8233 (pttt) REVERT: A 179 TYR cc_start: 0.8641 (t80) cc_final: 0.8214 (t80) REVERT: A 200 ASN cc_start: 0.9203 (m-40) cc_final: 0.8866 (m110) REVERT: A 225 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7021 (mp0) REVERT: A 228 PHE cc_start: 0.6910 (m-80) cc_final: 0.6034 (m-80) REVERT: A 239 MET cc_start: 0.7138 (mmp) cc_final: 0.6748 (mmp) REVERT: A 242 TYR cc_start: 0.7217 (m-80) cc_final: 0.6818 (m-80) REVERT: A 259 TYR cc_start: 0.7764 (m-80) cc_final: 0.7025 (m-80) REVERT: A 262 PHE cc_start: 0.8815 (m-80) cc_final: 0.7734 (m-80) REVERT: A 307 HIS cc_start: 0.8900 (m90) cc_final: 0.8494 (m90) REVERT: A 312 CYS cc_start: 0.8504 (m) cc_final: 0.8256 (m) REVERT: A 317 ILE cc_start: 0.8577 (mt) cc_final: 0.8238 (mm) REVERT: A 322 GLN cc_start: 0.8768 (mt0) cc_final: 0.8326 (mp10) REVERT: A 325 ILE cc_start: 0.9107 (tt) cc_final: 0.8782 (pt) REVERT: A 358 THR cc_start: 0.8360 (m) cc_final: 0.7882 (m) REVERT: A 364 MET cc_start: 0.7435 (mtt) cc_final: 0.7144 (mtt) REVERT: A 370 GLU cc_start: 0.8377 (tt0) cc_final: 0.8031 (tt0) REVERT: A 371 MET cc_start: 0.9160 (mtm) cc_final: 0.8625 (mpp) REVERT: A 373 HIS cc_start: 0.8469 (t70) cc_final: 0.8061 (t70) REVERT: A 408 TYR cc_start: 0.8806 (t80) cc_final: 0.8024 (t80) REVERT: A 417 ASP cc_start: 0.8737 (m-30) cc_final: 0.8438 (t0) REVERT: A 423 LEU cc_start: 0.6788 (mt) cc_final: 0.6511 (mt) REVERT: A 432 PHE cc_start: 0.7054 (p90) cc_final: 0.6573 (p90) REVERT: A 448 SER cc_start: 0.8076 (m) cc_final: 0.7843 (p) REVERT: A 451 GLN cc_start: 0.8759 (mp10) cc_final: 0.8333 (mp10) REVERT: A 453 CYS cc_start: 0.8742 (m) cc_final: 0.8528 (p) REVERT: A 458 ASN cc_start: 0.9136 (m-40) cc_final: 0.8784 (m110) REVERT: A 463 GLN cc_start: 0.9032 (tt0) cc_final: 0.8268 (tm-30) REVERT: A 468 HIS cc_start: 0.8226 (t-90) cc_final: 0.7816 (t-90) REVERT: A 475 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8173 (pp20) REVERT: A 476 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8208 (tm-30) REVERT: A 478 MET cc_start: 0.8881 (mtm) cc_final: 0.8536 (mtm) REVERT: A 498 LEU cc_start: 0.8953 (mp) cc_final: 0.8362 (tt) REVERT: A 509 LEU cc_start: 0.8997 (tp) cc_final: 0.8661 (mt) REVERT: A 512 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7806 (mt-10) REVERT: A 514 LYS cc_start: 0.8706 (tmtt) cc_final: 0.8449 (ptmt) REVERT: A 520 ASP cc_start: 0.8440 (m-30) cc_final: 0.8122 (p0) REVERT: A 521 ASP cc_start: 0.8671 (p0) cc_final: 0.8384 (p0) REVERT: A 525 GLN cc_start: 0.8329 (tp40) cc_final: 0.7501 (tp-100) REVERT: A 526 LYS cc_start: 0.8991 (tttt) cc_final: 0.8456 (mmmt) REVERT: A 528 TYR cc_start: 0.7885 (m-10) cc_final: 0.7561 (m-10) REVERT: A 532 LEU cc_start: 0.7897 (mt) cc_final: 0.7394 (mt) REVERT: A 535 CYS cc_start: 0.6044 (p) cc_final: 0.5757 (p) REVERT: A 537 LEU cc_start: 0.8813 (mp) cc_final: 0.8520 (mp) REVERT: A 555 ASP cc_start: 0.8156 (t0) cc_final: 0.7928 (t0) REVERT: A 556 LYS cc_start: 0.8710 (mttt) cc_final: 0.8095 (mttm) REVERT: A 558 GLU cc_start: 0.7878 (tt0) cc_final: 0.7424 (tm-30) REVERT: A 559 TYR cc_start: 0.7537 (m-80) cc_final: 0.7075 (m-80) REVERT: A 560 GLN cc_start: 0.7176 (mp10) cc_final: 0.6420 (mp10) REVERT: A 568 ASN cc_start: 0.7965 (t0) cc_final: 0.7741 (t0) REVERT: A 579 VAL cc_start: 0.9121 (m) cc_final: 0.8882 (t) REVERT: A 637 HIS cc_start: 0.8322 (t-90) cc_final: 0.8068 (t-90) REVERT: A 638 GLN cc_start: 0.9009 (tt0) cc_final: 0.8688 (pt0) REVERT: A 640 ARG cc_start: 0.8655 (ptp-170) cc_final: 0.8352 (ptm160) REVERT: A 641 ASN cc_start: 0.9084 (m110) cc_final: 0.8722 (m-40) REVERT: A 643 LEU cc_start: 0.8781 (tp) cc_final: 0.7953 (tp) REVERT: A 656 HIS cc_start: 0.5762 (m-70) cc_final: 0.4174 (m-70) REVERT: A 657 TYR cc_start: 0.6687 (m-80) cc_final: 0.6300 (m-80) REVERT: A 666 PHE cc_start: 0.8252 (m-10) cc_final: 0.8049 (m-10) REVERT: A 691 ARG cc_start: 0.8672 (mtm110) cc_final: 0.8319 (mtm110) REVERT: A 700 ARG cc_start: 0.7142 (mtt90) cc_final: 0.6290 (mpt180) REVERT: A 750 PHE cc_start: 0.8160 (m-80) cc_final: 0.7944 (m-80) REVERT: A 757 TYR cc_start: 0.8846 (t80) cc_final: 0.8489 (t80) REVERT: B 48 MET cc_start: 0.6813 (mtt) cc_final: 0.6416 (tpp) REVERT: B 54 TYR cc_start: 0.7565 (m-80) cc_final: 0.6905 (m-10) REVERT: B 62 LYS cc_start: 0.8460 (mttm) cc_final: 0.7673 (mttm) REVERT: B 66 LEU cc_start: 0.8324 (mt) cc_final: 0.8082 (mt) REVERT: B 77 ILE cc_start: 0.8669 (mm) cc_final: 0.8136 (tt) REVERT: B 83 MET cc_start: 0.8212 (tpp) cc_final: 0.7549 (tpp) REVERT: B 84 GLU cc_start: 0.8748 (tt0) cc_final: 0.8387 (tm-30) REVERT: B 85 LYS cc_start: 0.9116 (mttm) cc_final: 0.8882 (mttm) REVERT: B 106 LEU cc_start: 0.7716 (mt) cc_final: 0.7209 (mt) REVERT: B 119 LYS cc_start: 0.8486 (tppt) cc_final: 0.6853 (tppt) REVERT: B 120 MET cc_start: 0.8569 (ttm) cc_final: 0.7722 (tmm) REVERT: B 122 GLN cc_start: 0.8446 (tt0) cc_final: 0.8135 (tm-30) REVERT: B 123 ILE cc_start: 0.8574 (mt) cc_final: 0.7768 (mt) REVERT: B 124 MET cc_start: 0.8371 (tpp) cc_final: 0.7533 (tpp) REVERT: B 126 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7465 (mt-10) REVERT: B 128 PHE cc_start: 0.8022 (m-80) cc_final: 0.6846 (m-10) REVERT: B 129 ASN cc_start: 0.8502 (m-40) cc_final: 0.8284 (m-40) REVERT: B 133 MET cc_start: 0.7621 (ttp) cc_final: 0.6391 (ttp) REVERT: B 134 TYR cc_start: 0.7290 (t80) cc_final: 0.6995 (t80) REVERT: B 162 HIS cc_start: 0.5818 (p90) cc_final: 0.5572 (p90) REVERT: B 163 ASN cc_start: 0.8298 (t0) cc_final: 0.7812 (t0) REVERT: B 168 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7405 (mm-30) REVERT: B 174 HIS cc_start: 0.7683 (p-80) cc_final: 0.7191 (p-80) REVERT: B 177 MET cc_start: 0.7093 (mmm) cc_final: 0.6703 (mmm) REVERT: B 181 LEU cc_start: 0.7849 (tp) cc_final: 0.7594 (tp) REVERT: B 186 LEU cc_start: 0.8146 (mt) cc_final: 0.7852 (mt) REVERT: B 207 ARG cc_start: 0.8657 (ttm170) cc_final: 0.8296 (ttm170) REVERT: B 208 GLU cc_start: 0.7699 (pp20) cc_final: 0.7061 (pp20) REVERT: B 214 LYS cc_start: 0.9054 (ttpt) cc_final: 0.8535 (ttpt) REVERT: B 216 LYS cc_start: 0.8837 (mttt) cc_final: 0.8632 (mmmt) REVERT: B 239 LYS cc_start: 0.8581 (mttt) cc_final: 0.8348 (mmtt) REVERT: B 260 GLU cc_start: 0.8405 (tp30) cc_final: 0.7896 (tm-30) REVERT: B 263 PHE cc_start: 0.8427 (m-80) cc_final: 0.7429 (m-80) REVERT: B 264 GLN cc_start: 0.8108 (mt0) cc_final: 0.6708 (mm-40) REVERT: B 267 PHE cc_start: 0.7545 (m-10) cc_final: 0.6901 (m-10) REVERT: B 277 GLU cc_start: 0.7924 (tp30) cc_final: 0.7220 (tp30) REVERT: B 281 ASN cc_start: 0.8023 (m-40) cc_final: 0.7744 (m-40) REVERT: B 285 LYS cc_start: 0.8402 (mmmm) cc_final: 0.7962 (mtmm) REVERT: B 306 MET cc_start: 0.6985 (mmm) cc_final: 0.5654 (mmt) REVERT: B 313 ARG cc_start: 0.8755 (tpt-90) cc_final: 0.7869 (tpp-160) REVERT: B 314 MET cc_start: 0.8435 (tpt) cc_final: 0.7761 (mmp) REVERT: B 316 LYS cc_start: 0.8839 (ptpt) cc_final: 0.8478 (ptpt) REVERT: B 326 MET cc_start: 0.7402 (mmp) cc_final: 0.6854 (mmm) REVERT: B 329 LYS cc_start: 0.7502 (mttt) cc_final: 0.7298 (tptm) REVERT: B 335 GLU cc_start: 0.8183 (mp0) cc_final: 0.7613 (mp0) REVERT: B 353 PHE cc_start: 0.7720 (t80) cc_final: 0.7203 (t80) REVERT: B 355 GLN cc_start: 0.8428 (pp30) cc_final: 0.7639 (pp30) REVERT: B 356 MET cc_start: 0.8701 (mtm) cc_final: 0.8301 (mmm) REVERT: B 361 GLN cc_start: 0.8924 (pp30) cc_final: 0.8671 (pp30) REVERT: B 372 HIS cc_start: 0.7088 (m-70) cc_final: 0.6750 (m-70) REVERT: C 51 ASP cc_start: 0.7861 (p0) cc_final: 0.7617 (p0) REVERT: C 54 VAL cc_start: 0.7632 (t) cc_final: 0.6643 (p) REVERT: C 57 GLU cc_start: 0.8413 (pt0) cc_final: 0.8173 (pm20) REVERT: C 64 ILE cc_start: 0.7844 (mt) cc_final: 0.7262 (tp) REVERT: C 71 ILE cc_start: 0.7413 (mm) cc_final: 0.6839 (tp) REVERT: C 72 GLU cc_start: 0.8367 (pp20) cc_final: 0.8116 (pp20) REVERT: C 75 ILE cc_start: 0.7838 (pt) cc_final: 0.7486 (pt) REVERT: C 79 TRP cc_start: 0.6904 (m100) cc_final: 0.6449 (m100) REVERT: C 82 MET cc_start: 0.8001 (tpp) cc_final: 0.6856 (tpp) REVERT: C 87 HIS cc_start: 0.8200 (t70) cc_final: 0.7621 (t-90) REVERT: C 90 PHE cc_start: 0.7535 (m-10) cc_final: 0.7114 (m-80) REVERT: C 91 TYR cc_start: 0.7846 (m-80) cc_final: 0.7395 (m-80) REVERT: C 118 LYS cc_start: 0.8164 (tptt) cc_final: 0.7543 (tptt) REVERT: C 119 MET cc_start: 0.8436 (ttm) cc_final: 0.8206 (ttm) REVERT: C 121 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8591 (tm-30) REVERT: C 123 MET cc_start: 0.8129 (tpp) cc_final: 0.7037 (tpp) REVERT: C 124 PHE cc_start: 0.7726 (m-80) cc_final: 0.7330 (m-80) REVERT: C 127 PHE cc_start: 0.8001 (m-80) cc_final: 0.7602 (m-80) REVERT: C 140 LEU cc_start: 0.8429 (mt) cc_final: 0.8163 (mt) REVERT: C 157 ASP cc_start: 0.6889 (t0) cc_final: 0.6432 (t0) REVERT: C 161 HIS cc_start: 0.6940 (p-80) cc_final: 0.6656 (p-80) REVERT: C 167 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7892 (mp0) REVERT: C 169 TYR cc_start: 0.7668 (m-80) cc_final: 0.7360 (t80) REVERT: C 177 ARG cc_start: 0.7956 (ttm170) cc_final: 0.7742 (ttm170) REVERT: C 191 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8718 (mtpp) REVERT: C 192 ILE cc_start: 0.8489 (pt) cc_final: 0.8115 (mm) REVERT: C 202 THR cc_start: 0.7614 (p) cc_final: 0.7371 (p) REVERT: C 205 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7392 (mt-10) REVERT: C 211 ASP cc_start: 0.8436 (m-30) cc_final: 0.8097 (m-30) REVERT: C 242 LEU cc_start: 0.8595 (mt) cc_final: 0.7834 (mt) REVERT: C 256 ARG cc_start: 0.8462 (mtp180) cc_final: 0.7463 (mtp180) REVERT: C 259 GLU cc_start: 0.8787 (tp30) cc_final: 0.7618 (tm-30) REVERT: C 262 PHE cc_start: 0.8716 (m-10) cc_final: 0.8487 (m-10) REVERT: C 263 GLN cc_start: 0.7892 (mt0) cc_final: 0.7168 (mt0) REVERT: C 275 HIS cc_start: 0.8289 (p90) cc_final: 0.7650 (p90) REVERT: C 276 GLU cc_start: 0.8549 (tp30) cc_final: 0.7902 (tp30) REVERT: C 280 ASN cc_start: 0.8597 (m110) cc_final: 0.7981 (m110) REVERT: C 282 ILE cc_start: 0.8549 (mt) cc_final: 0.8304 (mt) REVERT: C 283 MET cc_start: 0.8270 (mmm) cc_final: 0.7821 (mmm) REVERT: C 284 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8244 (mtpp) REVERT: C 286 ASP cc_start: 0.8255 (t0) cc_final: 0.7429 (p0) REVERT: C 294 TYR cc_start: 0.7709 (m-80) cc_final: 0.7406 (m-80) REVERT: C 296 ASN cc_start: 0.7596 (p0) cc_final: 0.7151 (p0) REVERT: C 299 MET cc_start: 0.8128 (mmm) cc_final: 0.7631 (mmm) REVERT: C 303 THR cc_start: 0.8437 (m) cc_final: 0.8215 (p) REVERT: C 313 MET cc_start: 0.8433 (tpp) cc_final: 0.7403 (tpp) REVERT: C 314 GLN cc_start: 0.8619 (tt0) cc_final: 0.8016 (tt0) REVERT: C 327 ILE cc_start: 0.8683 (mm) cc_final: 0.8158 (pt) REVERT: C 329 ILE cc_start: 0.8366 (mm) cc_final: 0.7994 (mt) REVERT: C 352 PHE cc_start: 0.7856 (t80) cc_final: 0.7475 (t80) REVERT: C 356 TRP cc_start: 0.7202 (m100) cc_final: 0.6802 (m100) REVERT: C 361 GLU cc_start: 0.8532 (tp30) cc_final: 0.7991 (tp30) REVERT: D 12 ASN cc_start: 0.7357 (m110) cc_final: 0.6921 (m110) REVERT: D 28 ARG cc_start: 0.7153 (ttp80) cc_final: 0.6430 (ttp-170) REVERT: D 34 ILE cc_start: 0.8340 (mt) cc_final: 0.7923 (mp) REVERT: D 44 MET cc_start: 0.5992 (mmm) cc_final: 0.5609 (mmm) REVERT: D 49 GLN cc_start: 0.6614 (pm20) cc_final: 0.6410 (pm20) REVERT: D 50 LYS cc_start: 0.7895 (mtmm) cc_final: 0.7214 (mtmm) REVERT: D 51 ASP cc_start: 0.6578 (p0) cc_final: 0.5653 (p0) REVERT: D 52 SER cc_start: 0.7188 (t) cc_final: 0.6880 (m) REVERT: D 57 GLU cc_start: 0.8345 (tt0) cc_final: 0.7320 (tt0) REVERT: D 61 LYS cc_start: 0.8202 (mttm) cc_final: 0.7757 (mttt) REVERT: D 68 LYS cc_start: 0.7657 (mmtt) cc_final: 0.7291 (mmtt) REVERT: D 84 LYS cc_start: 0.8753 (mmtp) cc_final: 0.8521 (mmtt) REVERT: D 86 TRP cc_start: 0.8021 (m-10) cc_final: 0.7109 (m-90) REVERT: D 93 GLU cc_start: 0.7472 (tp30) cc_final: 0.7228 (tp30) REVERT: D 94 LEU cc_start: 0.8233 (mt) cc_final: 0.7539 (mt) REVERT: D 107 GLU cc_start: 0.7069 (pt0) cc_final: 0.5619 (pt0) REVERT: D 111 ASN cc_start: 0.7876 (m-40) cc_final: 0.6631 (m-40) REVERT: D 116 ARG cc_start: 0.8599 (ttm-80) cc_final: 0.8233 (ttm-80) REVERT: D 117 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8131 (mt-10) REVERT: D 118 LYS cc_start: 0.9141 (tptt) cc_final: 0.7792 (tppt) REVERT: D 119 MET cc_start: 0.9000 (ttm) cc_final: 0.8286 (ttm) REVERT: D 123 MET cc_start: 0.8132 (mmp) cc_final: 0.7734 (mmp) REVERT: D 125 GLU cc_start: 0.8853 (pt0) cc_final: 0.8493 (pt0) REVERT: D 133 TYR cc_start: 0.7364 (t80) cc_final: 0.7098 (t80) REVERT: D 137 GLN cc_start: 0.8050 (mt0) cc_final: 0.7599 (mt0) REVERT: D 139 VAL cc_start: 0.8621 (m) cc_final: 0.8274 (p) REVERT: D 165 ILE cc_start: 0.7752 (mt) cc_final: 0.7423 (tt) REVERT: D 176 MET cc_start: 0.6925 (mmm) cc_final: 0.6667 (mmm) REVERT: D 187 ASP cc_start: 0.8720 (m-30) cc_final: 0.8439 (m-30) REVERT: D 191 LYS cc_start: 0.9182 (ttpt) cc_final: 0.8827 (ttpt) REVERT: D 205 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8292 (mt-10) REVERT: D 207 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7476 (tp30) REVERT: D 209 VAL cc_start: 0.8713 (t) cc_final: 0.8402 (t) REVERT: D 211 ASP cc_start: 0.8840 (m-30) cc_final: 0.7537 (m-30) REVERT: D 213 LYS cc_start: 0.8717 (ttpt) cc_final: 0.8250 (ttpt) REVERT: D 214 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7460 (mm-30) REVERT: D 224 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8892 (tm-30) REVERT: D 238 LYS cc_start: 0.7090 (mttm) cc_final: 0.6850 (mmtm) REVERT: D 240 TYR cc_start: 0.7827 (t80) cc_final: 0.7471 (t80) REVERT: D 286 ASP cc_start: 0.8324 (t0) cc_final: 0.7888 (t0) REVERT: D 288 ASP cc_start: 0.8649 (m-30) cc_final: 0.8074 (m-30) REVERT: D 290 ARG cc_start: 0.7598 (mtt180) cc_final: 0.6610 (mtt180) REVERT: D 294 TYR cc_start: 0.8231 (m-80) cc_final: 0.7646 (m-80) REVERT: D 299 MET cc_start: 0.8082 (mmm) cc_final: 0.7500 (mmm) REVERT: D 303 THR cc_start: 0.7847 (m) cc_final: 0.7470 (p) REVERT: D 309 ILE cc_start: 0.8349 (tt) cc_final: 0.8122 (tp) REVERT: D 312 ARG cc_start: 0.8906 (tpt-90) cc_final: 0.7577 (tpp80) REVERT: D 314 GLN cc_start: 0.8950 (tt0) cc_final: 0.8682 (tm-30) REVERT: D 316 GLU cc_start: 0.8619 (mm-30) cc_final: 0.7805 (mm-30) outliers start: 1 outliers final: 0 residues processed: 769 average time/residue: 0.1195 time to fit residues: 128.1588 Evaluate side-chains 700 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 700 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 149 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 125 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 125 ASN A 157 GLN A 200 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 HIS ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS D 12 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.113619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.087173 restraints weight = 42873.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.091007 restraints weight = 25940.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.093729 restraints weight = 17646.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.095691 restraints weight = 12950.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.097142 restraints weight = 10089.032| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 15178 Z= 0.209 Angle : 0.719 7.687 20547 Z= 0.374 Chirality : 0.046 0.181 2251 Planarity : 0.006 0.152 2631 Dihedral : 9.671 166.511 2071 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.25 % Allowed : 2.39 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.19), residues: 1847 helix: 0.71 (0.17), residues: 834 sheet: -1.45 (0.28), residues: 301 loop : -0.07 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 62 TYR 0.035 0.002 TYR D 166 PHE 0.016 0.002 PHE A 672 TRP 0.017 0.002 TRP D 79 HIS 0.012 0.002 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00417 (15177) covalent geometry : angle 0.71906 (20547) hydrogen bonds : bond 0.04505 ( 724) hydrogen bonds : angle 5.38828 ( 2007) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 777 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7390 (mm-30) REVERT: A 38 LEU cc_start: 0.8403 (mm) cc_final: 0.8066 (mm) REVERT: A 87 HIS cc_start: 0.8535 (t-90) cc_final: 0.8316 (t-90) REVERT: A 89 LEU cc_start: 0.8358 (mt) cc_final: 0.8007 (pp) REVERT: A 99 ILE cc_start: 0.8096 (pt) cc_final: 0.7791 (pt) REVERT: A 101 THR cc_start: 0.8056 (m) cc_final: 0.7766 (t) REVERT: A 110 ILE cc_start: 0.7614 (mp) cc_final: 0.7138 (tp) REVERT: A 116 LEU cc_start: 0.8859 (tp) cc_final: 0.8641 (tp) REVERT: A 122 ASP cc_start: 0.9178 (m-30) cc_final: 0.8654 (p0) REVERT: A 127 TYR cc_start: 0.7735 (m-80) cc_final: 0.7503 (m-80) REVERT: A 144 GLU cc_start: 0.8672 (tp30) cc_final: 0.8470 (tt0) REVERT: A 145 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 148 LYS cc_start: 0.8963 (mtmt) cc_final: 0.8666 (mtmm) REVERT: A 149 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8123 (mm-40) REVERT: A 179 TYR cc_start: 0.8497 (t80) cc_final: 0.8088 (t80) REVERT: A 194 GLU cc_start: 0.7177 (tp30) cc_final: 0.6825 (tm-30) REVERT: A 223 TYR cc_start: 0.7816 (t80) cc_final: 0.6848 (t80) REVERT: A 225 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7191 (mp0) REVERT: A 240 ARG cc_start: 0.7669 (ttm170) cc_final: 0.7143 (ttm170) REVERT: A 242 TYR cc_start: 0.7501 (m-80) cc_final: 0.7028 (m-80) REVERT: A 248 ARG cc_start: 0.7989 (tpm170) cc_final: 0.7628 (tpp-160) REVERT: A 259 TYR cc_start: 0.7717 (m-80) cc_final: 0.6571 (m-80) REVERT: A 260 HIS cc_start: 0.8415 (m-70) cc_final: 0.8142 (m90) REVERT: A 262 PHE cc_start: 0.8771 (m-80) cc_final: 0.8121 (m-80) REVERT: A 286 HIS cc_start: 0.6573 (t-90) cc_final: 0.6359 (t-90) REVERT: A 307 HIS cc_start: 0.8844 (m90) cc_final: 0.8616 (m90) REVERT: A 322 GLN cc_start: 0.8889 (mt0) cc_final: 0.8599 (mt0) REVERT: A 327 ARG cc_start: 0.8586 (mpt180) cc_final: 0.8140 (mmt180) REVERT: A 329 LEU cc_start: 0.8476 (mt) cc_final: 0.8208 (mt) REVERT: A 364 MET cc_start: 0.7391 (mtt) cc_final: 0.7152 (mtt) REVERT: A 370 GLU cc_start: 0.8354 (tt0) cc_final: 0.8034 (tt0) REVERT: A 371 MET cc_start: 0.8985 (mtm) cc_final: 0.8534 (mtp) REVERT: A 373 HIS cc_start: 0.8462 (t70) cc_final: 0.8035 (t70) REVERT: A 408 TYR cc_start: 0.8830 (t80) cc_final: 0.7955 (t80) REVERT: A 413 ASN cc_start: 0.8802 (m-40) cc_final: 0.8220 (t0) REVERT: A 417 ASP cc_start: 0.8641 (m-30) cc_final: 0.8330 (m-30) REVERT: A 423 LEU cc_start: 0.7379 (mt) cc_final: 0.6983 (mt) REVERT: A 450 GLU cc_start: 0.9062 (mp0) cc_final: 0.8799 (mp0) REVERT: A 452 PHE cc_start: 0.8526 (t80) cc_final: 0.8039 (t80) REVERT: A 453 CYS cc_start: 0.8821 (m) cc_final: 0.8562 (p) REVERT: A 467 MET cc_start: 0.8459 (mtm) cc_final: 0.8185 (mtm) REVERT: A 468 HIS cc_start: 0.8263 (t-90) cc_final: 0.7684 (t-90) REVERT: A 475 GLU cc_start: 0.8396 (mp0) cc_final: 0.7951 (mp0) REVERT: A 476 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8307 (tm-30) REVERT: A 478 MET cc_start: 0.8837 (mtm) cc_final: 0.8411 (mtm) REVERT: A 498 LEU cc_start: 0.9055 (mp) cc_final: 0.8436 (tt) REVERT: A 505 ILE cc_start: 0.8710 (mt) cc_final: 0.8458 (pt) REVERT: A 506 LEU cc_start: 0.8881 (mt) cc_final: 0.8663 (mt) REVERT: A 509 LEU cc_start: 0.8894 (tp) cc_final: 0.8530 (mt) REVERT: A 511 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8064 (mm-30) REVERT: A 512 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7855 (mm-30) REVERT: A 514 LYS cc_start: 0.8724 (tmtt) cc_final: 0.8412 (ptmm) REVERT: A 525 GLN cc_start: 0.8423 (tp40) cc_final: 0.7561 (tp-100) REVERT: A 526 LYS cc_start: 0.9030 (tttt) cc_final: 0.8368 (mmmt) REVERT: A 529 ASN cc_start: 0.8570 (m-40) cc_final: 0.7669 (m110) REVERT: A 532 LEU cc_start: 0.7841 (mt) cc_final: 0.7264 (mt) REVERT: A 534 LYS cc_start: 0.8391 (pttt) cc_final: 0.8040 (pttm) REVERT: A 535 CYS cc_start: 0.6349 (p) cc_final: 0.6140 (p) REVERT: A 537 LEU cc_start: 0.9023 (mp) cc_final: 0.8633 (mp) REVERT: A 538 PHE cc_start: 0.8236 (t80) cc_final: 0.7898 (t80) REVERT: A 555 ASP cc_start: 0.8187 (t0) cc_final: 0.7890 (t0) REVERT: A 556 LYS cc_start: 0.8631 (mttt) cc_final: 0.7872 (mttm) REVERT: A 558 GLU cc_start: 0.7886 (tt0) cc_final: 0.7492 (tm-30) REVERT: A 559 TYR cc_start: 0.7496 (m-80) cc_final: 0.7022 (m-80) REVERT: A 568 ASN cc_start: 0.8142 (t0) cc_final: 0.7937 (t0) REVERT: A 637 HIS cc_start: 0.8418 (t-90) cc_final: 0.7976 (t-90) REVERT: A 638 GLN cc_start: 0.8998 (tt0) cc_final: 0.8733 (pt0) REVERT: A 641 ASN cc_start: 0.9133 (m110) cc_final: 0.8528 (m110) REVERT: A 643 LEU cc_start: 0.8675 (tp) cc_final: 0.7599 (tp) REVERT: A 645 LEU cc_start: 0.9190 (mt) cc_final: 0.8944 (tp) REVERT: A 647 MET cc_start: 0.8732 (mmm) cc_final: 0.7755 (mmm) REVERT: A 648 GLU cc_start: 0.8952 (tp30) cc_final: 0.8498 (tm-30) REVERT: A 649 THR cc_start: 0.9106 (p) cc_final: 0.8683 (p) REVERT: A 650 LEU cc_start: 0.8693 (mm) cc_final: 0.8249 (pp) REVERT: A 657 TYR cc_start: 0.6680 (m-80) cc_final: 0.5907 (m-80) REVERT: A 666 PHE cc_start: 0.8373 (m-10) cc_final: 0.8061 (m-10) REVERT: A 676 ARG cc_start: 0.8505 (mmp80) cc_final: 0.7968 (mtp85) REVERT: A 688 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7295 (tp30) REVERT: A 691 ARG cc_start: 0.8970 (mtm110) cc_final: 0.8687 (mtm-85) REVERT: A 700 ARG cc_start: 0.7201 (mtt90) cc_final: 0.6410 (mpt180) REVERT: A 757 TYR cc_start: 0.8893 (t80) cc_final: 0.8552 (t80) REVERT: B 17 LEU cc_start: 0.7126 (mt) cc_final: 0.6918 (mt) REVERT: B 54 TYR cc_start: 0.7940 (m-80) cc_final: 0.6991 (m-10) REVERT: B 62 LYS cc_start: 0.8751 (mttm) cc_final: 0.8104 (mttm) REVERT: B 66 LEU cc_start: 0.8328 (mt) cc_final: 0.7947 (mt) REVERT: B 76 ILE cc_start: 0.8513 (pt) cc_final: 0.8219 (pt) REVERT: B 83 MET cc_start: 0.8249 (tpp) cc_final: 0.7689 (tpp) REVERT: B 84 GLU cc_start: 0.8794 (tt0) cc_final: 0.8378 (tm-30) REVERT: B 85 LYS cc_start: 0.9189 (mttm) cc_final: 0.8893 (mttm) REVERT: B 100 GLU cc_start: 0.8355 (mp0) cc_final: 0.8112 (mp0) REVERT: B 106 LEU cc_start: 0.7814 (mt) cc_final: 0.7319 (mt) REVERT: B 114 LYS cc_start: 0.8538 (ptmm) cc_final: 0.7660 (ptmm) REVERT: B 120 MET cc_start: 0.8552 (ttm) cc_final: 0.7870 (tmm) REVERT: B 121 THR cc_start: 0.8663 (p) cc_final: 0.7862 (p) REVERT: B 123 ILE cc_start: 0.8602 (mt) cc_final: 0.7815 (mt) REVERT: B 124 MET cc_start: 0.8397 (tpp) cc_final: 0.7773 (tpp) REVERT: B 128 PHE cc_start: 0.8160 (m-80) cc_final: 0.7216 (m-10) REVERT: B 133 MET cc_start: 0.7374 (ttp) cc_final: 0.6631 (ttp) REVERT: B 134 TYR cc_start: 0.7310 (t80) cc_final: 0.6942 (t80) REVERT: B 167 TYR cc_start: 0.8068 (t80) cc_final: 0.7860 (t80) REVERT: B 168 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7808 (tp30) REVERT: B 179 LEU cc_start: 0.6860 (tp) cc_final: 0.6554 (tp) REVERT: B 181 LEU cc_start: 0.7976 (tp) cc_final: 0.7751 (tp) REVERT: B 186 LEU cc_start: 0.8473 (mt) cc_final: 0.8234 (mt) REVERT: B 191 MET cc_start: 0.8504 (ttm) cc_final: 0.8202 (ttm) REVERT: B 192 LYS cc_start: 0.8366 (ptmt) cc_final: 0.8030 (ptmt) REVERT: B 208 GLU cc_start: 0.8039 (pp20) cc_final: 0.7447 (pm20) REVERT: B 209 ILE cc_start: 0.8766 (mm) cc_final: 0.8301 (mm) REVERT: B 211 ARG cc_start: 0.8881 (ptt90) cc_final: 0.8635 (ptm-80) REVERT: B 214 LYS cc_start: 0.9024 (ttpt) cc_final: 0.8563 (ttpt) REVERT: B 219 TYR cc_start: 0.7422 (p90) cc_final: 0.7197 (p90) REVERT: B 239 LYS cc_start: 0.8618 (mttt) cc_final: 0.8357 (mmtt) REVERT: B 256 PHE cc_start: 0.8407 (p90) cc_final: 0.8025 (p90) REVERT: B 260 GLU cc_start: 0.8430 (tp30) cc_final: 0.8007 (tp30) REVERT: B 263 PHE cc_start: 0.8555 (m-80) cc_final: 0.7918 (m-80) REVERT: B 264 GLN cc_start: 0.8413 (mt0) cc_final: 0.7458 (mt0) REVERT: B 267 PHE cc_start: 0.7879 (m-10) cc_final: 0.7419 (m-10) REVERT: B 291 ARG cc_start: 0.7912 (mtt180) cc_final: 0.7571 (mtt180) REVERT: B 292 LYS cc_start: 0.8713 (pttm) cc_final: 0.8460 (pttm) REVERT: B 299 VAL cc_start: 0.8243 (t) cc_final: 0.8007 (p) REVERT: B 300 MET cc_start: 0.7833 (mmm) cc_final: 0.7520 (mmm) REVERT: B 310 ILE cc_start: 0.8764 (tt) cc_final: 0.8419 (pt) REVERT: B 313 ARG cc_start: 0.8907 (tpt-90) cc_final: 0.8120 (tpp-160) REVERT: B 314 MET cc_start: 0.8394 (tpt) cc_final: 0.7734 (mmm) REVERT: B 315 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8067 (tp40) REVERT: B 316 LYS cc_start: 0.8919 (ptpt) cc_final: 0.8567 (ptpt) REVERT: B 326 MET cc_start: 0.7430 (mmp) cc_final: 0.7080 (mmm) REVERT: B 329 LYS cc_start: 0.7686 (mttt) cc_final: 0.7370 (mttt) REVERT: B 351 SER cc_start: 0.7978 (t) cc_final: 0.7537 (p) REVERT: B 353 PHE cc_start: 0.8117 (t80) cc_final: 0.7881 (t80) REVERT: B 362 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8228 (tp30) REVERT: B 365 GLU cc_start: 0.8197 (pt0) cc_final: 0.7672 (pp20) REVERT: B 370 ILE cc_start: 0.8380 (tp) cc_final: 0.8039 (tp) REVERT: B 372 HIS cc_start: 0.7817 (m-70) cc_final: 0.7124 (m90) REVERT: C 50 LYS cc_start: 0.8182 (mttt) cc_final: 0.7792 (mttt) REVERT: C 51 ASP cc_start: 0.8254 (p0) cc_final: 0.7489 (p0) REVERT: C 54 VAL cc_start: 0.7882 (t) cc_final: 0.7416 (p) REVERT: C 57 GLU cc_start: 0.8431 (pt0) cc_final: 0.8152 (pt0) REVERT: C 64 ILE cc_start: 0.8596 (mt) cc_final: 0.8394 (tp) REVERT: C 71 ILE cc_start: 0.7478 (mm) cc_final: 0.7040 (tp) REVERT: C 72 GLU cc_start: 0.8376 (pp20) cc_final: 0.8100 (pp20) REVERT: C 75 ILE cc_start: 0.7945 (pt) cc_final: 0.7590 (pt) REVERT: C 76 ILE cc_start: 0.7366 (mm) cc_final: 0.7049 (mm) REVERT: C 79 TRP cc_start: 0.7100 (m100) cc_final: 0.6158 (m100) REVERT: C 82 MET cc_start: 0.7974 (tpp) cc_final: 0.6948 (tpp) REVERT: C 83 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8661 (pp20) REVERT: C 84 LYS cc_start: 0.9233 (ttmm) cc_final: 0.9011 (ttmm) REVERT: C 87 HIS cc_start: 0.8203 (t70) cc_final: 0.7584 (t-90) REVERT: C 90 PHE cc_start: 0.7722 (m-10) cc_final: 0.7313 (m-80) REVERT: C 91 TYR cc_start: 0.8009 (m-80) cc_final: 0.7541 (m-80) REVERT: C 105 LEU cc_start: 0.8221 (mt) cc_final: 0.7947 (mm) REVERT: C 113 LYS cc_start: 0.8503 (mttp) cc_final: 0.8124 (mttp) REVERT: C 118 LYS cc_start: 0.8172 (tptt) cc_final: 0.7639 (tptm) REVERT: C 119 MET cc_start: 0.8478 (ttm) cc_final: 0.8251 (ttm) REVERT: C 121 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8737 (tm-30) REVERT: C 123 MET cc_start: 0.8247 (tpp) cc_final: 0.7402 (tpp) REVERT: C 127 PHE cc_start: 0.7882 (m-80) cc_final: 0.7475 (m-80) REVERT: C 140 LEU cc_start: 0.8789 (mt) cc_final: 0.8574 (mt) REVERT: C 142 LEU cc_start: 0.8521 (tp) cc_final: 0.8274 (tp) REVERT: C 161 HIS cc_start: 0.6982 (p-80) cc_final: 0.6590 (p-80) REVERT: C 163 VAL cc_start: 0.7818 (t) cc_final: 0.7578 (t) REVERT: C 167 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8096 (mm-30) REVERT: C 176 MET cc_start: 0.6791 (mtt) cc_final: 0.6558 (mtt) REVERT: C 178 LEU cc_start: 0.7643 (tp) cc_final: 0.7419 (tp) REVERT: C 185 LEU cc_start: 0.8852 (mt) cc_final: 0.8599 (mt) REVERT: C 187 ASP cc_start: 0.8873 (m-30) cc_final: 0.8589 (m-30) REVERT: C 191 LYS cc_start: 0.9001 (ttpt) cc_final: 0.8713 (mtpp) REVERT: C 205 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7423 (mt-10) REVERT: C 206 ARG cc_start: 0.8250 (ptp-110) cc_final: 0.7809 (ptp-170) REVERT: C 211 ASP cc_start: 0.8653 (m-30) cc_final: 0.7901 (m-30) REVERT: C 216 LEU cc_start: 0.8339 (mt) cc_final: 0.8131 (mt) REVERT: C 242 LEU cc_start: 0.8773 (mt) cc_final: 0.7936 (mt) REVERT: C 252 ASN cc_start: 0.8139 (p0) cc_final: 0.7680 (p0) REVERT: C 253 GLU cc_start: 0.8358 (mp0) cc_final: 0.7840 (mp0) REVERT: C 254 ARG cc_start: 0.7836 (mtp-110) cc_final: 0.7544 (mtp-110) REVERT: C 256 ARG cc_start: 0.8684 (mtp180) cc_final: 0.8034 (mtp180) REVERT: C 259 GLU cc_start: 0.8830 (tp30) cc_final: 0.7838 (tm-30) REVERT: C 263 GLN cc_start: 0.8081 (mt0) cc_final: 0.7758 (mt0) REVERT: C 276 GLU cc_start: 0.8393 (tp30) cc_final: 0.8164 (mm-30) REVERT: C 279 TYR cc_start: 0.8638 (t80) cc_final: 0.8377 (t80) REVERT: C 282 ILE cc_start: 0.8708 (mt) cc_final: 0.8484 (mt) REVERT: C 283 MET cc_start: 0.8323 (mmm) cc_final: 0.7914 (mmm) REVERT: C 284 LYS cc_start: 0.8744 (mtpt) cc_final: 0.8433 (mtpp) REVERT: C 286 ASP cc_start: 0.8304 (t0) cc_final: 0.7639 (p0) REVERT: C 289 ILE cc_start: 0.8190 (pt) cc_final: 0.7899 (mm) REVERT: C 294 TYR cc_start: 0.7912 (m-80) cc_final: 0.7583 (m-80) REVERT: C 296 ASN cc_start: 0.7357 (p0) cc_final: 0.6617 (p0) REVERT: C 299 MET cc_start: 0.8018 (mmm) cc_final: 0.7316 (mpp) REVERT: C 305 MET cc_start: 0.6736 (mmm) cc_final: 0.6245 (mmm) REVERT: C 313 MET cc_start: 0.8350 (tpp) cc_final: 0.6982 (tpp) REVERT: C 314 GLN cc_start: 0.8634 (tt0) cc_final: 0.7806 (mm-40) REVERT: C 316 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7728 (tm-30) REVERT: C 317 ILE cc_start: 0.8862 (mm) cc_final: 0.8028 (mm) REVERT: C 327 ILE cc_start: 0.8716 (mm) cc_final: 0.8354 (pt) REVERT: C 328 LYS cc_start: 0.8468 (mttp) cc_final: 0.8093 (mttp) REVERT: C 329 ILE cc_start: 0.8619 (mm) cc_final: 0.7172 (mm) REVERT: C 330 ILE cc_start: 0.8669 (tt) cc_final: 0.8192 (tt) REVERT: C 356 TRP cc_start: 0.6928 (m100) cc_final: 0.6395 (m100) REVERT: C 361 GLU cc_start: 0.8648 (tp30) cc_final: 0.8086 (tp30) REVERT: C 371 HIS cc_start: 0.7013 (m-70) cc_final: 0.6098 (m-70) REVERT: D 37 ARG cc_start: 0.7955 (tpp80) cc_final: 0.7383 (tpp80) REVERT: D 41 GLN cc_start: 0.8150 (tp40) cc_final: 0.7654 (tm-30) REVERT: D 52 SER cc_start: 0.7571 (t) cc_final: 0.6975 (m) REVERT: D 57 GLU cc_start: 0.8325 (tt0) cc_final: 0.7806 (tp30) REVERT: D 61 LYS cc_start: 0.7879 (mttm) cc_final: 0.7103 (mttt) REVERT: D 62 ARG cc_start: 0.8291 (mtt90) cc_final: 0.7771 (mtt90) REVERT: D 64 ILE cc_start: 0.8074 (tp) cc_final: 0.7300 (tp) REVERT: D 68 LYS cc_start: 0.7665 (mmtt) cc_final: 0.7404 (mmtt) REVERT: D 81 ASP cc_start: 0.8462 (m-30) cc_final: 0.8192 (m-30) REVERT: D 103 THR cc_start: 0.7825 (m) cc_final: 0.7602 (t) REVERT: D 111 ASN cc_start: 0.8027 (m-40) cc_final: 0.6801 (m-40) REVERT: D 117 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8110 (mt-10) REVERT: D 121 GLN cc_start: 0.8618 (pp30) cc_final: 0.8360 (pp30) REVERT: D 124 PHE cc_start: 0.7840 (m-80) cc_final: 0.7207 (m-80) REVERT: D 127 PHE cc_start: 0.8523 (m-10) cc_final: 0.8076 (m-10) REVERT: D 132 MET cc_start: 0.6792 (mmp) cc_final: 0.6098 (mmp) REVERT: D 133 TYR cc_start: 0.7506 (t80) cc_final: 0.7145 (t80) REVERT: D 137 GLN cc_start: 0.7981 (mt0) cc_final: 0.7600 (mt0) REVERT: D 139 VAL cc_start: 0.8520 (m) cc_final: 0.8089 (p) REVERT: D 165 ILE cc_start: 0.7808 (mt) cc_final: 0.7422 (tt) REVERT: D 176 MET cc_start: 0.7064 (mmm) cc_final: 0.6728 (mmm) REVERT: D 178 LEU cc_start: 0.8338 (tp) cc_final: 0.8025 (tp) REVERT: D 187 ASP cc_start: 0.8804 (m-30) cc_final: 0.8596 (m-30) REVERT: D 196 ARG cc_start: 0.8055 (tpp80) cc_final: 0.7710 (tpp80) REVERT: D 205 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8359 (mt-10) REVERT: D 211 ASP cc_start: 0.8743 (m-30) cc_final: 0.8439 (m-30) REVERT: D 213 LYS cc_start: 0.8721 (ttpt) cc_final: 0.8434 (ttpt) REVERT: D 214 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7751 (mt-10) REVERT: D 238 LYS cc_start: 0.7408 (mttp) cc_final: 0.6974 (mmtp) REVERT: D 240 TYR cc_start: 0.7942 (t80) cc_final: 0.7672 (t80) REVERT: D 259 GLU cc_start: 0.8565 (tp30) cc_final: 0.8154 (tp30) REVERT: D 283 MET cc_start: 0.8471 (mmp) cc_final: 0.8173 (mmp) REVERT: D 286 ASP cc_start: 0.8524 (t0) cc_final: 0.7935 (t0) REVERT: D 288 ASP cc_start: 0.8531 (m-30) cc_final: 0.7837 (m-30) REVERT: D 289 ILE cc_start: 0.8208 (pt) cc_final: 0.7685 (mp) REVERT: D 290 ARG cc_start: 0.8068 (mtt180) cc_final: 0.6792 (mtt90) REVERT: D 294 TYR cc_start: 0.8343 (m-80) cc_final: 0.7611 (m-80) REVERT: D 299 MET cc_start: 0.8222 (mmm) cc_final: 0.7704 (mmm) REVERT: D 303 THR cc_start: 0.7973 (m) cc_final: 0.7641 (p) REVERT: D 312 ARG cc_start: 0.8956 (tpt-90) cc_final: 0.8532 (tpt-90) REVERT: D 314 GLN cc_start: 0.9059 (tt0) cc_final: 0.8841 (mt0) REVERT: D 352 PHE cc_start: 0.8944 (t80) cc_final: 0.8461 (t80) REVERT: D 356 TRP cc_start: 0.6369 (m100) cc_final: 0.6041 (m100) outliers start: 4 outliers final: 0 residues processed: 780 average time/residue: 0.1230 time to fit residues: 134.1693 Evaluate side-chains 719 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 718 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 61 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 78 optimal weight: 0.0970 chunk 8 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 0.0970 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 156 ASN ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 286 HIS A 334 HIS A 406 HIS ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN C 280 ASN C 353 GLN D 12 ASN D 92 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.112991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.087071 restraints weight = 43043.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.090888 restraints weight = 25861.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.093577 restraints weight = 17521.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.095419 restraints weight = 12848.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.096920 restraints weight = 10068.704| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15178 Z= 0.181 Angle : 0.657 6.992 20547 Z= 0.340 Chirality : 0.044 0.203 2251 Planarity : 0.005 0.065 2631 Dihedral : 9.404 164.017 2071 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.13 % Allowed : 1.95 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.20), residues: 1847 helix: 0.87 (0.18), residues: 837 sheet: -1.41 (0.27), residues: 311 loop : 0.08 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 207 TYR 0.030 0.002 TYR A 439 PHE 0.018 0.001 PHE A 750 TRP 0.038 0.002 TRP C 340 HIS 0.006 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00356 (15177) covalent geometry : angle 0.65713 (20547) hydrogen bonds : bond 0.03937 ( 724) hydrogen bonds : angle 5.12655 ( 2007) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 760 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7326 (mm-30) REVERT: A 92 ARG cc_start: 0.7727 (mmm160) cc_final: 0.6982 (mmt-90) REVERT: A 99 ILE cc_start: 0.8006 (pt) cc_final: 0.7639 (pt) REVERT: A 103 CYS cc_start: 0.6191 (t) cc_final: 0.5897 (t) REVERT: A 110 ILE cc_start: 0.7509 (mp) cc_final: 0.7049 (tp) REVERT: A 121 GLU cc_start: 0.8593 (pm20) cc_final: 0.8384 (tm-30) REVERT: A 122 ASP cc_start: 0.9005 (m-30) cc_final: 0.8690 (p0) REVERT: A 138 HIS cc_start: 0.6413 (t-90) cc_final: 0.5430 (t-90) REVERT: A 144 GLU cc_start: 0.8611 (tp30) cc_final: 0.8354 (tt0) REVERT: A 145 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8461 (tm-30) REVERT: A 150 MET cc_start: 0.8101 (ttp) cc_final: 0.6803 (tpp) REVERT: A 174 LYS cc_start: 0.8776 (ptpp) cc_final: 0.8484 (ptpp) REVERT: A 178 ARG cc_start: 0.8094 (ptt90) cc_final: 0.7720 (ppt170) REVERT: A 179 TYR cc_start: 0.8553 (t80) cc_final: 0.8150 (t80) REVERT: A 220 PHE cc_start: 0.7818 (p90) cc_final: 0.7328 (p90) REVERT: A 223 TYR cc_start: 0.8020 (t80) cc_final: 0.7340 (t80) REVERT: A 225 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7373 (mp0) REVERT: A 240 ARG cc_start: 0.7786 (ttm170) cc_final: 0.6998 (ttm170) REVERT: A 242 TYR cc_start: 0.7279 (m-80) cc_final: 0.6620 (m-80) REVERT: A 248 ARG cc_start: 0.8171 (tpm170) cc_final: 0.7897 (tpm170) REVERT: A 255 GLU cc_start: 0.8410 (pm20) cc_final: 0.7763 (pm20) REVERT: A 256 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7384 (mp0) REVERT: A 259 TYR cc_start: 0.7591 (m-80) cc_final: 0.6908 (m-80) REVERT: A 260 HIS cc_start: 0.8322 (m-70) cc_final: 0.8042 (m90) REVERT: A 262 PHE cc_start: 0.8687 (m-80) cc_final: 0.7945 (m-80) REVERT: A 286 HIS cc_start: 0.6809 (t70) cc_final: 0.6431 (t-90) REVERT: A 304 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7928 (mp0) REVERT: A 327 ARG cc_start: 0.8517 (mmt-90) cc_final: 0.8305 (mmt180) REVERT: A 354 HIS cc_start: 0.7596 (t-90) cc_final: 0.7018 (t-90) REVERT: A 370 GLU cc_start: 0.8330 (tt0) cc_final: 0.8036 (tt0) REVERT: A 371 MET cc_start: 0.9079 (mtm) cc_final: 0.8611 (ptm) REVERT: A 373 HIS cc_start: 0.8459 (t70) cc_final: 0.8054 (t70) REVERT: A 400 ARG cc_start: 0.8503 (ptt90) cc_final: 0.8100 (ttp-110) REVERT: A 407 ILE cc_start: 0.8710 (mt) cc_final: 0.8482 (mm) REVERT: A 408 TYR cc_start: 0.8767 (t80) cc_final: 0.7813 (t80) REVERT: A 413 ASN cc_start: 0.8769 (m-40) cc_final: 0.8545 (m-40) REVERT: A 419 VAL cc_start: 0.8824 (m) cc_final: 0.8570 (m) REVERT: A 420 ASN cc_start: 0.8298 (t0) cc_final: 0.8036 (m110) REVERT: A 423 LEU cc_start: 0.7360 (mt) cc_final: 0.6885 (mt) REVERT: A 451 GLN cc_start: 0.8791 (mp10) cc_final: 0.8468 (mp10) REVERT: A 452 PHE cc_start: 0.8421 (t80) cc_final: 0.7892 (t80) REVERT: A 460 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8466 (mmtm) REVERT: A 463 GLN cc_start: 0.8904 (tt0) cc_final: 0.8195 (mm110) REVERT: A 468 HIS cc_start: 0.8210 (t-90) cc_final: 0.7521 (t-90) REVERT: A 475 GLU cc_start: 0.8306 (mp0) cc_final: 0.7899 (mp0) REVERT: A 478 MET cc_start: 0.8834 (mtm) cc_final: 0.8448 (mtm) REVERT: A 493 GLN cc_start: 0.8707 (tp-100) cc_final: 0.8044 (tp40) REVERT: A 498 LEU cc_start: 0.9039 (mp) cc_final: 0.8403 (tt) REVERT: A 505 ILE cc_start: 0.8683 (mt) cc_final: 0.8371 (pt) REVERT: A 509 LEU cc_start: 0.8892 (tp) cc_final: 0.8559 (mt) REVERT: A 511 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8053 (mm-30) REVERT: A 512 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7333 (mm-30) REVERT: A 515 MET cc_start: 0.7050 (ttm) cc_final: 0.6465 (ttm) REVERT: A 520 ASP cc_start: 0.8469 (p0) cc_final: 0.8215 (m-30) REVERT: A 526 LYS cc_start: 0.9004 (tttt) cc_final: 0.8428 (mmmt) REVERT: A 529 ASN cc_start: 0.8576 (m-40) cc_final: 0.8348 (m-40) REVERT: A 532 LEU cc_start: 0.7916 (mt) cc_final: 0.7344 (mt) REVERT: A 534 LYS cc_start: 0.8318 (pttt) cc_final: 0.8097 (pttt) REVERT: A 537 LEU cc_start: 0.9006 (mp) cc_final: 0.8678 (mp) REVERT: A 538 PHE cc_start: 0.8153 (t80) cc_final: 0.7834 (t80) REVERT: A 543 MET cc_start: 0.7552 (mmt) cc_final: 0.7227 (mmm) REVERT: A 545 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.7921 (t0) REVERT: A 555 ASP cc_start: 0.8182 (t0) cc_final: 0.7879 (t0) REVERT: A 556 LYS cc_start: 0.8613 (mttt) cc_final: 0.7773 (mtpp) REVERT: A 558 GLU cc_start: 0.7862 (tt0) cc_final: 0.7489 (tm-30) REVERT: A 559 TYR cc_start: 0.7373 (m-80) cc_final: 0.6742 (m-80) REVERT: A 574 GLU cc_start: 0.8566 (tp30) cc_final: 0.8161 (pm20) REVERT: A 637 HIS cc_start: 0.8407 (t-90) cc_final: 0.7887 (t-90) REVERT: A 638 GLN cc_start: 0.8977 (tt0) cc_final: 0.8683 (pt0) REVERT: A 641 ASN cc_start: 0.9232 (m110) cc_final: 0.8568 (m110) REVERT: A 643 LEU cc_start: 0.8664 (tp) cc_final: 0.7468 (tp) REVERT: A 644 HIS cc_start: 0.8489 (m90) cc_final: 0.8119 (m90) REVERT: A 645 LEU cc_start: 0.9153 (mt) cc_final: 0.8932 (tp) REVERT: A 647 MET cc_start: 0.8541 (mmm) cc_final: 0.7599 (mmm) REVERT: A 648 GLU cc_start: 0.8822 (tp30) cc_final: 0.8398 (tm-30) REVERT: A 650 LEU cc_start: 0.8752 (mm) cc_final: 0.8317 (pp) REVERT: A 656 HIS cc_start: 0.5819 (m-70) cc_final: 0.5475 (m170) REVERT: A 657 TYR cc_start: 0.6497 (m-80) cc_final: 0.5580 (m-80) REVERT: A 688 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7865 (mm-30) REVERT: A 689 THR cc_start: 0.8852 (m) cc_final: 0.8581 (p) REVERT: A 697 PHE cc_start: 0.7776 (m-80) cc_final: 0.7353 (m-80) REVERT: A 700 ARG cc_start: 0.7260 (mtt90) cc_final: 0.6675 (mtm-85) REVERT: A 757 TYR cc_start: 0.8931 (t80) cc_final: 0.8604 (t80) REVERT: B 48 MET cc_start: 0.7002 (mmt) cc_final: 0.6555 (tpp) REVERT: B 54 TYR cc_start: 0.7990 (m-80) cc_final: 0.7288 (m-10) REVERT: B 62 LYS cc_start: 0.8745 (mttm) cc_final: 0.8479 (mttm) REVERT: B 76 ILE cc_start: 0.8512 (pt) cc_final: 0.8252 (pt) REVERT: B 83 MET cc_start: 0.8286 (tpp) cc_final: 0.7692 (tpp) REVERT: B 84 GLU cc_start: 0.8779 (tt0) cc_final: 0.8454 (tm-30) REVERT: B 85 LYS cc_start: 0.9203 (mttm) cc_final: 0.8826 (mttm) REVERT: B 93 ASN cc_start: 0.8063 (m110) cc_final: 0.7698 (m110) REVERT: B 100 GLU cc_start: 0.8443 (mp0) cc_final: 0.8237 (mp0) REVERT: B 106 LEU cc_start: 0.7926 (mt) cc_final: 0.6937 (mt) REVERT: B 114 LYS cc_start: 0.8523 (ptmm) cc_final: 0.7997 (ptmm) REVERT: B 118 GLU cc_start: 0.8105 (mt-10) cc_final: 0.6824 (mm-30) REVERT: B 119 LYS cc_start: 0.8457 (tppt) cc_final: 0.7072 (tppt) REVERT: B 120 MET cc_start: 0.8560 (ttm) cc_final: 0.7883 (tmm) REVERT: B 121 THR cc_start: 0.8623 (p) cc_final: 0.7871 (p) REVERT: B 122 GLN cc_start: 0.8477 (tm-30) cc_final: 0.7944 (tm-30) REVERT: B 123 ILE cc_start: 0.8399 (mt) cc_final: 0.7815 (mt) REVERT: B 124 MET cc_start: 0.8346 (tpp) cc_final: 0.7808 (tpp) REVERT: B 128 PHE cc_start: 0.8038 (m-80) cc_final: 0.7196 (m-10) REVERT: B 133 MET cc_start: 0.7411 (ttp) cc_final: 0.6696 (ttp) REVERT: B 134 TYR cc_start: 0.7317 (t80) cc_final: 0.7037 (t80) REVERT: B 155 ASP cc_start: 0.6784 (t0) cc_final: 0.6225 (t0) REVERT: B 167 TYR cc_start: 0.8050 (t80) cc_final: 0.7501 (t80) REVERT: B 168 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7286 (mm-30) REVERT: B 179 LEU cc_start: 0.6863 (tp) cc_final: 0.6598 (tp) REVERT: B 186 LEU cc_start: 0.8673 (mt) cc_final: 0.8448 (mt) REVERT: B 191 MET cc_start: 0.8486 (ttm) cc_final: 0.8209 (ttm) REVERT: B 192 LYS cc_start: 0.8349 (ptmt) cc_final: 0.8026 (ptmt) REVERT: B 203 THR cc_start: 0.8264 (t) cc_final: 0.8034 (p) REVERT: B 208 GLU cc_start: 0.8083 (pp20) cc_final: 0.7642 (pm20) REVERT: B 209 ILE cc_start: 0.8679 (mm) cc_final: 0.8174 (mm) REVERT: B 211 ARG cc_start: 0.8874 (ptt90) cc_final: 0.8659 (ptm-80) REVERT: B 214 LYS cc_start: 0.9032 (ttpt) cc_final: 0.8605 (ttpt) REVERT: B 215 GLU cc_start: 0.8421 (pp20) cc_final: 0.7032 (pp20) REVERT: B 216 LYS cc_start: 0.8575 (mttt) cc_final: 0.8353 (mmmt) REVERT: B 219 TYR cc_start: 0.7520 (p90) cc_final: 0.7234 (p90) REVERT: B 239 LYS cc_start: 0.8582 (mttt) cc_final: 0.8327 (mmtt) REVERT: B 256 PHE cc_start: 0.8453 (p90) cc_final: 0.8153 (p90) REVERT: B 263 PHE cc_start: 0.8552 (m-80) cc_final: 0.7804 (m-80) REVERT: B 264 GLN cc_start: 0.8508 (mt0) cc_final: 0.7889 (mt0) REVERT: B 267 PHE cc_start: 0.7934 (m-10) cc_final: 0.7672 (m-10) REVERT: B 291 ARG cc_start: 0.7868 (mtt180) cc_final: 0.7571 (mtt180) REVERT: B 292 LYS cc_start: 0.8705 (pttm) cc_final: 0.8374 (pttm) REVERT: B 293 ASP cc_start: 0.8729 (m-30) cc_final: 0.8481 (m-30) REVERT: B 298 ASN cc_start: 0.7095 (m-40) cc_final: 0.6542 (m-40) REVERT: B 300 MET cc_start: 0.7958 (mmm) cc_final: 0.7718 (mmm) REVERT: B 306 MET cc_start: 0.7394 (mmt) cc_final: 0.7149 (mmt) REVERT: B 310 ILE cc_start: 0.8782 (tt) cc_final: 0.8296 (pt) REVERT: B 313 ARG cc_start: 0.8782 (tpt-90) cc_final: 0.8177 (tpp-160) REVERT: B 314 MET cc_start: 0.8391 (tpt) cc_final: 0.7764 (mmm) REVERT: B 316 LYS cc_start: 0.8924 (ptpt) cc_final: 0.8570 (ptpt) REVERT: B 326 MET cc_start: 0.7363 (mmp) cc_final: 0.7080 (mmm) REVERT: B 336 ARG cc_start: 0.8070 (mtt90) cc_final: 0.7814 (mpt180) REVERT: B 338 TYR cc_start: 0.7980 (m-80) cc_final: 0.7333 (m-80) REVERT: B 345 SER cc_start: 0.7473 (t) cc_final: 0.7121 (p) REVERT: B 351 SER cc_start: 0.7972 (t) cc_final: 0.7521 (p) REVERT: B 353 PHE cc_start: 0.8295 (t80) cc_final: 0.7984 (t80) REVERT: B 355 GLN cc_start: 0.8663 (pp30) cc_final: 0.7436 (pp30) REVERT: B 356 MET cc_start: 0.8857 (mtm) cc_final: 0.8115 (mmm) REVERT: B 359 THR cc_start: 0.7502 (p) cc_final: 0.6848 (m) REVERT: B 365 GLU cc_start: 0.8229 (pt0) cc_final: 0.8024 (pp20) REVERT: B 372 HIS cc_start: 0.7841 (m-70) cc_final: 0.7265 (m90) REVERT: C 16 LEU cc_start: 0.7276 (tp) cc_final: 0.6448 (pp) REVERT: C 44 MET cc_start: 0.8552 (ppp) cc_final: 0.8015 (ppp) REVERT: C 61 LYS cc_start: 0.8695 (mmtm) cc_final: 0.8159 (mmtm) REVERT: C 64 ILE cc_start: 0.8592 (mt) cc_final: 0.7960 (tp) REVERT: C 76 ILE cc_start: 0.7356 (mm) cc_final: 0.7098 (mm) REVERT: C 82 MET cc_start: 0.7930 (tpp) cc_final: 0.6930 (tpp) REVERT: C 84 LYS cc_start: 0.9214 (ttmm) cc_final: 0.8968 (ttmm) REVERT: C 87 HIS cc_start: 0.8222 (t70) cc_final: 0.7563 (t-90) REVERT: C 90 PHE cc_start: 0.7691 (m-10) cc_final: 0.7204 (m-80) REVERT: C 91 TYR cc_start: 0.7983 (m-80) cc_final: 0.7560 (m-80) REVERT: C 111 ASN cc_start: 0.8778 (t0) cc_final: 0.8314 (t0) REVERT: C 117 GLU cc_start: 0.8410 (pp20) cc_final: 0.8118 (pp20) REVERT: C 121 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8739 (tm-30) REVERT: C 123 MET cc_start: 0.8219 (tpp) cc_final: 0.7345 (tpp) REVERT: C 127 PHE cc_start: 0.7576 (m-80) cc_final: 0.7059 (m-80) REVERT: C 151 ILE cc_start: 0.8245 (tt) cc_final: 0.7636 (tp) REVERT: C 153 LEU cc_start: 0.8301 (tp) cc_final: 0.7945 (pp) REVERT: C 157 ASP cc_start: 0.7143 (t0) cc_final: 0.6499 (t0) REVERT: C 161 HIS cc_start: 0.6702 (p-80) cc_final: 0.6417 (p-80) REVERT: C 167 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8141 (mm-30) REVERT: C 176 MET cc_start: 0.6923 (mtt) cc_final: 0.6399 (mtt) REVERT: C 183 ARG cc_start: 0.8325 (ttm-80) cc_final: 0.8074 (ttm-80) REVERT: C 187 ASP cc_start: 0.8810 (m-30) cc_final: 0.8564 (m-30) REVERT: C 191 LYS cc_start: 0.9026 (ttpt) cc_final: 0.8729 (mtpp) REVERT: C 205 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7397 (mt-10) REVERT: C 206 ARG cc_start: 0.8138 (ptp-170) cc_final: 0.7575 (ptp-170) REVERT: C 211 ASP cc_start: 0.8523 (m-30) cc_final: 0.7990 (m-30) REVERT: C 215 LYS cc_start: 0.9024 (mmtp) cc_final: 0.8701 (mmmm) REVERT: C 252 ASN cc_start: 0.8087 (p0) cc_final: 0.7699 (p0) REVERT: C 253 GLU cc_start: 0.8324 (mp0) cc_final: 0.7682 (mp0) REVERT: C 256 ARG cc_start: 0.8693 (mtp180) cc_final: 0.7945 (mtp180) REVERT: C 259 GLU cc_start: 0.8820 (tp30) cc_final: 0.7965 (tm-30) REVERT: C 263 GLN cc_start: 0.8108 (mt0) cc_final: 0.7729 (mt0) REVERT: C 276 GLU cc_start: 0.8495 (tp30) cc_final: 0.8216 (mm-30) REVERT: C 282 ILE cc_start: 0.8723 (mt) cc_final: 0.8403 (mt) REVERT: C 283 MET cc_start: 0.8322 (mmm) cc_final: 0.7886 (mmm) REVERT: C 284 LYS cc_start: 0.8746 (mtpt) cc_final: 0.8385 (mtpt) REVERT: C 289 ILE cc_start: 0.8233 (pt) cc_final: 0.7965 (pt) REVERT: C 296 ASN cc_start: 0.7337 (p0) cc_final: 0.6822 (p0) REVERT: C 299 MET cc_start: 0.7924 (mmm) cc_final: 0.6488 (mmm) REVERT: C 313 MET cc_start: 0.8314 (tpp) cc_final: 0.7093 (tpp) REVERT: C 314 GLN cc_start: 0.8514 (tt0) cc_final: 0.8188 (mt0) REVERT: C 316 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7574 (tm-30) REVERT: C 317 ILE cc_start: 0.8887 (mm) cc_final: 0.8048 (mm) REVERT: C 325 MET cc_start: 0.7486 (tpt) cc_final: 0.7226 (tpt) REVERT: C 340 TRP cc_start: 0.6672 (t60) cc_final: 0.6386 (t60) REVERT: C 361 GLU cc_start: 0.8630 (tp30) cc_final: 0.8089 (tp30) REVERT: D 34 ILE cc_start: 0.8280 (mt) cc_final: 0.7635 (tt) REVERT: D 37 ARG cc_start: 0.7953 (tpp80) cc_final: 0.7445 (tpp80) REVERT: D 41 GLN cc_start: 0.8097 (tp40) cc_final: 0.7631 (tm-30) REVERT: D 50 LYS cc_start: 0.7756 (mtmm) cc_final: 0.7496 (mtmm) REVERT: D 52 SER cc_start: 0.7624 (t) cc_final: 0.7023 (m) REVERT: D 68 LYS cc_start: 0.7711 (mmtt) cc_final: 0.7481 (mmtt) REVERT: D 81 ASP cc_start: 0.8304 (m-30) cc_final: 0.7922 (m-30) REVERT: D 87 HIS cc_start: 0.8611 (t-90) cc_final: 0.8064 (t-90) REVERT: D 91 TYR cc_start: 0.8333 (m-80) cc_final: 0.7819 (m-80) REVERT: D 105 LEU cc_start: 0.7773 (mm) cc_final: 0.7110 (mm) REVERT: D 107 GLU cc_start: 0.6820 (pt0) cc_final: 0.5861 (pt0) REVERT: D 111 ASN cc_start: 0.8330 (m-40) cc_final: 0.6571 (m-40) REVERT: D 117 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8063 (mt-10) REVERT: D 119 MET cc_start: 0.8919 (ttm) cc_final: 0.8544 (ttm) REVERT: D 121 GLN cc_start: 0.8589 (pp30) cc_final: 0.8221 (pp30) REVERT: D 124 PHE cc_start: 0.7957 (m-80) cc_final: 0.7274 (m-80) REVERT: D 132 MET cc_start: 0.6825 (mmp) cc_final: 0.6201 (mmp) REVERT: D 137 GLN cc_start: 0.7999 (mt0) cc_final: 0.7633 (mt0) REVERT: D 139 VAL cc_start: 0.8499 (m) cc_final: 0.8082 (p) REVERT: D 165 ILE cc_start: 0.7909 (mt) cc_final: 0.7531 (tt) REVERT: D 167 GLU cc_start: 0.8042 (mp0) cc_final: 0.7833 (mp0) REVERT: D 176 MET cc_start: 0.7079 (mmm) cc_final: 0.6797 (mmm) REVERT: D 187 ASP cc_start: 0.8776 (m-30) cc_final: 0.8494 (m-30) REVERT: D 191 LYS cc_start: 0.9028 (ttpt) cc_final: 0.8775 (ttpt) REVERT: D 196 ARG cc_start: 0.8063 (tpp80) cc_final: 0.7845 (tpp80) REVERT: D 207 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7224 (mm-30) REVERT: D 211 ASP cc_start: 0.8690 (m-30) cc_final: 0.7790 (m-30) REVERT: D 213 LYS cc_start: 0.8684 (ttpt) cc_final: 0.8411 (ttpt) REVERT: D 214 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7821 (mt-10) REVERT: D 240 TYR cc_start: 0.7994 (t80) cc_final: 0.7720 (t80) REVERT: D 259 GLU cc_start: 0.8472 (tp30) cc_final: 0.8095 (tp30) REVERT: D 283 MET cc_start: 0.8375 (mmp) cc_final: 0.8150 (mmp) REVERT: D 286 ASP cc_start: 0.8526 (t0) cc_final: 0.8032 (t0) REVERT: D 287 ILE cc_start: 0.8468 (tp) cc_final: 0.8175 (tt) REVERT: D 288 ASP cc_start: 0.8382 (m-30) cc_final: 0.7773 (m-30) REVERT: D 289 ILE cc_start: 0.8089 (pt) cc_final: 0.7636 (mt) REVERT: D 290 ARG cc_start: 0.8024 (mtt180) cc_final: 0.6956 (mtt180) REVERT: D 294 TYR cc_start: 0.8236 (m-80) cc_final: 0.7641 (m-80) REVERT: D 297 ASN cc_start: 0.8167 (m-40) cc_final: 0.7864 (m-40) REVERT: D 299 MET cc_start: 0.8157 (mmm) cc_final: 0.7860 (mmm) REVERT: D 312 ARG cc_start: 0.8961 (tpt-90) cc_final: 0.7709 (tpt-90) REVERT: D 313 MET cc_start: 0.8485 (tpp) cc_final: 0.8130 (tpp) REVERT: D 314 GLN cc_start: 0.9056 (tt0) cc_final: 0.8764 (mt0) REVERT: D 316 GLU cc_start: 0.8827 (mm-30) cc_final: 0.7943 (mm-30) REVERT: D 325 MET cc_start: 0.7031 (tpt) cc_final: 0.6811 (tpt) REVERT: D 328 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8147 (mmtt) REVERT: D 352 PHE cc_start: 0.8869 (t80) cc_final: 0.8412 (t80) outliers start: 2 outliers final: 0 residues processed: 760 average time/residue: 0.1203 time to fit residues: 127.2876 Evaluate side-chains 709 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 708 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 141 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 139 optimal weight: 0.0980 chunk 62 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 156 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 ASN B 162 HIS B 174 HIS ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN C 280 ASN C 353 GLN C 371 HIS ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.113981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.088089 restraints weight = 42491.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.091843 restraints weight = 25510.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.094491 restraints weight = 17291.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.096462 restraints weight = 12698.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.097911 restraints weight = 9854.804| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.6711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15178 Z= 0.130 Angle : 0.633 8.447 20547 Z= 0.321 Chirality : 0.044 0.185 2251 Planarity : 0.005 0.077 2631 Dihedral : 9.112 164.944 2071 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.06 % Allowed : 1.63 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.20), residues: 1847 helix: 0.97 (0.18), residues: 832 sheet: -1.29 (0.27), residues: 309 loop : 0.14 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 256 TYR 0.044 0.002 TYR C 294 PHE 0.016 0.001 PHE D 255 TRP 0.024 0.002 TRP C 340 HIS 0.009 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00271 (15177) covalent geometry : angle 0.63278 (20547) hydrogen bonds : bond 0.03730 ( 724) hydrogen bonds : angle 4.98941 ( 2007) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 771 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7236 (mm-30) REVERT: A 79 TYR cc_start: 0.7720 (m-80) cc_final: 0.7413 (m-80) REVERT: A 92 ARG cc_start: 0.7768 (mmm160) cc_final: 0.7199 (mmm-85) REVERT: A 103 CYS cc_start: 0.6283 (t) cc_final: 0.5881 (t) REVERT: A 127 TYR cc_start: 0.8185 (m-10) cc_final: 0.7846 (m-80) REVERT: A 128 SER cc_start: 0.8834 (m) cc_final: 0.8599 (p) REVERT: A 138 HIS cc_start: 0.6047 (t-90) cc_final: 0.5549 (t-90) REVERT: A 144 GLU cc_start: 0.8585 (tp30) cc_final: 0.8362 (tt0) REVERT: A 149 GLN cc_start: 0.8757 (mm110) cc_final: 0.8372 (mm-40) REVERT: A 150 MET cc_start: 0.8328 (ttp) cc_final: 0.6643 (tpt) REVERT: A 174 LYS cc_start: 0.8797 (ptpp) cc_final: 0.8451 (ptpp) REVERT: A 177 MET cc_start: 0.8359 (mtp) cc_final: 0.8081 (mtp) REVERT: A 178 ARG cc_start: 0.8069 (ptt90) cc_final: 0.7739 (ppt170) REVERT: A 179 TYR cc_start: 0.8475 (t80) cc_final: 0.8095 (t80) REVERT: A 180 PHE cc_start: 0.8598 (m-80) cc_final: 0.8217 (m-80) REVERT: A 219 ARG cc_start: 0.6898 (mmm160) cc_final: 0.5729 (mmm160) REVERT: A 220 PHE cc_start: 0.7696 (p90) cc_final: 0.7238 (p90) REVERT: A 223 TYR cc_start: 0.7998 (t80) cc_final: 0.7114 (t80) REVERT: A 225 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7489 (mp0) REVERT: A 239 MET cc_start: 0.6785 (mmp) cc_final: 0.6477 (mmp) REVERT: A 240 ARG cc_start: 0.7722 (ttm170) cc_final: 0.6670 (ttm170) REVERT: A 242 TYR cc_start: 0.7158 (m-80) cc_final: 0.6481 (m-80) REVERT: A 248 ARG cc_start: 0.8222 (tpm170) cc_final: 0.7987 (tpm170) REVERT: A 259 TYR cc_start: 0.7578 (m-80) cc_final: 0.6870 (m-80) REVERT: A 260 HIS cc_start: 0.8283 (m-70) cc_final: 0.7964 (m-70) REVERT: A 262 PHE cc_start: 0.8480 (m-80) cc_final: 0.7830 (m-80) REVERT: A 286 HIS cc_start: 0.6775 (t70) cc_final: 0.6385 (t-90) REVERT: A 305 MET cc_start: 0.8277 (mmm) cc_final: 0.7964 (mmp) REVERT: A 307 HIS cc_start: 0.8704 (m90) cc_final: 0.8407 (m90) REVERT: A 309 ARG cc_start: 0.8836 (pmt-80) cc_final: 0.8204 (ttp80) REVERT: A 327 ARG cc_start: 0.8503 (mmt-90) cc_final: 0.8235 (mmt180) REVERT: A 354 HIS cc_start: 0.7584 (t-90) cc_final: 0.6775 (t-90) REVERT: A 364 MET cc_start: 0.7696 (mtt) cc_final: 0.7328 (mtt) REVERT: A 371 MET cc_start: 0.9031 (mtm) cc_final: 0.8592 (ptm) REVERT: A 373 HIS cc_start: 0.8453 (t70) cc_final: 0.8039 (t70) REVERT: A 400 ARG cc_start: 0.8599 (ptt90) cc_final: 0.8056 (ttp-110) REVERT: A 408 TYR cc_start: 0.8703 (t80) cc_final: 0.7718 (t80) REVERT: A 413 ASN cc_start: 0.8733 (m-40) cc_final: 0.8503 (m-40) REVERT: A 419 VAL cc_start: 0.8793 (m) cc_final: 0.8559 (m) REVERT: A 420 ASN cc_start: 0.8271 (t0) cc_final: 0.8028 (m110) REVERT: A 423 LEU cc_start: 0.7464 (mt) cc_final: 0.7012 (mt) REVERT: A 433 ILE cc_start: 0.8339 (tp) cc_final: 0.7120 (tp) REVERT: A 451 GLN cc_start: 0.8670 (mp10) cc_final: 0.8215 (mp10) REVERT: A 452 PHE cc_start: 0.8428 (t80) cc_final: 0.7800 (t80) REVERT: A 468 HIS cc_start: 0.8147 (t-90) cc_final: 0.7424 (t-90) REVERT: A 478 MET cc_start: 0.8807 (mtm) cc_final: 0.8365 (mtm) REVERT: A 498 LEU cc_start: 0.9014 (mp) cc_final: 0.8378 (tt) REVERT: A 505 ILE cc_start: 0.8641 (mt) cc_final: 0.8385 (pt) REVERT: A 509 LEU cc_start: 0.8895 (tp) cc_final: 0.8595 (mt) REVERT: A 512 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7205 (tp30) REVERT: A 515 MET cc_start: 0.6941 (ttm) cc_final: 0.6427 (ttm) REVERT: A 520 ASP cc_start: 0.8506 (p0) cc_final: 0.8202 (m-30) REVERT: A 522 THR cc_start: 0.8882 (m) cc_final: 0.8396 (m) REVERT: A 526 LYS cc_start: 0.9012 (tttt) cc_final: 0.8319 (mmmt) REVERT: A 529 ASN cc_start: 0.8448 (m-40) cc_final: 0.8050 (m-40) REVERT: A 532 LEU cc_start: 0.7939 (mt) cc_final: 0.7353 (mt) REVERT: A 534 LYS cc_start: 0.8293 (pttt) cc_final: 0.8033 (pttt) REVERT: A 537 LEU cc_start: 0.8970 (mp) cc_final: 0.8665 (mp) REVERT: A 538 PHE cc_start: 0.8131 (t80) cc_final: 0.7740 (t80) REVERT: A 543 MET cc_start: 0.7529 (mmt) cc_final: 0.7326 (mmt) REVERT: A 545 ASN cc_start: 0.8254 (t0) cc_final: 0.7706 (t0) REVERT: A 546 LYS cc_start: 0.7614 (mptt) cc_final: 0.7409 (mmtm) REVERT: A 555 ASP cc_start: 0.8113 (t0) cc_final: 0.7803 (t0) REVERT: A 556 LYS cc_start: 0.8609 (mttt) cc_final: 0.7779 (mtpp) REVERT: A 558 GLU cc_start: 0.7786 (tt0) cc_final: 0.7447 (tm-30) REVERT: A 559 TYR cc_start: 0.7277 (m-80) cc_final: 0.6738 (m-80) REVERT: A 574 GLU cc_start: 0.8607 (tp30) cc_final: 0.8334 (pm20) REVERT: A 637 HIS cc_start: 0.8065 (t-90) cc_final: 0.7511 (t-90) REVERT: A 640 ARG cc_start: 0.9083 (ptm160) cc_final: 0.8529 (ptm160) REVERT: A 641 ASN cc_start: 0.9068 (m110) cc_final: 0.8589 (m-40) REVERT: A 643 LEU cc_start: 0.8648 (tp) cc_final: 0.7645 (tp) REVERT: A 644 HIS cc_start: 0.8539 (m90) cc_final: 0.8118 (m90) REVERT: A 647 MET cc_start: 0.8589 (mmm) cc_final: 0.7783 (mmm) REVERT: A 648 GLU cc_start: 0.8776 (tp30) cc_final: 0.8272 (tm-30) REVERT: A 649 THR cc_start: 0.9072 (p) cc_final: 0.8605 (p) REVERT: A 650 LEU cc_start: 0.8654 (mm) cc_final: 0.8266 (pp) REVERT: A 657 TYR cc_start: 0.6414 (m-80) cc_final: 0.5500 (m-80) REVERT: A 682 ARG cc_start: 0.8889 (ptt-90) cc_final: 0.8683 (ptt90) REVERT: A 688 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7919 (mm-30) REVERT: A 689 THR cc_start: 0.8982 (m) cc_final: 0.8777 (p) REVERT: A 757 TYR cc_start: 0.8953 (t80) cc_final: 0.8600 (t80) REVERT: B 48 MET cc_start: 0.7147 (mmt) cc_final: 0.6760 (tpp) REVERT: B 54 TYR cc_start: 0.7926 (m-80) cc_final: 0.7604 (m-10) REVERT: B 62 LYS cc_start: 0.8672 (mttm) cc_final: 0.8360 (mttm) REVERT: B 83 MET cc_start: 0.8302 (tpp) cc_final: 0.7786 (tpp) REVERT: B 84 GLU cc_start: 0.8766 (tt0) cc_final: 0.8340 (tm-30) REVERT: B 85 LYS cc_start: 0.9202 (mttm) cc_final: 0.8868 (mttm) REVERT: B 102 HIS cc_start: 0.7912 (m90) cc_final: 0.7602 (m90) REVERT: B 106 LEU cc_start: 0.7881 (mt) cc_final: 0.7658 (mt) REVERT: B 114 LYS cc_start: 0.8499 (ptmm) cc_final: 0.7932 (ptmm) REVERT: B 118 GLU cc_start: 0.8093 (mt-10) cc_final: 0.6827 (mm-30) REVERT: B 120 MET cc_start: 0.8577 (ttm) cc_final: 0.7915 (tmm) REVERT: B 123 ILE cc_start: 0.8440 (mt) cc_final: 0.8210 (mt) REVERT: B 124 MET cc_start: 0.8303 (tpp) cc_final: 0.7652 (tpp) REVERT: B 128 PHE cc_start: 0.7935 (m-80) cc_final: 0.7048 (m-10) REVERT: B 133 MET cc_start: 0.7480 (ttp) cc_final: 0.6834 (ttp) REVERT: B 134 TYR cc_start: 0.7256 (t80) cc_final: 0.7044 (t80) REVERT: B 155 ASP cc_start: 0.6745 (t0) cc_final: 0.6241 (t0) REVERT: B 168 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7702 (tp30) REVERT: B 179 LEU cc_start: 0.6859 (tp) cc_final: 0.6617 (tp) REVERT: B 191 MET cc_start: 0.8442 (ttm) cc_final: 0.8185 (ttm) REVERT: B 192 LYS cc_start: 0.8306 (ptmt) cc_final: 0.7975 (ptmt) REVERT: B 208 GLU cc_start: 0.7932 (pp20) cc_final: 0.7457 (pm20) REVERT: B 209 ILE cc_start: 0.8629 (mm) cc_final: 0.8189 (mm) REVERT: B 214 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8583 (ttpt) REVERT: B 215 GLU cc_start: 0.8367 (pp20) cc_final: 0.7924 (pp20) REVERT: B 219 TYR cc_start: 0.7548 (p90) cc_final: 0.7293 (p90) REVERT: B 226 ASN cc_start: 0.8471 (t0) cc_final: 0.8211 (t0) REVERT: B 239 LYS cc_start: 0.8556 (mttt) cc_final: 0.8306 (mmtt) REVERT: B 256 PHE cc_start: 0.8425 (p90) cc_final: 0.8181 (p90) REVERT: B 260 GLU cc_start: 0.8352 (tp30) cc_final: 0.8036 (tp30) REVERT: B 263 PHE cc_start: 0.8552 (m-80) cc_final: 0.7767 (m-80) REVERT: B 264 GLN cc_start: 0.8357 (mt0) cc_final: 0.7607 (mt0) REVERT: B 267 PHE cc_start: 0.7896 (m-10) cc_final: 0.7487 (m-10) REVERT: B 277 GLU cc_start: 0.8415 (tp30) cc_final: 0.8132 (tp30) REVERT: B 292 LYS cc_start: 0.8648 (pttm) cc_final: 0.8292 (pttm) REVERT: B 293 ASP cc_start: 0.8739 (m-30) cc_final: 0.8484 (m-30) REVERT: B 298 ASN cc_start: 0.6957 (m-40) cc_final: 0.6531 (m-40) REVERT: B 306 MET cc_start: 0.7362 (mmt) cc_final: 0.7131 (mmt) REVERT: B 310 ILE cc_start: 0.8771 (tt) cc_final: 0.8110 (mm) REVERT: B 313 ARG cc_start: 0.8830 (tpt-90) cc_final: 0.8201 (tpp-160) REVERT: B 314 MET cc_start: 0.8359 (tpt) cc_final: 0.7805 (mmp) REVERT: B 316 LYS cc_start: 0.8959 (ptpt) cc_final: 0.8606 (ptpt) REVERT: B 326 MET cc_start: 0.7356 (mmp) cc_final: 0.7124 (mmm) REVERT: B 335 GLU cc_start: 0.7976 (mm-30) cc_final: 0.6743 (mm-30) REVERT: B 338 TYR cc_start: 0.7948 (m-80) cc_final: 0.7166 (m-80) REVERT: B 351 SER cc_start: 0.8010 (t) cc_final: 0.7661 (p) REVERT: B 353 PHE cc_start: 0.8186 (t80) cc_final: 0.7937 (t80) REVERT: B 355 GLN cc_start: 0.8712 (pp30) cc_final: 0.7803 (pp30) REVERT: B 356 MET cc_start: 0.8850 (mtm) cc_final: 0.8153 (mmm) REVERT: B 359 THR cc_start: 0.7486 (p) cc_final: 0.6676 (m) REVERT: B 362 GLU cc_start: 0.8593 (mt-10) cc_final: 0.7964 (tm-30) REVERT: B 365 GLU cc_start: 0.8276 (pt0) cc_final: 0.8046 (pp20) REVERT: B 370 ILE cc_start: 0.8446 (tp) cc_final: 0.7646 (tp) REVERT: B 372 HIS cc_start: 0.7836 (m-70) cc_final: 0.7330 (m-70) REVERT: C 44 MET cc_start: 0.8526 (ppp) cc_final: 0.7814 (ppp) REVERT: C 50 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8396 (mtmt) REVERT: C 51 ASP cc_start: 0.8505 (p0) cc_final: 0.7852 (p0) REVERT: C 57 GLU cc_start: 0.8179 (pm20) cc_final: 0.7907 (pm20) REVERT: C 61 LYS cc_start: 0.8775 (mmtm) cc_final: 0.8310 (mmtm) REVERT: C 64 ILE cc_start: 0.8712 (mt) cc_final: 0.8494 (tp) REVERT: C 71 ILE cc_start: 0.7320 (mm) cc_final: 0.6934 (tp) REVERT: C 75 ILE cc_start: 0.8092 (pt) cc_final: 0.7818 (mp) REVERT: C 82 MET cc_start: 0.7861 (tpp) cc_final: 0.6931 (tpp) REVERT: C 84 LYS cc_start: 0.9139 (ttmm) cc_final: 0.8719 (ttmm) REVERT: C 87 HIS cc_start: 0.8219 (t70) cc_final: 0.7577 (t-90) REVERT: C 90 PHE cc_start: 0.7773 (m-10) cc_final: 0.7253 (m-80) REVERT: C 91 TYR cc_start: 0.8018 (m-80) cc_final: 0.7550 (m-80) REVERT: C 107 GLU cc_start: 0.7381 (pm20) cc_final: 0.7082 (pm20) REVERT: C 111 ASN cc_start: 0.8725 (t0) cc_final: 0.8202 (t0) REVERT: C 113 LYS cc_start: 0.8711 (mttp) cc_final: 0.8253 (mttp) REVERT: C 116 ARG cc_start: 0.8456 (ttm110) cc_final: 0.8134 (ttm170) REVERT: C 117 GLU cc_start: 0.8397 (pp20) cc_final: 0.8137 (pp20) REVERT: C 119 MET cc_start: 0.8287 (ttm) cc_final: 0.8008 (ttm) REVERT: C 121 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8632 (tm-30) REVERT: C 123 MET cc_start: 0.8103 (tpp) cc_final: 0.7209 (tpp) REVERT: C 127 PHE cc_start: 0.7578 (m-80) cc_final: 0.7365 (m-80) REVERT: C 140 LEU cc_start: 0.8765 (mt) cc_final: 0.8554 (mt) REVERT: C 142 LEU cc_start: 0.8534 (tp) cc_final: 0.8268 (tp) REVERT: C 157 ASP cc_start: 0.7138 (t0) cc_final: 0.6665 (t0) REVERT: C 161 HIS cc_start: 0.6565 (p-80) cc_final: 0.6355 (p-80) REVERT: C 176 MET cc_start: 0.6892 (mtt) cc_final: 0.6386 (mtt) REVERT: C 177 ARG cc_start: 0.8077 (tpp80) cc_final: 0.7732 (tpp80) REVERT: C 183 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.8037 (ttm-80) REVERT: C 187 ASP cc_start: 0.8802 (m-30) cc_final: 0.8545 (m-30) REVERT: C 191 LYS cc_start: 0.8991 (ttpt) cc_final: 0.8720 (mtpp) REVERT: C 205 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7400 (mt-10) REVERT: C 206 ARG cc_start: 0.8116 (ptp-170) cc_final: 0.7648 (ptp-170) REVERT: C 211 ASP cc_start: 0.8456 (m-30) cc_final: 0.7903 (m-30) REVERT: C 248 ILE cc_start: 0.8816 (pt) cc_final: 0.8605 (tt) REVERT: C 254 ARG cc_start: 0.7688 (mtp-110) cc_final: 0.7202 (mtp85) REVERT: C 259 GLU cc_start: 0.8837 (tp30) cc_final: 0.8145 (tp30) REVERT: C 262 PHE cc_start: 0.8582 (m-10) cc_final: 0.8201 (m-10) REVERT: C 263 GLN cc_start: 0.8109 (mt0) cc_final: 0.7829 (mt0) REVERT: C 276 GLU cc_start: 0.8500 (tp30) cc_final: 0.7587 (tp30) REVERT: C 280 ASN cc_start: 0.8705 (m110) cc_final: 0.7812 (m-40) REVERT: C 283 MET cc_start: 0.8341 (mmm) cc_final: 0.7975 (mmm) REVERT: C 284 LYS cc_start: 0.8732 (mtpt) cc_final: 0.8358 (mtpt) REVERT: C 286 ASP cc_start: 0.8359 (t70) cc_final: 0.7628 (p0) REVERT: C 289 ILE cc_start: 0.8120 (pt) cc_final: 0.7698 (pt) REVERT: C 294 TYR cc_start: 0.7680 (m-80) cc_final: 0.7240 (m-80) REVERT: C 296 ASN cc_start: 0.7440 (p0) cc_final: 0.6852 (p0) REVERT: C 299 MET cc_start: 0.7872 (mmm) cc_final: 0.7408 (mmm) REVERT: C 313 MET cc_start: 0.8267 (tpp) cc_final: 0.7134 (tpp) REVERT: C 314 GLN cc_start: 0.8476 (tt0) cc_final: 0.7964 (mt0) REVERT: C 316 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7543 (tm-30) REVERT: C 317 ILE cc_start: 0.8847 (mm) cc_final: 0.8381 (mm) REVERT: C 325 MET cc_start: 0.7429 (tpt) cc_final: 0.7186 (tpt) REVERT: C 327 ILE cc_start: 0.8561 (mm) cc_final: 0.8307 (pt) REVERT: C 329 ILE cc_start: 0.8610 (mm) cc_final: 0.8014 (mm) REVERT: C 334 GLU cc_start: 0.8887 (pm20) cc_final: 0.8559 (pm20) REVERT: C 361 GLU cc_start: 0.8608 (tp30) cc_final: 0.8103 (tp30) REVERT: C 371 HIS cc_start: 0.7246 (m90) cc_final: 0.6290 (m-70) REVERT: D 37 ARG cc_start: 0.7945 (tpp80) cc_final: 0.7486 (tpp80) REVERT: D 41 GLN cc_start: 0.8172 (tp40) cc_final: 0.7815 (tm-30) REVERT: D 50 LYS cc_start: 0.7845 (mtmm) cc_final: 0.7520 (mtmm) REVERT: D 52 SER cc_start: 0.7724 (t) cc_final: 0.7152 (m) REVERT: D 62 ARG cc_start: 0.8179 (mtt90) cc_final: 0.7797 (mtm-85) REVERT: D 64 ILE cc_start: 0.8083 (tp) cc_final: 0.7259 (tp) REVERT: D 65 LEU cc_start: 0.8522 (mt) cc_final: 0.8257 (mt) REVERT: D 81 ASP cc_start: 0.8300 (m-30) cc_final: 0.7918 (m-30) REVERT: D 87 HIS cc_start: 0.8556 (t-90) cc_final: 0.7991 (t-90) REVERT: D 91 TYR cc_start: 0.8322 (m-80) cc_final: 0.7784 (m-80) REVERT: D 92 ASN cc_start: 0.7722 (m110) cc_final: 0.7521 (m110) REVERT: D 94 LEU cc_start: 0.8033 (mt) cc_final: 0.7801 (mt) REVERT: D 105 LEU cc_start: 0.7792 (mm) cc_final: 0.7141 (mm) REVERT: D 111 ASN cc_start: 0.8378 (m-40) cc_final: 0.7922 (m-40) REVERT: D 116 ARG cc_start: 0.8377 (mtt-85) cc_final: 0.8054 (mtt-85) REVERT: D 117 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7934 (mt-10) REVERT: D 119 MET cc_start: 0.8913 (ttm) cc_final: 0.8490 (ttm) REVERT: D 121 GLN cc_start: 0.8703 (pp30) cc_final: 0.8349 (pp30) REVERT: D 124 PHE cc_start: 0.7920 (m-80) cc_final: 0.7235 (m-80) REVERT: D 132 MET cc_start: 0.6854 (mmp) cc_final: 0.6158 (mmp) REVERT: D 139 VAL cc_start: 0.8482 (m) cc_final: 0.8087 (p) REVERT: D 165 ILE cc_start: 0.7994 (mt) cc_final: 0.7596 (tt) REVERT: D 175 ILE cc_start: 0.8523 (pt) cc_final: 0.7932 (pt) REVERT: D 176 MET cc_start: 0.7142 (mmm) cc_final: 0.6881 (mmm) REVERT: D 187 ASP cc_start: 0.8844 (m-30) cc_final: 0.8480 (m-30) REVERT: D 191 LYS cc_start: 0.8949 (ttpt) cc_final: 0.8551 (ttpt) REVERT: D 196 ARG cc_start: 0.7987 (tpp80) cc_final: 0.7778 (tpp80) REVERT: D 210 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7682 (ttp80) REVERT: D 211 ASP cc_start: 0.8390 (m-30) cc_final: 0.8188 (m-30) REVERT: D 213 LYS cc_start: 0.8719 (ttpt) cc_final: 0.8484 (ttpt) REVERT: D 214 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7781 (mt-10) REVERT: D 224 GLU cc_start: 0.8688 (pp20) cc_final: 0.8353 (pp20) REVERT: D 240 TYR cc_start: 0.7853 (t80) cc_final: 0.7604 (t80) REVERT: D 259 GLU cc_start: 0.8374 (tp30) cc_final: 0.8034 (tp30) REVERT: D 266 PHE cc_start: 0.8015 (m-10) cc_final: 0.7492 (m-10) REVERT: D 279 TYR cc_start: 0.7875 (t80) cc_final: 0.7304 (t80) REVERT: D 283 MET cc_start: 0.8444 (mmp) cc_final: 0.8237 (mmp) REVERT: D 286 ASP cc_start: 0.8512 (t0) cc_final: 0.8060 (t0) REVERT: D 287 ILE cc_start: 0.8352 (tp) cc_final: 0.8040 (tt) REVERT: D 288 ASP cc_start: 0.8334 (m-30) cc_final: 0.7793 (m-30) REVERT: D 289 ILE cc_start: 0.8051 (pt) cc_final: 0.7502 (mm) REVERT: D 290 ARG cc_start: 0.7939 (mtt180) cc_final: 0.6927 (mtt180) REVERT: D 294 TYR cc_start: 0.8259 (m-80) cc_final: 0.7688 (m-80) REVERT: D 297 ASN cc_start: 0.8286 (m-40) cc_final: 0.7959 (m-40) REVERT: D 299 MET cc_start: 0.8093 (mmm) cc_final: 0.7879 (mmm) REVERT: D 312 ARG cc_start: 0.8935 (tpt-90) cc_final: 0.7842 (tpt-90) REVERT: D 316 GLU cc_start: 0.8827 (mm-30) cc_final: 0.7959 (mm-30) REVERT: D 320 LEU cc_start: 0.8866 (mt) cc_final: 0.8443 (mt) REVERT: D 325 MET cc_start: 0.7265 (tpt) cc_final: 0.7064 (tpt) REVERT: D 361 GLU cc_start: 0.8744 (mp0) cc_final: 0.8269 (pm20) outliers start: 1 outliers final: 0 residues processed: 771 average time/residue: 0.1186 time to fit residues: 127.0666 Evaluate side-chains 718 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 718 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 115 optimal weight: 6.9990 chunk 57 optimal weight: 0.0870 chunk 152 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 149 GLN A 418 HIS ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 128 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.112983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.087413 restraints weight = 42671.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.091123 restraints weight = 25623.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.093752 restraints weight = 17355.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.095651 restraints weight = 12692.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.097062 restraints weight = 9874.351| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15178 Z= 0.144 Angle : 0.645 8.586 20547 Z= 0.329 Chirality : 0.044 0.204 2251 Planarity : 0.005 0.065 2631 Dihedral : 9.057 166.816 2071 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.20), residues: 1847 helix: 1.01 (0.18), residues: 833 sheet: -1.25 (0.27), residues: 313 loop : 0.10 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 256 TYR 0.026 0.001 TYR C 294 PHE 0.023 0.001 PHE C 124 TRP 0.021 0.002 TRP B 80 HIS 0.009 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00297 (15177) covalent geometry : angle 0.64489 (20547) hydrogen bonds : bond 0.03710 ( 724) hydrogen bonds : angle 4.99460 ( 2007) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 745 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7272 (mm-30) REVERT: A 79 TYR cc_start: 0.7711 (m-80) cc_final: 0.7404 (m-80) REVERT: A 92 ARG cc_start: 0.7863 (mmm160) cc_final: 0.7295 (mmm-85) REVERT: A 103 CYS cc_start: 0.6264 (t) cc_final: 0.5842 (t) REVERT: A 121 GLU cc_start: 0.8282 (tp30) cc_final: 0.7999 (tm-30) REVERT: A 127 TYR cc_start: 0.8199 (m-10) cc_final: 0.7826 (m-80) REVERT: A 128 SER cc_start: 0.8836 (m) cc_final: 0.8561 (p) REVERT: A 138 HIS cc_start: 0.5891 (t-170) cc_final: 0.5541 (t-90) REVERT: A 144 GLU cc_start: 0.8578 (tp30) cc_final: 0.8345 (tt0) REVERT: A 149 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8695 (pp30) REVERT: A 150 MET cc_start: 0.7697 (ttp) cc_final: 0.7421 (tpt) REVERT: A 156 ASN cc_start: 0.7110 (p0) cc_final: 0.6523 (t0) REVERT: A 177 MET cc_start: 0.8403 (mtp) cc_final: 0.8150 (mtp) REVERT: A 178 ARG cc_start: 0.8134 (ptt90) cc_final: 0.7719 (ppt170) REVERT: A 179 TYR cc_start: 0.8481 (t80) cc_final: 0.8011 (t80) REVERT: A 180 PHE cc_start: 0.8618 (m-80) cc_final: 0.8235 (m-80) REVERT: A 219 ARG cc_start: 0.6989 (mmm160) cc_final: 0.5846 (mmm160) REVERT: A 220 PHE cc_start: 0.7696 (p90) cc_final: 0.7177 (p90) REVERT: A 223 TYR cc_start: 0.7989 (t80) cc_final: 0.7099 (t80) REVERT: A 224 ILE cc_start: 0.8785 (pt) cc_final: 0.8278 (pt) REVERT: A 225 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7407 (mp0) REVERT: A 239 MET cc_start: 0.6822 (mmp) cc_final: 0.6448 (mmp) REVERT: A 240 ARG cc_start: 0.7750 (ttm170) cc_final: 0.6668 (ttm170) REVERT: A 242 TYR cc_start: 0.7136 (m-80) cc_final: 0.6562 (m-80) REVERT: A 248 ARG cc_start: 0.8228 (tpm170) cc_final: 0.7948 (tpm170) REVERT: A 259 TYR cc_start: 0.7702 (m-80) cc_final: 0.6873 (m-80) REVERT: A 260 HIS cc_start: 0.8240 (m-70) cc_final: 0.7918 (m-70) REVERT: A 262 PHE cc_start: 0.8555 (m-80) cc_final: 0.7895 (m-80) REVERT: A 286 HIS cc_start: 0.6845 (t70) cc_final: 0.6475 (t70) REVERT: A 307 HIS cc_start: 0.8780 (m90) cc_final: 0.8518 (m90) REVERT: A 309 ARG cc_start: 0.8801 (pmt-80) cc_final: 0.8281 (ttp80) REVERT: A 327 ARG cc_start: 0.8489 (mmt-90) cc_final: 0.8233 (mmt180) REVERT: A 371 MET cc_start: 0.9034 (mtm) cc_final: 0.8543 (ptm) REVERT: A 373 HIS cc_start: 0.8459 (t70) cc_final: 0.8049 (t70) REVERT: A 400 ARG cc_start: 0.8604 (ptt90) cc_final: 0.8059 (ttp-110) REVERT: A 408 TYR cc_start: 0.8704 (t80) cc_final: 0.7732 (t80) REVERT: A 413 ASN cc_start: 0.8693 (m-40) cc_final: 0.8470 (m-40) REVERT: A 420 ASN cc_start: 0.8278 (t0) cc_final: 0.8051 (m110) REVERT: A 423 LEU cc_start: 0.7412 (mt) cc_final: 0.6885 (mt) REVERT: A 433 ILE cc_start: 0.7809 (tp) cc_final: 0.7538 (tp) REVERT: A 451 GLN cc_start: 0.8692 (mp10) cc_final: 0.8350 (mp10) REVERT: A 452 PHE cc_start: 0.8408 (t80) cc_final: 0.7898 (t80) REVERT: A 453 CYS cc_start: 0.8727 (p) cc_final: 0.8519 (p) REVERT: A 460 LYS cc_start: 0.8948 (tptp) cc_final: 0.8689 (tppt) REVERT: A 468 HIS cc_start: 0.8127 (t-90) cc_final: 0.7868 (t-90) REVERT: A 473 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8191 (mm-30) REVERT: A 478 MET cc_start: 0.8819 (mtm) cc_final: 0.8420 (mtm) REVERT: A 498 LEU cc_start: 0.9031 (mp) cc_final: 0.8361 (tt) REVERT: A 512 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7493 (tp30) REVERT: A 520 ASP cc_start: 0.8497 (p0) cc_final: 0.8279 (m-30) REVERT: A 522 THR cc_start: 0.8836 (m) cc_final: 0.8262 (p) REVERT: A 526 LYS cc_start: 0.8979 (tttt) cc_final: 0.8297 (mmmt) REVERT: A 529 ASN cc_start: 0.8471 (m-40) cc_final: 0.8078 (m-40) REVERT: A 532 LEU cc_start: 0.7914 (mt) cc_final: 0.7329 (mt) REVERT: A 534 LYS cc_start: 0.8286 (pttt) cc_final: 0.8048 (pttt) REVERT: A 537 LEU cc_start: 0.8980 (mp) cc_final: 0.8682 (mp) REVERT: A 538 PHE cc_start: 0.8141 (t80) cc_final: 0.7739 (t80) REVERT: A 545 ASN cc_start: 0.8264 (t0) cc_final: 0.7737 (t0) REVERT: A 546 LYS cc_start: 0.7626 (mptt) cc_final: 0.7423 (mmtm) REVERT: A 555 ASP cc_start: 0.8113 (t0) cc_final: 0.7809 (t0) REVERT: A 556 LYS cc_start: 0.8615 (mttt) cc_final: 0.7778 (mtpp) REVERT: A 558 GLU cc_start: 0.7757 (tt0) cc_final: 0.7475 (tm-30) REVERT: A 559 TYR cc_start: 0.7283 (m-80) cc_final: 0.6650 (m-80) REVERT: A 569 LYS cc_start: 0.8254 (tptp) cc_final: 0.7898 (tptp) REVERT: A 579 VAL cc_start: 0.9019 (m) cc_final: 0.8818 (t) REVERT: A 633 LYS cc_start: 0.6446 (mmtt) cc_final: 0.6189 (mmtp) REVERT: A 637 HIS cc_start: 0.8219 (t-90) cc_final: 0.7641 (t-90) REVERT: A 640 ARG cc_start: 0.9138 (ptm160) cc_final: 0.8923 (ptm160) REVERT: A 641 ASN cc_start: 0.9047 (m110) cc_final: 0.8559 (m-40) REVERT: A 643 LEU cc_start: 0.8771 (tp) cc_final: 0.7751 (tp) REVERT: A 647 MET cc_start: 0.8381 (mmm) cc_final: 0.7819 (mmm) REVERT: A 648 GLU cc_start: 0.8732 (tp30) cc_final: 0.8223 (tm-30) REVERT: A 649 THR cc_start: 0.9061 (p) cc_final: 0.8530 (p) REVERT: A 650 LEU cc_start: 0.8662 (mm) cc_final: 0.8223 (pp) REVERT: A 651 ASN cc_start: 0.8701 (t0) cc_final: 0.8484 (m-40) REVERT: A 657 TYR cc_start: 0.6283 (m-80) cc_final: 0.5298 (m-80) REVERT: A 688 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8001 (tp30) REVERT: A 689 THR cc_start: 0.8975 (m) cc_final: 0.8757 (p) REVERT: A 757 TYR cc_start: 0.8968 (t80) cc_final: 0.8601 (t80) REVERT: B 48 MET cc_start: 0.7183 (mmt) cc_final: 0.6827 (tpp) REVERT: B 54 TYR cc_start: 0.7954 (m-80) cc_final: 0.7526 (m-10) REVERT: B 58 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7882 (pt0) REVERT: B 82 ASP cc_start: 0.8527 (m-30) cc_final: 0.8164 (m-30) REVERT: B 83 MET cc_start: 0.8308 (tpp) cc_final: 0.7830 (tpp) REVERT: B 84 GLU cc_start: 0.8788 (tt0) cc_final: 0.8336 (tm-30) REVERT: B 85 LYS cc_start: 0.9204 (mttm) cc_final: 0.8890 (mttm) REVERT: B 100 GLU cc_start: 0.8452 (mp0) cc_final: 0.8166 (mp0) REVERT: B 102 HIS cc_start: 0.7852 (m90) cc_final: 0.7586 (m90) REVERT: B 111 LEU cc_start: 0.8297 (mt) cc_final: 0.8042 (mt) REVERT: B 114 LYS cc_start: 0.8509 (ptmm) cc_final: 0.7991 (ptmm) REVERT: B 118 GLU cc_start: 0.8180 (mt-10) cc_final: 0.6863 (mm-30) REVERT: B 120 MET cc_start: 0.8433 (ttm) cc_final: 0.7785 (tmm) REVERT: B 121 THR cc_start: 0.8637 (p) cc_final: 0.7941 (p) REVERT: B 123 ILE cc_start: 0.8398 (mt) cc_final: 0.8176 (mt) REVERT: B 124 MET cc_start: 0.8302 (tpp) cc_final: 0.7654 (tpp) REVERT: B 128 PHE cc_start: 0.8013 (m-80) cc_final: 0.7154 (m-10) REVERT: B 133 MET cc_start: 0.7519 (ttp) cc_final: 0.6756 (ttp) REVERT: B 134 TYR cc_start: 0.7246 (t80) cc_final: 0.6948 (t80) REVERT: B 155 ASP cc_start: 0.6794 (t0) cc_final: 0.6501 (t0) REVERT: B 176 ILE cc_start: 0.8077 (mt) cc_final: 0.7873 (tp) REVERT: B 184 ARG cc_start: 0.8334 (ttm170) cc_final: 0.7942 (ttm110) REVERT: B 186 LEU cc_start: 0.8704 (mt) cc_final: 0.8487 (mt) REVERT: B 191 MET cc_start: 0.8447 (ttm) cc_final: 0.8186 (ttm) REVERT: B 192 LYS cc_start: 0.8352 (ptmt) cc_final: 0.8022 (ptmt) REVERT: B 207 ARG cc_start: 0.8577 (mtt90) cc_final: 0.8253 (mtt-85) REVERT: B 209 ILE cc_start: 0.8647 (mm) cc_final: 0.8030 (mm) REVERT: B 211 ARG cc_start: 0.8918 (tmm160) cc_final: 0.8506 (ptm-80) REVERT: B 214 LYS cc_start: 0.9022 (ttpt) cc_final: 0.8598 (ttpt) REVERT: B 215 GLU cc_start: 0.8405 (pp20) cc_final: 0.7902 (pp20) REVERT: B 219 TYR cc_start: 0.7620 (p90) cc_final: 0.7346 (p90) REVERT: B 226 ASN cc_start: 0.8524 (t0) cc_final: 0.8052 (t0) REVERT: B 230 THR cc_start: 0.8424 (m) cc_final: 0.8055 (p) REVERT: B 239 LYS cc_start: 0.8565 (mttt) cc_final: 0.8349 (mmtt) REVERT: B 256 PHE cc_start: 0.8419 (p90) cc_final: 0.8175 (p90) REVERT: B 260 GLU cc_start: 0.8398 (tp30) cc_final: 0.8048 (tp30) REVERT: B 263 PHE cc_start: 0.8619 (m-80) cc_final: 0.7745 (m-80) REVERT: B 264 GLN cc_start: 0.8364 (mt0) cc_final: 0.7518 (mt0) REVERT: B 267 PHE cc_start: 0.8033 (m-10) cc_final: 0.7608 (m-10) REVERT: B 277 GLU cc_start: 0.8325 (tp30) cc_final: 0.8073 (tp30) REVERT: B 280 TYR cc_start: 0.8105 (t80) cc_final: 0.7883 (t80) REVERT: B 287 ASP cc_start: 0.7960 (t70) cc_final: 0.7658 (t70) REVERT: B 292 LYS cc_start: 0.8600 (pttm) cc_final: 0.8261 (pttm) REVERT: B 298 ASN cc_start: 0.7078 (m-40) cc_final: 0.6518 (m-40) REVERT: B 300 MET cc_start: 0.8129 (mmm) cc_final: 0.7800 (mmm) REVERT: B 306 MET cc_start: 0.7391 (mmt) cc_final: 0.7151 (mmt) REVERT: B 310 ILE cc_start: 0.8804 (tt) cc_final: 0.8119 (mm) REVERT: B 313 ARG cc_start: 0.8838 (tpt-90) cc_final: 0.6950 (tpp-160) REVERT: B 314 MET cc_start: 0.8427 (tpt) cc_final: 0.7860 (mmp) REVERT: B 316 LYS cc_start: 0.8970 (ptpt) cc_final: 0.8006 (ptpt) REVERT: B 317 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7665 (mm-30) REVERT: B 335 GLU cc_start: 0.7923 (mm-30) cc_final: 0.6953 (mm-30) REVERT: B 338 TYR cc_start: 0.8053 (m-80) cc_final: 0.7295 (m-80) REVERT: B 351 SER cc_start: 0.7756 (t) cc_final: 0.7192 (p) REVERT: B 353 PHE cc_start: 0.8264 (t80) cc_final: 0.7851 (t80) REVERT: B 355 GLN cc_start: 0.8677 (pp30) cc_final: 0.7879 (pp30) REVERT: B 356 MET cc_start: 0.8833 (mtm) cc_final: 0.8145 (mmm) REVERT: B 357 TRP cc_start: 0.7109 (m-10) cc_final: 0.6873 (m-10) REVERT: B 359 THR cc_start: 0.7553 (p) cc_final: 0.7270 (m) REVERT: B 360 LYS cc_start: 0.8303 (tptp) cc_final: 0.7450 (tptp) REVERT: B 362 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8162 (tm-30) REVERT: B 370 ILE cc_start: 0.8462 (tp) cc_final: 0.7702 (tp) REVERT: B 372 HIS cc_start: 0.7960 (m-70) cc_final: 0.7373 (m90) REVERT: C 50 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8528 (mtmt) REVERT: C 54 VAL cc_start: 0.7276 (t) cc_final: 0.6981 (t) REVERT: C 61 LYS cc_start: 0.8737 (mmtm) cc_final: 0.8285 (mmtm) REVERT: C 64 ILE cc_start: 0.8681 (mt) cc_final: 0.8413 (tp) REVERT: C 76 ILE cc_start: 0.7458 (mm) cc_final: 0.6746 (tp) REVERT: C 82 MET cc_start: 0.7862 (tpp) cc_final: 0.6970 (tpp) REVERT: C 84 LYS cc_start: 0.9106 (ttmm) cc_final: 0.8679 (ttmm) REVERT: C 87 HIS cc_start: 0.8225 (t70) cc_final: 0.7529 (t-90) REVERT: C 90 PHE cc_start: 0.7817 (m-10) cc_final: 0.7275 (m-80) REVERT: C 91 TYR cc_start: 0.8019 (m-80) cc_final: 0.7530 (m-80) REVERT: C 105 LEU cc_start: 0.8134 (mm) cc_final: 0.7706 (mm) REVERT: C 111 ASN cc_start: 0.8726 (t0) cc_final: 0.8179 (t0) REVERT: C 113 LYS cc_start: 0.8633 (mttp) cc_final: 0.8146 (mttp) REVERT: C 116 ARG cc_start: 0.8461 (ttm110) cc_final: 0.8165 (ttm170) REVERT: C 117 GLU cc_start: 0.8434 (pp20) cc_final: 0.8148 (pp20) REVERT: C 119 MET cc_start: 0.8326 (ttm) cc_final: 0.7994 (ttm) REVERT: C 121 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8485 (tm-30) REVERT: C 123 MET cc_start: 0.8189 (tpp) cc_final: 0.7328 (tpp) REVERT: C 127 PHE cc_start: 0.7977 (m-80) cc_final: 0.7336 (m-80) REVERT: C 140 LEU cc_start: 0.8826 (mt) cc_final: 0.8614 (mt) REVERT: C 151 ILE cc_start: 0.8060 (tt) cc_final: 0.7534 (tp) REVERT: C 153 LEU cc_start: 0.8263 (tp) cc_final: 0.8037 (tp) REVERT: C 157 ASP cc_start: 0.7088 (t0) cc_final: 0.6878 (t0) REVERT: C 161 HIS cc_start: 0.6439 (p-80) cc_final: 0.6217 (p-80) REVERT: C 176 MET cc_start: 0.6892 (mtt) cc_final: 0.6408 (mtt) REVERT: C 187 ASP cc_start: 0.8787 (m-30) cc_final: 0.8581 (m-30) REVERT: C 205 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7467 (mt-10) REVERT: C 211 ASP cc_start: 0.8425 (m-30) cc_final: 0.7920 (m-30) REVERT: C 212 ILE cc_start: 0.8776 (mt) cc_final: 0.8421 (mm) REVERT: C 240 TYR cc_start: 0.8090 (t80) cc_final: 0.7692 (t80) REVERT: C 242 LEU cc_start: 0.8311 (mp) cc_final: 0.8110 (mp) REVERT: C 252 ASN cc_start: 0.8450 (p0) cc_final: 0.8156 (p0) REVERT: C 254 ARG cc_start: 0.7666 (mtp-110) cc_final: 0.7347 (mtm-85) REVERT: C 255 PHE cc_start: 0.8988 (p90) cc_final: 0.8763 (p90) REVERT: C 259 GLU cc_start: 0.8835 (tp30) cc_final: 0.8222 (tp30) REVERT: C 262 PHE cc_start: 0.8629 (m-10) cc_final: 0.8297 (m-10) REVERT: C 263 GLN cc_start: 0.8105 (mt0) cc_final: 0.7819 (mt0) REVERT: C 276 GLU cc_start: 0.8488 (tp30) cc_final: 0.7491 (tp30) REVERT: C 280 ASN cc_start: 0.8691 (m110) cc_final: 0.7835 (m-40) REVERT: C 282 ILE cc_start: 0.8690 (mt) cc_final: 0.8407 (pt) REVERT: C 283 MET cc_start: 0.8299 (mmm) cc_final: 0.7849 (mmm) REVERT: C 284 LYS cc_start: 0.8759 (mtpt) cc_final: 0.8345 (mtpt) REVERT: C 286 ASP cc_start: 0.8384 (t70) cc_final: 0.7633 (p0) REVERT: C 289 ILE cc_start: 0.8150 (pt) cc_final: 0.7743 (pt) REVERT: C 294 TYR cc_start: 0.7730 (m-80) cc_final: 0.7476 (m-80) REVERT: C 296 ASN cc_start: 0.7448 (p0) cc_final: 0.6993 (p0) REVERT: C 299 MET cc_start: 0.7825 (mmm) cc_final: 0.7542 (mmm) REVERT: C 305 MET cc_start: 0.6796 (mmm) cc_final: 0.6408 (mmm) REVERT: C 313 MET cc_start: 0.8275 (tpp) cc_final: 0.7084 (tpp) REVERT: C 314 GLN cc_start: 0.8474 (tt0) cc_final: 0.8137 (mt0) REVERT: C 317 ILE cc_start: 0.8856 (mm) cc_final: 0.8281 (mm) REVERT: C 334 GLU cc_start: 0.8941 (pm20) cc_final: 0.8634 (pm20) REVERT: C 361 GLU cc_start: 0.8621 (tp30) cc_final: 0.8195 (tm-30) REVERT: C 371 HIS cc_start: 0.7394 (m90) cc_final: 0.6573 (m-70) REVERT: D 24 ASP cc_start: 0.6603 (t0) cc_final: 0.6243 (t0) REVERT: D 33 SER cc_start: 0.8079 (p) cc_final: 0.7820 (p) REVERT: D 34 ILE cc_start: 0.8188 (mt) cc_final: 0.7662 (tt) REVERT: D 37 ARG cc_start: 0.7902 (tpp80) cc_final: 0.7606 (tpp80) REVERT: D 41 GLN cc_start: 0.8067 (tp40) cc_final: 0.7678 (tm-30) REVERT: D 50 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7459 (mtmm) REVERT: D 67 LEU cc_start: 0.7970 (mt) cc_final: 0.7658 (mt) REVERT: D 81 ASP cc_start: 0.8256 (m-30) cc_final: 0.8023 (m-30) REVERT: D 82 MET cc_start: 0.8251 (mmp) cc_final: 0.7741 (mmp) REVERT: D 84 LYS cc_start: 0.8692 (mmtp) cc_final: 0.8400 (mmtt) REVERT: D 87 HIS cc_start: 0.8558 (t-90) cc_final: 0.8011 (t-90) REVERT: D 91 TYR cc_start: 0.8331 (m-80) cc_final: 0.7765 (m-80) REVERT: D 92 ASN cc_start: 0.7755 (m110) cc_final: 0.7551 (m110) REVERT: D 94 LEU cc_start: 0.8024 (mt) cc_final: 0.7808 (mt) REVERT: D 99 GLU cc_start: 0.7207 (mp0) cc_final: 0.6967 (mp0) REVERT: D 105 LEU cc_start: 0.7870 (mm) cc_final: 0.7440 (mm) REVERT: D 111 ASN cc_start: 0.8357 (m-40) cc_final: 0.7906 (m-40) REVERT: D 116 ARG cc_start: 0.8375 (mtt-85) cc_final: 0.8002 (mtt-85) REVERT: D 117 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7876 (mt-10) REVERT: D 119 MET cc_start: 0.8952 (ttm) cc_final: 0.8557 (ttm) REVERT: D 121 GLN cc_start: 0.8666 (pp30) cc_final: 0.8271 (pp30) REVERT: D 124 PHE cc_start: 0.7902 (m-80) cc_final: 0.7247 (m-80) REVERT: D 139 VAL cc_start: 0.8498 (m) cc_final: 0.8113 (p) REVERT: D 165 ILE cc_start: 0.8029 (mt) cc_final: 0.7669 (tt) REVERT: D 175 ILE cc_start: 0.8512 (pt) cc_final: 0.7921 (pt) REVERT: D 176 MET cc_start: 0.7111 (mmm) cc_final: 0.6823 (mmm) REVERT: D 187 ASP cc_start: 0.8769 (m-30) cc_final: 0.8454 (m-30) REVERT: D 191 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8559 (ttpt) REVERT: D 195 GLU cc_start: 0.6611 (mp0) cc_final: 0.6248 (mp0) REVERT: D 196 ARG cc_start: 0.7852 (tpp80) cc_final: 0.7629 (tpp80) REVERT: D 210 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7473 (ttp80) REVERT: D 213 LYS cc_start: 0.8711 (ttpt) cc_final: 0.8458 (ttpt) REVERT: D 215 LYS cc_start: 0.9009 (mmpt) cc_final: 0.8781 (mmmt) REVERT: D 240 TYR cc_start: 0.7819 (t80) cc_final: 0.7597 (t80) REVERT: D 242 LEU cc_start: 0.7799 (mt) cc_final: 0.7596 (mt) REVERT: D 243 PRO cc_start: 0.8420 (Cg_exo) cc_final: 0.7436 (Cg_endo) REVERT: D 259 GLU cc_start: 0.8365 (tp30) cc_final: 0.8032 (tp30) REVERT: D 279 TYR cc_start: 0.7948 (t80) cc_final: 0.7355 (t80) REVERT: D 283 MET cc_start: 0.8467 (mmp) cc_final: 0.8182 (mmp) REVERT: D 286 ASP cc_start: 0.8508 (t0) cc_final: 0.7923 (t0) REVERT: D 287 ILE cc_start: 0.8337 (tp) cc_final: 0.7960 (tt) REVERT: D 288 ASP cc_start: 0.8318 (m-30) cc_final: 0.7785 (m-30) REVERT: D 289 ILE cc_start: 0.8070 (pt) cc_final: 0.7506 (mm) REVERT: D 290 ARG cc_start: 0.7978 (mtt180) cc_final: 0.6869 (mtt90) REVERT: D 293 LEU cc_start: 0.8991 (mt) cc_final: 0.8631 (mt) REVERT: D 294 TYR cc_start: 0.8292 (m-80) cc_final: 0.7713 (m-80) REVERT: D 297 ASN cc_start: 0.8171 (m-40) cc_final: 0.7871 (m-40) REVERT: D 299 MET cc_start: 0.8091 (mmm) cc_final: 0.7874 (mmm) REVERT: D 305 MET cc_start: 0.6976 (mmp) cc_final: 0.6492 (mmt) REVERT: D 312 ARG cc_start: 0.8915 (tpt-90) cc_final: 0.7878 (tpt-90) REVERT: D 314 GLN cc_start: 0.9028 (mt0) cc_final: 0.8548 (mm-40) REVERT: D 316 GLU cc_start: 0.8835 (mm-30) cc_final: 0.7975 (mm-30) REVERT: D 320 LEU cc_start: 0.8842 (mt) cc_final: 0.8439 (mt) REVERT: D 328 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8345 (mmtt) REVERT: D 346 LEU cc_start: 0.8294 (tp) cc_final: 0.7950 (tp) REVERT: D 352 PHE cc_start: 0.8825 (t80) cc_final: 0.8515 (t80) REVERT: D 361 GLU cc_start: 0.8783 (mp0) cc_final: 0.8266 (pm20) REVERT: D 371 HIS cc_start: 0.7669 (p90) cc_final: 0.7418 (p90) outliers start: 0 outliers final: 0 residues processed: 745 average time/residue: 0.1490 time to fit residues: 153.7960 Evaluate side-chains 704 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 704 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 135 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 16 optimal weight: 0.0870 chunk 70 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 418 HIS A 638 GLN ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN C 128 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.111290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.085935 restraints weight = 42770.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.089588 restraints weight = 25550.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.092201 restraints weight = 17252.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.094071 restraints weight = 12588.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.095456 restraints weight = 9778.044| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.7388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15178 Z= 0.166 Angle : 0.666 7.585 20547 Z= 0.341 Chirality : 0.044 0.220 2251 Planarity : 0.005 0.064 2631 Dihedral : 9.090 169.907 2071 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.06 % Allowed : 1.13 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.20), residues: 1847 helix: 0.87 (0.18), residues: 833 sheet: -1.20 (0.27), residues: 312 loop : -0.01 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 39 TYR 0.023 0.002 TYR C 294 PHE 0.018 0.001 PHE C 124 TRP 0.024 0.002 TRP B 80 HIS 0.006 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00338 (15177) covalent geometry : angle 0.66557 (20547) hydrogen bonds : bond 0.03866 ( 724) hydrogen bonds : angle 5.09386 ( 2007) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 766 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7318 (mm-30) REVERT: A 79 TYR cc_start: 0.7813 (m-80) cc_final: 0.7465 (m-80) REVERT: A 127 TYR cc_start: 0.8243 (m-10) cc_final: 0.7822 (m-80) REVERT: A 138 HIS cc_start: 0.5979 (t-170) cc_final: 0.5425 (t-90) REVERT: A 144 GLU cc_start: 0.8570 (tp30) cc_final: 0.8352 (tt0) REVERT: A 149 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8653 (pp30) REVERT: A 150 MET cc_start: 0.7806 (ttp) cc_final: 0.7478 (tpt) REVERT: A 156 ASN cc_start: 0.7081 (p0) cc_final: 0.6584 (t0) REVERT: A 175 TYR cc_start: 0.8082 (m-10) cc_final: 0.7561 (m-10) REVERT: A 177 MET cc_start: 0.8427 (mtp) cc_final: 0.8189 (mtp) REVERT: A 178 ARG cc_start: 0.8147 (ptt90) cc_final: 0.7862 (ppt90) REVERT: A 179 TYR cc_start: 0.8432 (t80) cc_final: 0.8008 (t80) REVERT: A 180 PHE cc_start: 0.8617 (m-80) cc_final: 0.8243 (m-80) REVERT: A 204 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8008 (mm-30) REVERT: A 210 LYS cc_start: 0.7290 (tttm) cc_final: 0.6909 (tmmt) REVERT: A 219 ARG cc_start: 0.7048 (mmm160) cc_final: 0.5782 (mmm160) REVERT: A 220 PHE cc_start: 0.7585 (p90) cc_final: 0.7079 (p90) REVERT: A 223 TYR cc_start: 0.7965 (t80) cc_final: 0.7234 (t80) REVERT: A 224 ILE cc_start: 0.8926 (pt) cc_final: 0.8505 (pt) REVERT: A 225 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7531 (mp0) REVERT: A 233 ARG cc_start: 0.8314 (mmm160) cc_final: 0.7888 (mmm160) REVERT: A 240 ARG cc_start: 0.7739 (ttm170) cc_final: 0.6635 (ttm170) REVERT: A 242 TYR cc_start: 0.7230 (m-80) cc_final: 0.6707 (m-80) REVERT: A 260 HIS cc_start: 0.8039 (m-70) cc_final: 0.7692 (m-70) REVERT: A 262 PHE cc_start: 0.8568 (m-80) cc_final: 0.8029 (m-80) REVERT: A 286 HIS cc_start: 0.6954 (t70) cc_final: 0.6679 (t70) REVERT: A 307 HIS cc_start: 0.8825 (m90) cc_final: 0.8575 (m90) REVERT: A 309 ARG cc_start: 0.8789 (pmt-80) cc_final: 0.7854 (ttp80) REVERT: A 317 ILE cc_start: 0.8602 (mm) cc_final: 0.8264 (mm) REVERT: A 327 ARG cc_start: 0.8473 (mmt-90) cc_final: 0.8178 (mmt180) REVERT: A 364 MET cc_start: 0.7892 (mtt) cc_final: 0.7594 (mtt) REVERT: A 371 MET cc_start: 0.9095 (mtm) cc_final: 0.8589 (ptm) REVERT: A 373 HIS cc_start: 0.8443 (t70) cc_final: 0.8032 (t70) REVERT: A 400 ARG cc_start: 0.8576 (ptt90) cc_final: 0.8020 (ttp-110) REVERT: A 408 TYR cc_start: 0.8705 (t80) cc_final: 0.7994 (t80) REVERT: A 413 ASN cc_start: 0.8676 (m-40) cc_final: 0.8449 (m-40) REVERT: A 423 LEU cc_start: 0.7522 (mt) cc_final: 0.7013 (mt) REVERT: A 451 GLN cc_start: 0.8784 (mp10) cc_final: 0.8478 (mp10) REVERT: A 452 PHE cc_start: 0.8541 (t80) cc_final: 0.7960 (t80) REVERT: A 453 CYS cc_start: 0.8742 (p) cc_final: 0.8529 (p) REVERT: A 463 GLN cc_start: 0.8732 (tt0) cc_final: 0.8148 (mm-40) REVERT: A 468 HIS cc_start: 0.8380 (t-90) cc_final: 0.7824 (t-90) REVERT: A 470 PHE cc_start: 0.8211 (m-80) cc_final: 0.7900 (m-80) REVERT: A 475 GLU cc_start: 0.8190 (mp0) cc_final: 0.7936 (mp0) REVERT: A 478 MET cc_start: 0.8829 (mtm) cc_final: 0.8454 (mtm) REVERT: A 493 GLN cc_start: 0.8771 (tp40) cc_final: 0.8087 (tp40) REVERT: A 498 LEU cc_start: 0.9057 (mp) cc_final: 0.8382 (tt) REVERT: A 509 LEU cc_start: 0.8881 (tp) cc_final: 0.8519 (mt) REVERT: A 512 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7243 (tp30) REVERT: A 515 MET cc_start: 0.7285 (ttt) cc_final: 0.6710 (tpt) REVERT: A 520 ASP cc_start: 0.8511 (p0) cc_final: 0.8291 (m-30) REVERT: A 522 THR cc_start: 0.8819 (m) cc_final: 0.8584 (m) REVERT: A 526 LYS cc_start: 0.8955 (tttt) cc_final: 0.8346 (mmmt) REVERT: A 532 LEU cc_start: 0.7914 (mt) cc_final: 0.7293 (mt) REVERT: A 534 LYS cc_start: 0.8294 (pttt) cc_final: 0.8023 (pttt) REVERT: A 537 LEU cc_start: 0.9006 (mp) cc_final: 0.8723 (mp) REVERT: A 538 PHE cc_start: 0.8106 (t80) cc_final: 0.7445 (t80) REVERT: A 545 ASN cc_start: 0.8268 (t0) cc_final: 0.7886 (t0) REVERT: A 555 ASP cc_start: 0.8096 (t0) cc_final: 0.7776 (t0) REVERT: A 556 LYS cc_start: 0.8626 (mttt) cc_final: 0.7775 (mtpp) REVERT: A 558 GLU cc_start: 0.7832 (tt0) cc_final: 0.7505 (tm-30) REVERT: A 559 TYR cc_start: 0.7235 (m-80) cc_final: 0.6733 (m-80) REVERT: A 585 PHE cc_start: 0.7786 (t80) cc_final: 0.6808 (t80) REVERT: A 587 MET cc_start: 0.8590 (mmp) cc_final: 0.8270 (mpp) REVERT: A 633 LYS cc_start: 0.6846 (mmtt) cc_final: 0.6545 (mmtm) REVERT: A 637 HIS cc_start: 0.8300 (t-90) cc_final: 0.7765 (t-90) REVERT: A 641 ASN cc_start: 0.9102 (m110) cc_final: 0.8598 (m-40) REVERT: A 643 LEU cc_start: 0.8752 (tp) cc_final: 0.7721 (tp) REVERT: A 647 MET cc_start: 0.8475 (mmm) cc_final: 0.7899 (mmm) REVERT: A 648 GLU cc_start: 0.8746 (tp30) cc_final: 0.8267 (tm-30) REVERT: A 649 THR cc_start: 0.9064 (p) cc_final: 0.8521 (p) REVERT: A 650 LEU cc_start: 0.8750 (mm) cc_final: 0.8276 (pp) REVERT: A 657 TYR cc_start: 0.6409 (m-80) cc_final: 0.5810 (m-80) REVERT: A 666 PHE cc_start: 0.8407 (m-10) cc_final: 0.8058 (m-10) REVERT: A 750 PHE cc_start: 0.8937 (m-10) cc_final: 0.8652 (m-10) REVERT: A 757 TYR cc_start: 0.8953 (t80) cc_final: 0.8574 (t80) REVERT: B 10 VAL cc_start: 0.8379 (p) cc_final: 0.8025 (p) REVERT: B 32 PHE cc_start: 0.7871 (p90) cc_final: 0.7616 (p90) REVERT: B 54 TYR cc_start: 0.8095 (m-80) cc_final: 0.7326 (m-10) REVERT: B 58 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8061 (pt0) REVERT: B 62 LYS cc_start: 0.8779 (mmtp) cc_final: 0.8188 (mmtp) REVERT: B 82 ASP cc_start: 0.8521 (m-30) cc_final: 0.8220 (m-30) REVERT: B 83 MET cc_start: 0.8353 (tpp) cc_final: 0.7820 (tpp) REVERT: B 84 GLU cc_start: 0.8779 (tt0) cc_final: 0.8332 (tm-30) REVERT: B 85 LYS cc_start: 0.9220 (mttm) cc_final: 0.8889 (mttm) REVERT: B 100 GLU cc_start: 0.8499 (mp0) cc_final: 0.8252 (mp0) REVERT: B 102 HIS cc_start: 0.7906 (m90) cc_final: 0.7606 (m90) REVERT: B 111 LEU cc_start: 0.8220 (mt) cc_final: 0.8003 (mt) REVERT: B 114 LYS cc_start: 0.8564 (ptmm) cc_final: 0.8025 (ptmm) REVERT: B 118 GLU cc_start: 0.8180 (mt-10) cc_final: 0.6991 (mm-30) REVERT: B 120 MET cc_start: 0.8565 (ttm) cc_final: 0.7985 (tmm) REVERT: B 121 THR cc_start: 0.8588 (p) cc_final: 0.7941 (p) REVERT: B 122 GLN cc_start: 0.8405 (pp30) cc_final: 0.8205 (pp30) REVERT: B 123 ILE cc_start: 0.8467 (mt) cc_final: 0.8099 (mt) REVERT: B 124 MET cc_start: 0.8315 (tpp) cc_final: 0.7580 (tpp) REVERT: B 128 PHE cc_start: 0.8135 (m-80) cc_final: 0.7222 (m-80) REVERT: B 133 MET cc_start: 0.7577 (ttp) cc_final: 0.6999 (ttp) REVERT: B 134 TYR cc_start: 0.7197 (t80) cc_final: 0.6980 (t80) REVERT: B 155 ASP cc_start: 0.6872 (t0) cc_final: 0.6501 (t0) REVERT: B 168 GLU cc_start: 0.8192 (tp30) cc_final: 0.7922 (tp30) REVERT: B 184 ARG cc_start: 0.8291 (ttm170) cc_final: 0.7907 (ttm110) REVERT: B 186 LEU cc_start: 0.8776 (mt) cc_final: 0.8556 (mt) REVERT: B 191 MET cc_start: 0.8437 (ttm) cc_final: 0.8162 (ttm) REVERT: B 192 LYS cc_start: 0.8427 (ptmt) cc_final: 0.8050 (ptmt) REVERT: B 207 ARG cc_start: 0.8564 (mtt90) cc_final: 0.8163 (mtt-85) REVERT: B 208 GLU cc_start: 0.7755 (pp20) cc_final: 0.7515 (pm20) REVERT: B 209 ILE cc_start: 0.8689 (mm) cc_final: 0.8295 (mm) REVERT: B 214 LYS cc_start: 0.9009 (ttpt) cc_final: 0.8622 (ttpt) REVERT: B 219 TYR cc_start: 0.7675 (p90) cc_final: 0.7423 (p90) REVERT: B 226 ASN cc_start: 0.8571 (t0) cc_final: 0.8122 (t0) REVERT: B 230 THR cc_start: 0.8442 (m) cc_final: 0.8124 (p) REVERT: B 239 LYS cc_start: 0.8584 (mttt) cc_final: 0.8349 (mmtt) REVERT: B 256 PHE cc_start: 0.8421 (p90) cc_final: 0.8209 (p90) REVERT: B 260 GLU cc_start: 0.8366 (tp30) cc_final: 0.8047 (tp30) REVERT: B 263 PHE cc_start: 0.8603 (m-80) cc_final: 0.7862 (m-80) REVERT: B 264 GLN cc_start: 0.8454 (mt0) cc_final: 0.7657 (mt0) REVERT: B 267 PHE cc_start: 0.8012 (m-10) cc_final: 0.7631 (m-10) REVERT: B 268 ILE cc_start: 0.8410 (tp) cc_final: 0.8137 (tp) REVERT: B 277 GLU cc_start: 0.8347 (tp30) cc_final: 0.8057 (tp30) REVERT: B 280 TYR cc_start: 0.8055 (t80) cc_final: 0.7425 (t80) REVERT: B 283 ILE cc_start: 0.8607 (tp) cc_final: 0.8394 (pt) REVERT: B 284 MET cc_start: 0.8111 (mmp) cc_final: 0.7780 (mmm) REVERT: B 287 ASP cc_start: 0.7997 (t70) cc_final: 0.7764 (t70) REVERT: B 293 ASP cc_start: 0.8563 (m-30) cc_final: 0.8322 (m-30) REVERT: B 298 ASN cc_start: 0.6952 (m-40) cc_final: 0.6465 (m-40) REVERT: B 300 MET cc_start: 0.8127 (mmm) cc_final: 0.7757 (mmm) REVERT: B 306 MET cc_start: 0.7388 (mmt) cc_final: 0.7178 (mmt) REVERT: B 310 ILE cc_start: 0.8819 (tt) cc_final: 0.8101 (mm) REVERT: B 313 ARG cc_start: 0.8846 (tpt-90) cc_final: 0.8372 (tpp-160) REVERT: B 314 MET cc_start: 0.8445 (tpt) cc_final: 0.7823 (mmm) REVERT: B 316 LYS cc_start: 0.8964 (ptpt) cc_final: 0.8599 (ptpt) REVERT: B 325 THR cc_start: 0.8701 (t) cc_final: 0.8453 (p) REVERT: B 326 MET cc_start: 0.7519 (mmm) cc_final: 0.7313 (mmm) REVERT: B 335 GLU cc_start: 0.8044 (mm-30) cc_final: 0.6656 (mm-30) REVERT: B 338 TYR cc_start: 0.8083 (m-80) cc_final: 0.7298 (m-80) REVERT: B 355 GLN cc_start: 0.8656 (pp30) cc_final: 0.7917 (pp30) REVERT: B 356 MET cc_start: 0.8851 (mtm) cc_final: 0.8004 (mmm) REVERT: B 359 THR cc_start: 0.7654 (p) cc_final: 0.6520 (m) REVERT: B 360 LYS cc_start: 0.8260 (tptp) cc_final: 0.7432 (tptp) REVERT: B 362 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8192 (mt-10) REVERT: B 372 HIS cc_start: 0.7962 (m-70) cc_final: 0.7328 (m90) REVERT: C 44 MET cc_start: 0.8464 (ppp) cc_final: 0.7814 (ppp) REVERT: C 50 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8528 (mtmt) REVERT: C 51 ASP cc_start: 0.8352 (p0) cc_final: 0.8142 (p0) REVERT: C 54 VAL cc_start: 0.7253 (t) cc_final: 0.6949 (t) REVERT: C 61 LYS cc_start: 0.8725 (mmtm) cc_final: 0.8197 (mmtm) REVERT: C 64 ILE cc_start: 0.8642 (mt) cc_final: 0.8359 (tp) REVERT: C 76 ILE cc_start: 0.7554 (mm) cc_final: 0.7091 (tp) REVERT: C 82 MET cc_start: 0.7939 (tpp) cc_final: 0.7049 (tpp) REVERT: C 84 LYS cc_start: 0.9104 (ttmm) cc_final: 0.8668 (ttmm) REVERT: C 87 HIS cc_start: 0.8260 (t70) cc_final: 0.7612 (t-90) REVERT: C 90 PHE cc_start: 0.7807 (m-10) cc_final: 0.7253 (m-80) REVERT: C 91 TYR cc_start: 0.8008 (m-80) cc_final: 0.7569 (m-80) REVERT: C 92 ASN cc_start: 0.7520 (m-40) cc_final: 0.7217 (m110) REVERT: C 105 LEU cc_start: 0.8016 (mm) cc_final: 0.7766 (mm) REVERT: C 111 ASN cc_start: 0.8747 (t0) cc_final: 0.8166 (t0) REVERT: C 113 LYS cc_start: 0.8589 (mttp) cc_final: 0.7836 (mttp) REVERT: C 116 ARG cc_start: 0.8480 (ttm110) cc_final: 0.8035 (ttm110) REVERT: C 117 GLU cc_start: 0.8455 (pp20) cc_final: 0.8177 (pp20) REVERT: C 119 MET cc_start: 0.8325 (ttm) cc_final: 0.8031 (ttm) REVERT: C 121 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8531 (tm-30) REVERT: C 123 MET cc_start: 0.8248 (tpp) cc_final: 0.7312 (tpp) REVERT: C 127 PHE cc_start: 0.8046 (m-80) cc_final: 0.7355 (m-80) REVERT: C 140 LEU cc_start: 0.8890 (mt) cc_final: 0.8667 (mt) REVERT: C 151 ILE cc_start: 0.8013 (tt) cc_final: 0.7262 (tp) REVERT: C 153 LEU cc_start: 0.8366 (tp) cc_final: 0.8096 (tp) REVERT: C 164 PRO cc_start: 0.7695 (Cg_endo) cc_final: 0.7408 (Cg_exo) REVERT: C 166 TYR cc_start: 0.8100 (t80) cc_final: 0.7186 (t80) REVERT: C 176 MET cc_start: 0.6894 (mtt) cc_final: 0.6489 (mtt) REVERT: C 187 ASP cc_start: 0.8839 (m-30) cc_final: 0.8599 (m-30) REVERT: C 200 PHE cc_start: 0.8221 (m-10) cc_final: 0.7933 (m-10) REVERT: C 205 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7470 (mt-10) REVERT: C 211 ASP cc_start: 0.8304 (m-30) cc_final: 0.7894 (m-30) REVERT: C 213 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8483 (ttpt) REVERT: C 240 TYR cc_start: 0.8133 (t80) cc_final: 0.7821 (t80) REVERT: C 252 ASN cc_start: 0.8517 (p0) cc_final: 0.8222 (p0) REVERT: C 254 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.6992 (ttp80) REVERT: C 255 PHE cc_start: 0.8999 (p90) cc_final: 0.8789 (p90) REVERT: C 259 GLU cc_start: 0.8854 (tp30) cc_final: 0.8573 (tp30) REVERT: C 262 PHE cc_start: 0.8643 (m-10) cc_final: 0.8372 (m-10) REVERT: C 276 GLU cc_start: 0.8470 (tp30) cc_final: 0.7562 (tp30) REVERT: C 280 ASN cc_start: 0.8672 (m110) cc_final: 0.7874 (m-40) REVERT: C 283 MET cc_start: 0.8361 (mmm) cc_final: 0.8021 (mmm) REVERT: C 284 LYS cc_start: 0.8803 (mtpt) cc_final: 0.8408 (mtpt) REVERT: C 286 ASP cc_start: 0.8479 (t70) cc_final: 0.7699 (p0) REVERT: C 289 ILE cc_start: 0.8220 (pt) cc_final: 0.7797 (pt) REVERT: C 294 TYR cc_start: 0.7812 (m-80) cc_final: 0.7242 (m-80) REVERT: C 296 ASN cc_start: 0.7429 (p0) cc_final: 0.6698 (p0) REVERT: C 299 MET cc_start: 0.7847 (mmm) cc_final: 0.7444 (mmm) REVERT: C 305 MET cc_start: 0.6961 (mmm) cc_final: 0.6680 (mmm) REVERT: C 313 MET cc_start: 0.8251 (tpp) cc_final: 0.6888 (tpp) REVERT: C 314 GLN cc_start: 0.8503 (tt0) cc_final: 0.8165 (mt0) REVERT: C 316 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7294 (tm-30) REVERT: C 317 ILE cc_start: 0.8866 (mm) cc_final: 0.7940 (mm) REVERT: C 361 GLU cc_start: 0.8644 (tp30) cc_final: 0.8127 (tp30) REVERT: C 371 HIS cc_start: 0.7468 (m90) cc_final: 0.6946 (m-70) REVERT: D 12 ASN cc_start: 0.7417 (m-40) cc_final: 0.6976 (m-40) REVERT: D 24 ASP cc_start: 0.6606 (t0) cc_final: 0.6245 (t0) REVERT: D 33 SER cc_start: 0.8068 (p) cc_final: 0.7728 (p) REVERT: D 34 ILE cc_start: 0.8184 (mt) cc_final: 0.7845 (mt) REVERT: D 37 ARG cc_start: 0.7872 (tpp80) cc_final: 0.7651 (tpp80) REVERT: D 41 GLN cc_start: 0.7988 (tp40) cc_final: 0.7496 (tm-30) REVERT: D 50 LYS cc_start: 0.7819 (mtmm) cc_final: 0.7507 (mtmm) REVERT: D 68 LYS cc_start: 0.7828 (mmtt) cc_final: 0.7614 (mmtt) REVERT: D 72 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7798 (tm-30) REVERT: D 81 ASP cc_start: 0.8292 (m-30) cc_final: 0.8008 (m-30) REVERT: D 82 MET cc_start: 0.8160 (mmp) cc_final: 0.7873 (mmp) REVERT: D 84 LYS cc_start: 0.8692 (mmtp) cc_final: 0.8414 (mmtt) REVERT: D 87 HIS cc_start: 0.8567 (t-90) cc_final: 0.8014 (t-90) REVERT: D 91 TYR cc_start: 0.8424 (m-80) cc_final: 0.7833 (m-80) REVERT: D 99 GLU cc_start: 0.7226 (mp0) cc_final: 0.6988 (mp0) REVERT: D 105 LEU cc_start: 0.7744 (mm) cc_final: 0.7538 (mm) REVERT: D 111 ASN cc_start: 0.8438 (m-40) cc_final: 0.8072 (m-40) REVERT: D 116 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.7984 (mtt-85) REVERT: D 117 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7950 (mt-10) REVERT: D 119 MET cc_start: 0.8920 (ttm) cc_final: 0.8548 (ttm) REVERT: D 121 GLN cc_start: 0.8666 (pp30) cc_final: 0.8290 (pp30) REVERT: D 124 PHE cc_start: 0.7974 (m-80) cc_final: 0.7285 (m-80) REVERT: D 137 GLN cc_start: 0.8145 (mt0) cc_final: 0.7686 (mt0) REVERT: D 139 VAL cc_start: 0.8514 (m) cc_final: 0.8223 (p) REVERT: D 175 ILE cc_start: 0.8554 (pt) cc_final: 0.8003 (pt) REVERT: D 176 MET cc_start: 0.6988 (mmm) cc_final: 0.6700 (mmm) REVERT: D 187 ASP cc_start: 0.8756 (m-30) cc_final: 0.8442 (m-30) REVERT: D 191 LYS cc_start: 0.8804 (ttpt) cc_final: 0.8557 (ttpt) REVERT: D 192 ILE cc_start: 0.8203 (tp) cc_final: 0.7533 (tp) REVERT: D 195 GLU cc_start: 0.6683 (mp0) cc_final: 0.6309 (mp0) REVERT: D 205 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8434 (mt-10) REVERT: D 210 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7603 (ttp80) REVERT: D 213 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8501 (ttpt) REVERT: D 214 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7839 (tt0) REVERT: D 215 LYS cc_start: 0.8979 (mmpt) cc_final: 0.8747 (mmmt) REVERT: D 238 LYS cc_start: 0.7257 (mppt) cc_final: 0.6699 (mptt) REVERT: D 240 TYR cc_start: 0.7812 (t80) cc_final: 0.7577 (t80) REVERT: D 243 PRO cc_start: 0.8516 (Cg_exo) cc_final: 0.8271 (Cg_endo) REVERT: D 254 ARG cc_start: 0.7308 (ptm160) cc_final: 0.7034 (ptm-80) REVERT: D 259 GLU cc_start: 0.8383 (tp30) cc_final: 0.7960 (tp30) REVERT: D 279 TYR cc_start: 0.7947 (t80) cc_final: 0.7396 (t80) REVERT: D 283 MET cc_start: 0.8434 (mmp) cc_final: 0.8084 (mmp) REVERT: D 286 ASP cc_start: 0.8494 (t0) cc_final: 0.7888 (t0) REVERT: D 288 ASP cc_start: 0.8312 (m-30) cc_final: 0.7738 (m-30) REVERT: D 289 ILE cc_start: 0.8150 (pt) cc_final: 0.7560 (mt) REVERT: D 290 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7001 (mtt90) REVERT: D 292 ASP cc_start: 0.8509 (m-30) cc_final: 0.7408 (t0) REVERT: D 293 LEU cc_start: 0.8970 (mt) cc_final: 0.8521 (mt) REVERT: D 294 TYR cc_start: 0.8346 (m-80) cc_final: 0.7735 (m-80) REVERT: D 297 ASN cc_start: 0.8144 (m-40) cc_final: 0.7842 (m-40) REVERT: D 299 MET cc_start: 0.8075 (mmm) cc_final: 0.7856 (mmm) REVERT: D 309 ILE cc_start: 0.8731 (pt) cc_final: 0.8321 (mt) REVERT: D 312 ARG cc_start: 0.8861 (tpt-90) cc_final: 0.8186 (tpt-90) REVERT: D 314 GLN cc_start: 0.9056 (mt0) cc_final: 0.8602 (mm-40) REVERT: D 316 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8224 (mt-10) REVERT: D 320 LEU cc_start: 0.8828 (mt) cc_final: 0.8423 (mt) REVERT: D 328 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8334 (mmtt) REVERT: D 346 LEU cc_start: 0.8281 (tp) cc_final: 0.8060 (tp) REVERT: D 352 PHE cc_start: 0.8854 (t80) cc_final: 0.8542 (t80) REVERT: D 360 GLN cc_start: 0.9004 (mp10) cc_final: 0.8763 (mp10) REVERT: D 361 GLU cc_start: 0.8802 (mp0) cc_final: 0.8404 (pm20) outliers start: 1 outliers final: 0 residues processed: 766 average time/residue: 0.1253 time to fit residues: 133.7301 Evaluate side-chains 718 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 718 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 83 optimal weight: 0.0000 chunk 157 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN C 263 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.113101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.087364 restraints weight = 42406.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.091102 restraints weight = 25309.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093740 restraints weight = 17053.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.095570 restraints weight = 12454.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097025 restraints weight = 9727.648| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.7634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15178 Z= 0.141 Angle : 0.669 9.130 20547 Z= 0.340 Chirality : 0.045 0.208 2251 Planarity : 0.005 0.062 2631 Dihedral : 9.045 166.573 2071 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.20), residues: 1847 helix: 0.89 (0.18), residues: 825 sheet: -1.13 (0.28), residues: 306 loop : -0.01 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 39 TYR 0.033 0.001 TYR A 439 PHE 0.027 0.001 PHE B 353 TRP 0.023 0.002 TRP B 80 HIS 0.007 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00304 (15177) covalent geometry : angle 0.66906 (20547) hydrogen bonds : bond 0.03782 ( 724) hydrogen bonds : angle 5.02953 ( 2007) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 749 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7300 (mm-30) REVERT: A 92 ARG cc_start: 0.8094 (mmp80) cc_final: 0.7460 (mtt90) REVERT: A 127 TYR cc_start: 0.8197 (m-10) cc_final: 0.7822 (m-80) REVERT: A 132 MET cc_start: 0.7414 (mtt) cc_final: 0.7210 (mtt) REVERT: A 138 HIS cc_start: 0.5933 (t-170) cc_final: 0.5594 (t-90) REVERT: A 144 GLU cc_start: 0.8579 (tp30) cc_final: 0.8319 (tt0) REVERT: A 149 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8660 (pp30) REVERT: A 150 MET cc_start: 0.7824 (ttp) cc_final: 0.7438 (tpt) REVERT: A 156 ASN cc_start: 0.7108 (p0) cc_final: 0.6523 (m-40) REVERT: A 157 GLN cc_start: 0.7087 (pm20) cc_final: 0.6621 (pm20) REVERT: A 179 TYR cc_start: 0.8363 (t80) cc_final: 0.7955 (t80) REVERT: A 180 PHE cc_start: 0.8627 (m-80) cc_final: 0.8240 (m-80) REVERT: A 204 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8022 (mm-30) REVERT: A 219 ARG cc_start: 0.6998 (mmm160) cc_final: 0.5682 (mmm160) REVERT: A 220 PHE cc_start: 0.7516 (p90) cc_final: 0.6916 (p90) REVERT: A 222 LYS cc_start: 0.7874 (tptp) cc_final: 0.7652 (tppt) REVERT: A 223 TYR cc_start: 0.8140 (t80) cc_final: 0.6224 (t80) REVERT: A 224 ILE cc_start: 0.8944 (pt) cc_final: 0.8484 (pt) REVERT: A 225 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7502 (mp0) REVERT: A 233 ARG cc_start: 0.8287 (mmm160) cc_final: 0.7736 (mmm160) REVERT: A 239 MET cc_start: 0.6906 (mmp) cc_final: 0.6517 (mmp) REVERT: A 240 ARG cc_start: 0.7756 (ttm170) cc_final: 0.6453 (ttm170) REVERT: A 242 TYR cc_start: 0.7211 (m-80) cc_final: 0.6658 (m-80) REVERT: A 244 LEU cc_start: 0.8416 (tp) cc_final: 0.8005 (tp) REVERT: A 260 HIS cc_start: 0.7992 (m-70) cc_final: 0.7669 (m-70) REVERT: A 262 PHE cc_start: 0.8577 (m-80) cc_final: 0.8055 (m-80) REVERT: A 277 LEU cc_start: 0.8674 (mt) cc_final: 0.8440 (mt) REVERT: A 286 HIS cc_start: 0.7065 (t70) cc_final: 0.6758 (t70) REVERT: A 307 HIS cc_start: 0.8900 (m90) cc_final: 0.8590 (m90) REVERT: A 309 ARG cc_start: 0.8723 (pmt-80) cc_final: 0.8447 (tpt90) REVERT: A 312 CYS cc_start: 0.8543 (m) cc_final: 0.8222 (m) REVERT: A 327 ARG cc_start: 0.8411 (mmt-90) cc_final: 0.8158 (mmt180) REVERT: A 329 LEU cc_start: 0.8488 (mt) cc_final: 0.8147 (pp) REVERT: A 364 MET cc_start: 0.8051 (mtt) cc_final: 0.7726 (mtt) REVERT: A 371 MET cc_start: 0.9170 (mtm) cc_final: 0.8599 (ptp) REVERT: A 373 HIS cc_start: 0.8428 (t70) cc_final: 0.8012 (t70) REVERT: A 400 ARG cc_start: 0.8582 (ptt90) cc_final: 0.8043 (ttp-110) REVERT: A 408 TYR cc_start: 0.8750 (t80) cc_final: 0.8023 (t80) REVERT: A 423 LEU cc_start: 0.7464 (mt) cc_final: 0.6867 (mt) REVERT: A 451 GLN cc_start: 0.8637 (mp10) cc_final: 0.8346 (mp10) REVERT: A 452 PHE cc_start: 0.8384 (t80) cc_final: 0.7859 (t80) REVERT: A 453 CYS cc_start: 0.8833 (p) cc_final: 0.8533 (p) REVERT: A 468 HIS cc_start: 0.8363 (t-90) cc_final: 0.7805 (t-90) REVERT: A 478 MET cc_start: 0.8809 (mtm) cc_final: 0.8408 (mtm) REVERT: A 496 ILE cc_start: 0.8621 (mt) cc_final: 0.8391 (mt) REVERT: A 498 LEU cc_start: 0.8930 (mp) cc_final: 0.8289 (tt) REVERT: A 506 LEU cc_start: 0.8906 (mt) cc_final: 0.8536 (mt) REVERT: A 509 LEU cc_start: 0.8867 (tp) cc_final: 0.8520 (mt) REVERT: A 515 MET cc_start: 0.7126 (ttt) cc_final: 0.6739 (tpt) REVERT: A 520 ASP cc_start: 0.8504 (p0) cc_final: 0.8298 (m-30) REVERT: A 525 GLN cc_start: 0.8555 (tp40) cc_final: 0.7447 (tp-100) REVERT: A 529 ASN cc_start: 0.8570 (m-40) cc_final: 0.7690 (m110) REVERT: A 532 LEU cc_start: 0.7858 (mt) cc_final: 0.7305 (mt) REVERT: A 534 LYS cc_start: 0.8309 (pttt) cc_final: 0.8034 (pttt) REVERT: A 537 LEU cc_start: 0.8999 (mp) cc_final: 0.8687 (mp) REVERT: A 538 PHE cc_start: 0.7960 (t80) cc_final: 0.7229 (t80) REVERT: A 543 MET cc_start: 0.7503 (mmt) cc_final: 0.6960 (mmm) REVERT: A 545 ASN cc_start: 0.8172 (t0) cc_final: 0.7942 (t0) REVERT: A 555 ASP cc_start: 0.8019 (t0) cc_final: 0.7756 (t0) REVERT: A 556 LYS cc_start: 0.8624 (mttt) cc_final: 0.7710 (mtpp) REVERT: A 558 GLU cc_start: 0.7806 (tt0) cc_final: 0.7379 (tm-30) REVERT: A 559 TYR cc_start: 0.7194 (m-80) cc_final: 0.6668 (m-80) REVERT: A 565 LEU cc_start: 0.7617 (pt) cc_final: 0.7250 (pt) REVERT: A 633 LYS cc_start: 0.7078 (mmtt) cc_final: 0.6480 (mmtm) REVERT: A 637 HIS cc_start: 0.8280 (t-90) cc_final: 0.7588 (t-90) REVERT: A 638 GLN cc_start: 0.8992 (pt0) cc_final: 0.8608 (pt0) REVERT: A 641 ASN cc_start: 0.9064 (m110) cc_final: 0.8528 (m-40) REVERT: A 643 LEU cc_start: 0.8774 (tp) cc_final: 0.7745 (tp) REVERT: A 647 MET cc_start: 0.8806 (mmm) cc_final: 0.8044 (mmm) REVERT: A 657 TYR cc_start: 0.6533 (m-80) cc_final: 0.5858 (m-80) REVERT: A 666 PHE cc_start: 0.8277 (m-10) cc_final: 0.7976 (m-10) REVERT: A 688 GLU cc_start: 0.8712 (tp30) cc_final: 0.8361 (tp30) REVERT: A 750 PHE cc_start: 0.8934 (m-10) cc_final: 0.8612 (m-10) REVERT: A 757 TYR cc_start: 0.8995 (t80) cc_final: 0.8595 (t80) REVERT: B 48 MET cc_start: 0.7116 (mmt) cc_final: 0.6676 (tpp) REVERT: B 51 LYS cc_start: 0.8097 (mppt) cc_final: 0.7878 (mmtm) REVERT: B 54 TYR cc_start: 0.8065 (m-80) cc_final: 0.7323 (m-10) REVERT: B 58 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8050 (pt0) REVERT: B 62 LYS cc_start: 0.8819 (mmtp) cc_final: 0.8250 (mmtp) REVERT: B 82 ASP cc_start: 0.8524 (m-30) cc_final: 0.8112 (m-30) REVERT: B 83 MET cc_start: 0.8223 (tpp) cc_final: 0.7857 (tpp) REVERT: B 84 GLU cc_start: 0.8762 (tt0) cc_final: 0.8287 (tm-30) REVERT: B 85 LYS cc_start: 0.9221 (mttm) cc_final: 0.8877 (mttm) REVERT: B 93 ASN cc_start: 0.8072 (m110) cc_final: 0.7799 (m110) REVERT: B 102 HIS cc_start: 0.7622 (m90) cc_final: 0.7419 (m90) REVERT: B 114 LYS cc_start: 0.8508 (ptmm) cc_final: 0.7950 (ptmm) REVERT: B 118 GLU cc_start: 0.8138 (mt-10) cc_final: 0.6930 (mm-30) REVERT: B 120 MET cc_start: 0.8460 (ttm) cc_final: 0.7866 (tmm) REVERT: B 121 THR cc_start: 0.8582 (p) cc_final: 0.7949 (p) REVERT: B 123 ILE cc_start: 0.8459 (mt) cc_final: 0.8163 (mt) REVERT: B 124 MET cc_start: 0.8320 (tpp) cc_final: 0.7522 (tpp) REVERT: B 128 PHE cc_start: 0.8173 (m-80) cc_final: 0.7132 (m-80) REVERT: B 133 MET cc_start: 0.7590 (ttp) cc_final: 0.6956 (ttp) REVERT: B 134 TYR cc_start: 0.7349 (t80) cc_final: 0.6839 (t80) REVERT: B 155 ASP cc_start: 0.6856 (t0) cc_final: 0.6484 (t0) REVERT: B 163 ASN cc_start: 0.8079 (t0) cc_final: 0.7539 (t0) REVERT: B 168 GLU cc_start: 0.8179 (tp30) cc_final: 0.7809 (mm-30) REVERT: B 184 ARG cc_start: 0.8255 (ttm170) cc_final: 0.7856 (ttm110) REVERT: B 186 LEU cc_start: 0.8802 (mt) cc_final: 0.8581 (mt) REVERT: B 191 MET cc_start: 0.8419 (ttm) cc_final: 0.8136 (ttm) REVERT: B 192 LYS cc_start: 0.8320 (ptmt) cc_final: 0.7970 (ptmt) REVERT: B 207 ARG cc_start: 0.8604 (mtt90) cc_final: 0.7994 (mtt-85) REVERT: B 214 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8608 (ttpt) REVERT: B 219 TYR cc_start: 0.7621 (p90) cc_final: 0.7410 (p90) REVERT: B 226 ASN cc_start: 0.8588 (t0) cc_final: 0.8057 (t0) REVERT: B 230 THR cc_start: 0.8468 (m) cc_final: 0.8122 (p) REVERT: B 260 GLU cc_start: 0.8347 (tp30) cc_final: 0.8039 (tp30) REVERT: B 263 PHE cc_start: 0.8597 (m-80) cc_final: 0.7839 (m-80) REVERT: B 264 GLN cc_start: 0.8498 (mt0) cc_final: 0.7675 (mt0) REVERT: B 267 PHE cc_start: 0.8034 (m-10) cc_final: 0.7616 (m-10) REVERT: B 268 ILE cc_start: 0.8395 (tp) cc_final: 0.8149 (tp) REVERT: B 277 GLU cc_start: 0.8349 (tp30) cc_final: 0.8122 (tp30) REVERT: B 280 TYR cc_start: 0.8089 (t80) cc_final: 0.7857 (t80) REVERT: B 283 ILE cc_start: 0.8637 (tp) cc_final: 0.8400 (pt) REVERT: B 287 ASP cc_start: 0.7889 (t70) cc_final: 0.7643 (t70) REVERT: B 292 LYS cc_start: 0.8641 (pttm) cc_final: 0.8238 (pttm) REVERT: B 293 ASP cc_start: 0.8575 (m-30) cc_final: 0.8367 (m-30) REVERT: B 298 ASN cc_start: 0.6983 (m-40) cc_final: 0.6490 (m-40) REVERT: B 300 MET cc_start: 0.8076 (mmm) cc_final: 0.7611 (mmm) REVERT: B 306 MET cc_start: 0.7454 (mmt) cc_final: 0.7113 (mmt) REVERT: B 310 ILE cc_start: 0.8821 (tt) cc_final: 0.8120 (mm) REVERT: B 313 ARG cc_start: 0.8866 (tpt-90) cc_final: 0.8399 (tpp-160) REVERT: B 314 MET cc_start: 0.8427 (tpt) cc_final: 0.7864 (mmm) REVERT: B 316 LYS cc_start: 0.8934 (ptpt) cc_final: 0.8622 (ptpt) REVERT: B 325 THR cc_start: 0.8702 (t) cc_final: 0.8466 (p) REVERT: B 326 MET cc_start: 0.7481 (mmm) cc_final: 0.7264 (mmm) REVERT: B 335 GLU cc_start: 0.7881 (mm-30) cc_final: 0.6986 (mm-30) REVERT: B 338 TYR cc_start: 0.8044 (m-80) cc_final: 0.7261 (m-80) REVERT: B 359 THR cc_start: 0.7674 (p) cc_final: 0.6872 (m) REVERT: B 360 LYS cc_start: 0.8250 (tptp) cc_final: 0.7507 (tptp) REVERT: B 362 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8327 (mt-10) REVERT: B 364 ASP cc_start: 0.7883 (m-30) cc_final: 0.7241 (m-30) REVERT: B 372 HIS cc_start: 0.8004 (m-70) cc_final: 0.7386 (m90) REVERT: C 34 ILE cc_start: 0.8239 (mt) cc_final: 0.7946 (tt) REVERT: C 44 MET cc_start: 0.8457 (ppp) cc_final: 0.8024 (ppp) REVERT: C 50 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8517 (mtmt) REVERT: C 54 VAL cc_start: 0.7332 (t) cc_final: 0.7068 (t) REVERT: C 57 GLU cc_start: 0.8050 (pm20) cc_final: 0.7686 (pm20) REVERT: C 76 ILE cc_start: 0.7438 (mm) cc_final: 0.7188 (tp) REVERT: C 82 MET cc_start: 0.7864 (tpp) cc_final: 0.6709 (tpp) REVERT: C 84 LYS cc_start: 0.9133 (ttmm) cc_final: 0.8712 (ttmm) REVERT: C 87 HIS cc_start: 0.8318 (t70) cc_final: 0.7637 (t-90) REVERT: C 90 PHE cc_start: 0.7765 (m-10) cc_final: 0.7245 (m-80) REVERT: C 91 TYR cc_start: 0.7988 (m-80) cc_final: 0.7538 (m-80) REVERT: C 92 ASN cc_start: 0.7525 (m-40) cc_final: 0.7227 (m-40) REVERT: C 105 LEU cc_start: 0.8055 (mm) cc_final: 0.7844 (mm) REVERT: C 111 ASN cc_start: 0.8725 (t0) cc_final: 0.8114 (t0) REVERT: C 113 LYS cc_start: 0.8575 (mttp) cc_final: 0.7745 (mttp) REVERT: C 115 ASN cc_start: 0.8483 (t0) cc_final: 0.8268 (t0) REVERT: C 116 ARG cc_start: 0.8480 (ttm110) cc_final: 0.7857 (ttm110) REVERT: C 117 GLU cc_start: 0.8398 (pp20) cc_final: 0.8105 (pp20) REVERT: C 119 MET cc_start: 0.8403 (ttm) cc_final: 0.8115 (ttm) REVERT: C 121 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8599 (tm-30) REVERT: C 123 MET cc_start: 0.8219 (tpp) cc_final: 0.7264 (tpp) REVERT: C 127 PHE cc_start: 0.8000 (m-80) cc_final: 0.7367 (m-80) REVERT: C 140 LEU cc_start: 0.8894 (mt) cc_final: 0.8629 (mt) REVERT: C 151 ILE cc_start: 0.7924 (tt) cc_final: 0.7128 (tp) REVERT: C 153 LEU cc_start: 0.8306 (tp) cc_final: 0.8079 (tp) REVERT: C 164 PRO cc_start: 0.7631 (Cg_endo) cc_final: 0.7333 (Cg_exo) REVERT: C 167 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8137 (mm-30) REVERT: C 176 MET cc_start: 0.6869 (mtt) cc_final: 0.6513 (mtt) REVERT: C 187 ASP cc_start: 0.8810 (m-30) cc_final: 0.8571 (m-30) REVERT: C 192 ILE cc_start: 0.8794 (pt) cc_final: 0.8385 (pt) REVERT: C 200 PHE cc_start: 0.8167 (m-10) cc_final: 0.7824 (m-10) REVERT: C 205 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7464 (mt-10) REVERT: C 211 ASP cc_start: 0.8309 (m-30) cc_final: 0.7904 (m-30) REVERT: C 213 LYS cc_start: 0.8924 (ttpt) cc_final: 0.8417 (ttpt) REVERT: C 240 TYR cc_start: 0.8010 (t80) cc_final: 0.7692 (t80) REVERT: C 242 LEU cc_start: 0.8718 (mp) cc_final: 0.8175 (mp) REVERT: C 252 ASN cc_start: 0.8493 (p0) cc_final: 0.7936 (p0) REVERT: C 255 PHE cc_start: 0.9002 (p90) cc_final: 0.8741 (p90) REVERT: C 256 ARG cc_start: 0.8581 (mtp180) cc_final: 0.7912 (mtp180) REVERT: C 259 GLU cc_start: 0.8862 (tp30) cc_final: 0.8561 (tp30) REVERT: C 276 GLU cc_start: 0.8472 (tp30) cc_final: 0.8185 (mm-30) REVERT: C 280 ASN cc_start: 0.8726 (m110) cc_final: 0.8489 (m-40) REVERT: C 283 MET cc_start: 0.8351 (mmm) cc_final: 0.8014 (mmm) REVERT: C 284 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8397 (mtpt) REVERT: C 286 ASP cc_start: 0.8490 (t70) cc_final: 0.7738 (p0) REVERT: C 289 ILE cc_start: 0.8234 (pt) cc_final: 0.7841 (pt) REVERT: C 294 TYR cc_start: 0.7837 (m-80) cc_final: 0.7541 (m-80) REVERT: C 296 ASN cc_start: 0.7415 (p0) cc_final: 0.6898 (p0) REVERT: C 299 MET cc_start: 0.7811 (mmm) cc_final: 0.7451 (mmm) REVERT: C 305 MET cc_start: 0.7106 (mmm) cc_final: 0.6806 (mmm) REVERT: C 313 MET cc_start: 0.8202 (tpp) cc_final: 0.6578 (tpp) REVERT: C 314 GLN cc_start: 0.8477 (tt0) cc_final: 0.8134 (mt0) REVERT: C 316 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7532 (tm-30) REVERT: C 317 ILE cc_start: 0.8852 (mm) cc_final: 0.7841 (mm) REVERT: C 361 GLU cc_start: 0.8640 (tp30) cc_final: 0.8119 (tp30) REVERT: C 371 HIS cc_start: 0.7295 (m90) cc_final: 0.6720 (m-70) REVERT: D 10 CYS cc_start: 0.7672 (p) cc_final: 0.6272 (m) REVERT: D 12 ASN cc_start: 0.7442 (m-40) cc_final: 0.7106 (m-40) REVERT: D 34 ILE cc_start: 0.8245 (mt) cc_final: 0.7575 (tp) REVERT: D 41 GLN cc_start: 0.8027 (tp40) cc_final: 0.7556 (tm-30) REVERT: D 50 LYS cc_start: 0.7897 (mtmm) cc_final: 0.7521 (mtmm) REVERT: D 68 LYS cc_start: 0.7834 (mmtt) cc_final: 0.7602 (mmtt) REVERT: D 84 LYS cc_start: 0.8693 (mmtp) cc_final: 0.8443 (mmtt) REVERT: D 87 HIS cc_start: 0.8597 (t-90) cc_final: 0.8031 (t-90) REVERT: D 91 TYR cc_start: 0.8399 (m-80) cc_final: 0.7815 (m-80) REVERT: D 92 ASN cc_start: 0.7846 (m110) cc_final: 0.7521 (m110) REVERT: D 111 ASN cc_start: 0.8406 (m-40) cc_final: 0.8066 (m-40) REVERT: D 116 ARG cc_start: 0.8383 (mtt-85) cc_final: 0.8028 (mtt-85) REVERT: D 119 MET cc_start: 0.8891 (ttm) cc_final: 0.8485 (ttm) REVERT: D 121 GLN cc_start: 0.8649 (pp30) cc_final: 0.8430 (pp30) REVERT: D 124 PHE cc_start: 0.8014 (m-80) cc_final: 0.7379 (m-80) REVERT: D 137 GLN cc_start: 0.8028 (mt0) cc_final: 0.7590 (mt0) REVERT: D 175 ILE cc_start: 0.8599 (pt) cc_final: 0.8076 (pt) REVERT: D 176 MET cc_start: 0.6973 (mmm) cc_final: 0.6669 (mmm) REVERT: D 187 ASP cc_start: 0.8764 (m-30) cc_final: 0.8442 (m-30) REVERT: D 191 LYS cc_start: 0.8825 (ttpt) cc_final: 0.8544 (ttpt) REVERT: D 192 ILE cc_start: 0.8228 (tp) cc_final: 0.7563 (tp) REVERT: D 195 GLU cc_start: 0.6658 (mp0) cc_final: 0.6271 (mp0) REVERT: D 196 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7482 (tpp80) REVERT: D 205 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8350 (mt-10) REVERT: D 207 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7020 (mm-30) REVERT: D 210 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7517 (ttp-110) REVERT: D 213 LYS cc_start: 0.8687 (ttpt) cc_final: 0.8450 (ttpt) REVERT: D 214 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7879 (tt0) REVERT: D 215 LYS cc_start: 0.8978 (mmpt) cc_final: 0.8734 (mmmt) REVERT: D 238 LYS cc_start: 0.7297 (mppt) cc_final: 0.6977 (mptt) REVERT: D 243 PRO cc_start: 0.8524 (Cg_exo) cc_final: 0.7513 (Cg_endo) REVERT: D 259 GLU cc_start: 0.8311 (tp30) cc_final: 0.7924 (tp30) REVERT: D 279 TYR cc_start: 0.7967 (t80) cc_final: 0.7456 (t80) REVERT: D 283 MET cc_start: 0.8431 (mmp) cc_final: 0.7969 (mmp) REVERT: D 286 ASP cc_start: 0.8437 (t0) cc_final: 0.7979 (t0) REVERT: D 288 ASP cc_start: 0.8193 (m-30) cc_final: 0.7614 (m-30) REVERT: D 289 ILE cc_start: 0.8016 (pt) cc_final: 0.7743 (mt) REVERT: D 290 ARG cc_start: 0.7977 (mtt180) cc_final: 0.7071 (mtt180) REVERT: D 294 TYR cc_start: 0.8293 (m-80) cc_final: 0.7682 (m-80) REVERT: D 298 VAL cc_start: 0.8413 (t) cc_final: 0.7828 (t) REVERT: D 299 MET cc_start: 0.8105 (mmm) cc_final: 0.7874 (mmm) REVERT: D 305 MET cc_start: 0.6915 (mmp) cc_final: 0.6632 (mmt) REVERT: D 309 ILE cc_start: 0.8670 (pt) cc_final: 0.8282 (mt) REVERT: D 312 ARG cc_start: 0.8845 (tpt-90) cc_final: 0.7831 (tpt-90) REVERT: D 314 GLN cc_start: 0.9041 (mt0) cc_final: 0.8547 (mm-40) REVERT: D 316 GLU cc_start: 0.8774 (mm-30) cc_final: 0.7965 (mm-30) REVERT: D 320 LEU cc_start: 0.8826 (mt) cc_final: 0.8439 (mt) REVERT: D 328 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8324 (mmtt) REVERT: D 329 ILE cc_start: 0.8713 (mm) cc_final: 0.7829 (mm) REVERT: D 340 TRP cc_start: 0.7724 (t60) cc_final: 0.6961 (t60) REVERT: D 345 ILE cc_start: 0.8380 (tp) cc_final: 0.8043 (pt) REVERT: D 346 LEU cc_start: 0.8288 (tp) cc_final: 0.7905 (tp) REVERT: D 352 PHE cc_start: 0.8764 (t80) cc_final: 0.8537 (t80) REVERT: D 360 GLN cc_start: 0.9039 (mp10) cc_final: 0.8810 (mp10) REVERT: D 361 GLU cc_start: 0.8799 (mp0) cc_final: 0.8433 (pm20) REVERT: D 371 HIS cc_start: 0.7449 (p90) cc_final: 0.7051 (p90) outliers start: 0 outliers final: 0 residues processed: 749 average time/residue: 0.1207 time to fit residues: 125.8431 Evaluate side-chains 695 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 695 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 81 optimal weight: 0.1980 chunk 10 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 53 optimal weight: 0.0270 chunk 181 optimal weight: 2.9990 chunk 29 optimal weight: 0.0870 chunk 42 optimal weight: 0.0270 chunk 168 optimal weight: 0.9990 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 GLN B 74 HIS ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN C 263 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 297 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.113880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.088049 restraints weight = 42020.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.091903 restraints weight = 24910.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.094594 restraints weight = 16708.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.096548 restraints weight = 12160.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.097918 restraints weight = 9389.235| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.7815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15178 Z= 0.120 Angle : 0.662 7.560 20547 Z= 0.334 Chirality : 0.044 0.179 2251 Planarity : 0.005 0.077 2631 Dihedral : 8.900 165.537 2071 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.20), residues: 1847 helix: 0.94 (0.18), residues: 827 sheet: -1.03 (0.28), residues: 294 loop : -0.04 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 691 TYR 0.032 0.002 TYR A 439 PHE 0.016 0.001 PHE D 352 TRP 0.024 0.002 TRP C 79 HIS 0.005 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00267 (15177) covalent geometry : angle 0.66244 (20547) hydrogen bonds : bond 0.03579 ( 724) hydrogen bonds : angle 4.93668 ( 2007) Misc. bond : bond 0.00071 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 741 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7243 (mm-30) REVERT: A 92 ARG cc_start: 0.8105 (mmp80) cc_final: 0.7573 (mmp-170) REVERT: A 107 LEU cc_start: 0.7799 (tt) cc_final: 0.7588 (tp) REVERT: A 119 TYR cc_start: 0.6974 (m-80) cc_final: 0.6704 (m-80) REVERT: A 127 TYR cc_start: 0.8221 (m-10) cc_final: 0.7843 (m-80) REVERT: A 132 MET cc_start: 0.7322 (mtt) cc_final: 0.7104 (mtt) REVERT: A 138 HIS cc_start: 0.6119 (t-170) cc_final: 0.5658 (t-90) REVERT: A 149 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8723 (pp30) REVERT: A 150 MET cc_start: 0.7861 (ttp) cc_final: 0.7430 (tpt) REVERT: A 156 ASN cc_start: 0.6972 (p0) cc_final: 0.6444 (t0) REVERT: A 157 GLN cc_start: 0.7025 (pm20) cc_final: 0.6537 (pm20) REVERT: A 177 MET cc_start: 0.8111 (mtp) cc_final: 0.7658 (mtp) REVERT: A 179 TYR cc_start: 0.8421 (t80) cc_final: 0.8015 (t80) REVERT: A 180 PHE cc_start: 0.8660 (m-80) cc_final: 0.8279 (m-80) REVERT: A 204 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8067 (mm-30) REVERT: A 219 ARG cc_start: 0.7040 (mmm160) cc_final: 0.5841 (mmm160) REVERT: A 220 PHE cc_start: 0.7312 (p90) cc_final: 0.6851 (p90) REVERT: A 223 TYR cc_start: 0.8163 (t80) cc_final: 0.6599 (t80) REVERT: A 225 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7272 (mp0) REVERT: A 239 MET cc_start: 0.6826 (mmp) cc_final: 0.6581 (mmp) REVERT: A 240 ARG cc_start: 0.7777 (ttm170) cc_final: 0.6581 (ttm170) REVERT: A 242 TYR cc_start: 0.7024 (m-80) cc_final: 0.6536 (m-80) REVERT: A 244 LEU cc_start: 0.8395 (tp) cc_final: 0.8015 (tp) REVERT: A 256 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6565 (mp0) REVERT: A 260 HIS cc_start: 0.7924 (m-70) cc_final: 0.7551 (m-70) REVERT: A 262 PHE cc_start: 0.8498 (m-80) cc_final: 0.7995 (m-80) REVERT: A 277 LEU cc_start: 0.8686 (mt) cc_final: 0.8406 (mt) REVERT: A 286 HIS cc_start: 0.7043 (t70) cc_final: 0.6737 (t70) REVERT: A 307 HIS cc_start: 0.8886 (m90) cc_final: 0.8590 (m90) REVERT: A 309 ARG cc_start: 0.8758 (pmt-80) cc_final: 0.8325 (ttp80) REVERT: A 317 ILE cc_start: 0.8484 (mm) cc_final: 0.8246 (mm) REVERT: A 325 ILE cc_start: 0.9057 (tp) cc_final: 0.8797 (pt) REVERT: A 327 ARG cc_start: 0.8407 (mmt-90) cc_final: 0.8143 (mmt180) REVERT: A 364 MET cc_start: 0.8078 (mtt) cc_final: 0.7769 (mtt) REVERT: A 371 MET cc_start: 0.9223 (mtm) cc_final: 0.8662 (ptp) REVERT: A 373 HIS cc_start: 0.8415 (t70) cc_final: 0.8004 (t70) REVERT: A 400 ARG cc_start: 0.8563 (ptt90) cc_final: 0.8014 (ttp-110) REVERT: A 408 TYR cc_start: 0.8753 (t80) cc_final: 0.8006 (t80) REVERT: A 423 LEU cc_start: 0.7474 (mt) cc_final: 0.6889 (mt) REVERT: A 451 GLN cc_start: 0.8609 (mp10) cc_final: 0.8265 (mp10) REVERT: A 452 PHE cc_start: 0.8388 (t80) cc_final: 0.7830 (t80) REVERT: A 453 CYS cc_start: 0.8803 (p) cc_final: 0.8534 (p) REVERT: A 456 TYR cc_start: 0.8732 (t80) cc_final: 0.8349 (t80) REVERT: A 466 ASN cc_start: 0.8158 (m-40) cc_final: 0.7899 (m-40) REVERT: A 467 MET cc_start: 0.8681 (tmm) cc_final: 0.8220 (tpt) REVERT: A 468 HIS cc_start: 0.8365 (t-90) cc_final: 0.7481 (t-90) REVERT: A 471 LYS cc_start: 0.8317 (mmtp) cc_final: 0.7926 (mmtt) REVERT: A 473 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8238 (mm-30) REVERT: A 475 GLU cc_start: 0.8552 (mp0) cc_final: 0.8217 (mp0) REVERT: A 478 MET cc_start: 0.8815 (mtm) cc_final: 0.8416 (mtm) REVERT: A 511 GLU cc_start: 0.8459 (tt0) cc_final: 0.8171 (tt0) REVERT: A 515 MET cc_start: 0.7209 (ttt) cc_final: 0.6629 (tpt) REVERT: A 529 ASN cc_start: 0.8566 (m-40) cc_final: 0.8238 (m-40) REVERT: A 532 LEU cc_start: 0.7809 (mt) cc_final: 0.7292 (mt) REVERT: A 534 LYS cc_start: 0.8311 (pttt) cc_final: 0.8033 (pttt) REVERT: A 537 LEU cc_start: 0.9013 (mp) cc_final: 0.8686 (mp) REVERT: A 538 PHE cc_start: 0.7893 (t80) cc_final: 0.7172 (t80) REVERT: A 542 ARG cc_start: 0.8251 (ttp-110) cc_final: 0.7681 (ttp80) REVERT: A 543 MET cc_start: 0.7301 (mmt) cc_final: 0.5933 (mmt) REVERT: A 545 ASN cc_start: 0.8207 (t0) cc_final: 0.7858 (t0) REVERT: A 556 LYS cc_start: 0.8657 (mttt) cc_final: 0.8097 (mtpp) REVERT: A 558 GLU cc_start: 0.7812 (tt0) cc_final: 0.7408 (tm-30) REVERT: A 559 TYR cc_start: 0.7100 (m-80) cc_final: 0.6605 (m-80) REVERT: A 568 ASN cc_start: 0.8326 (t0) cc_final: 0.7962 (t0) REVERT: A 633 LYS cc_start: 0.7132 (mmtt) cc_final: 0.6758 (mmtm) REVERT: A 637 HIS cc_start: 0.8238 (t-90) cc_final: 0.7673 (t-90) REVERT: A 638 GLN cc_start: 0.9000 (pt0) cc_final: 0.8643 (pt0) REVERT: A 640 ARG cc_start: 0.9174 (ptm160) cc_final: 0.8915 (ptm160) REVERT: A 641 ASN cc_start: 0.9061 (m110) cc_final: 0.8560 (m-40) REVERT: A 643 LEU cc_start: 0.8761 (tp) cc_final: 0.7607 (tp) REVERT: A 647 MET cc_start: 0.8795 (mmm) cc_final: 0.8024 (mmm) REVERT: A 657 TYR cc_start: 0.6263 (m-80) cc_final: 0.5344 (m-80) REVERT: A 666 PHE cc_start: 0.8365 (m-10) cc_final: 0.7974 (m-10) REVERT: A 667 LYS cc_start: 0.8876 (pttm) cc_final: 0.8485 (mptt) REVERT: A 682 ARG cc_start: 0.8743 (ptt90) cc_final: 0.8427 (ptt180) REVERT: A 688 GLU cc_start: 0.8748 (tp30) cc_final: 0.8376 (tp30) REVERT: A 706 PHE cc_start: 0.8431 (t80) cc_final: 0.8207 (t80) REVERT: A 741 TYR cc_start: 0.8606 (p90) cc_final: 0.8038 (p90) REVERT: A 750 PHE cc_start: 0.8923 (m-10) cc_final: 0.8561 (m-10) REVERT: A 757 TYR cc_start: 0.9016 (t80) cc_final: 0.8615 (t80) REVERT: B 32 PHE cc_start: 0.7911 (p90) cc_final: 0.7631 (p90) REVERT: B 48 MET cc_start: 0.7203 (mmt) cc_final: 0.6572 (tpp) REVERT: B 51 LYS cc_start: 0.8125 (mppt) cc_final: 0.7921 (mmtm) REVERT: B 54 TYR cc_start: 0.7995 (m-80) cc_final: 0.7403 (m-10) REVERT: B 58 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8005 (tt0) REVERT: B 62 LYS cc_start: 0.8786 (mmtp) cc_final: 0.8219 (mmtp) REVERT: B 82 ASP cc_start: 0.8506 (m-30) cc_final: 0.8112 (m-30) REVERT: B 83 MET cc_start: 0.8202 (tpp) cc_final: 0.7843 (tpp) REVERT: B 84 GLU cc_start: 0.8744 (tt0) cc_final: 0.8262 (tm-30) REVERT: B 85 LYS cc_start: 0.9201 (mttm) cc_final: 0.8885 (mttm) REVERT: B 92 TYR cc_start: 0.8333 (m-80) cc_final: 0.7897 (m-80) REVERT: B 111 LEU cc_start: 0.8181 (mt) cc_final: 0.7946 (mt) REVERT: B 114 LYS cc_start: 0.8522 (ptmm) cc_final: 0.7989 (ptmm) REVERT: B 118 GLU cc_start: 0.8160 (mt-10) cc_final: 0.6898 (mm-30) REVERT: B 120 MET cc_start: 0.8469 (ttm) cc_final: 0.7863 (tmm) REVERT: B 121 THR cc_start: 0.8593 (p) cc_final: 0.7977 (p) REVERT: B 123 ILE cc_start: 0.8443 (mt) cc_final: 0.8100 (mt) REVERT: B 124 MET cc_start: 0.8335 (tpp) cc_final: 0.7683 (tpp) REVERT: B 128 PHE cc_start: 0.8201 (m-80) cc_final: 0.7441 (m-80) REVERT: B 133 MET cc_start: 0.7503 (ttp) cc_final: 0.6860 (ttp) REVERT: B 134 TYR cc_start: 0.7234 (t80) cc_final: 0.6892 (t80) REVERT: B 155 ASP cc_start: 0.6714 (t0) cc_final: 0.6467 (t0) REVERT: B 184 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7831 (ttm110) REVERT: B 191 MET cc_start: 0.8418 (ttm) cc_final: 0.8124 (ttm) REVERT: B 192 LYS cc_start: 0.8313 (ptmt) cc_final: 0.8000 (ptmt) REVERT: B 207 ARG cc_start: 0.8585 (mtt90) cc_final: 0.8134 (mtt-85) REVERT: B 208 GLU cc_start: 0.7893 (pp20) cc_final: 0.7616 (pm20) REVERT: B 211 ARG cc_start: 0.8699 (ppt170) cc_final: 0.8423 (ttp80) REVERT: B 214 LYS cc_start: 0.8974 (ttpt) cc_final: 0.8718 (ttpt) REVERT: B 219 TYR cc_start: 0.7581 (p90) cc_final: 0.7358 (p90) REVERT: B 226 ASN cc_start: 0.8378 (t0) cc_final: 0.8043 (t0) REVERT: B 230 THR cc_start: 0.8451 (m) cc_final: 0.8107 (p) REVERT: B 257 ARG cc_start: 0.8515 (mtp180) cc_final: 0.8204 (mtp180) REVERT: B 260 GLU cc_start: 0.8372 (tp30) cc_final: 0.7918 (tp30) REVERT: B 263 PHE cc_start: 0.8576 (m-80) cc_final: 0.7833 (m-80) REVERT: B 264 GLN cc_start: 0.8480 (mt0) cc_final: 0.7564 (mt0) REVERT: B 267 PHE cc_start: 0.8056 (m-10) cc_final: 0.7530 (m-10) REVERT: B 277 GLU cc_start: 0.8328 (tp30) cc_final: 0.8113 (tp30) REVERT: B 280 TYR cc_start: 0.8071 (t80) cc_final: 0.7685 (t80) REVERT: B 283 ILE cc_start: 0.8637 (tp) cc_final: 0.8310 (pt) REVERT: B 287 ASP cc_start: 0.7764 (t70) cc_final: 0.7539 (t70) REVERT: B 292 LYS cc_start: 0.8619 (pttm) cc_final: 0.8217 (pttm) REVERT: B 293 ASP cc_start: 0.8501 (m-30) cc_final: 0.8051 (m-30) REVERT: B 297 ASN cc_start: 0.7700 (m-40) cc_final: 0.7402 (m-40) REVERT: B 298 ASN cc_start: 0.6888 (m-40) cc_final: 0.6402 (m-40) REVERT: B 300 MET cc_start: 0.8079 (mmm) cc_final: 0.7585 (mmm) REVERT: B 306 MET cc_start: 0.7450 (mmt) cc_final: 0.7168 (mmt) REVERT: B 310 ILE cc_start: 0.8767 (tt) cc_final: 0.8286 (pt) REVERT: B 313 ARG cc_start: 0.8893 (tpt-90) cc_final: 0.7166 (tpp-160) REVERT: B 314 MET cc_start: 0.8512 (tpt) cc_final: 0.7922 (mmm) REVERT: B 315 GLN cc_start: 0.8235 (mm110) cc_final: 0.7997 (mm110) REVERT: B 316 LYS cc_start: 0.8912 (ptpt) cc_final: 0.8058 (ptpt) REVERT: B 317 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7839 (mm-30) REVERT: B 325 THR cc_start: 0.8698 (t) cc_final: 0.8493 (p) REVERT: B 326 MET cc_start: 0.7458 (mmm) cc_final: 0.7215 (mmm) REVERT: B 335 GLU cc_start: 0.7825 (mm-30) cc_final: 0.6490 (mm-30) REVERT: B 338 TYR cc_start: 0.8014 (m-80) cc_final: 0.7233 (m-80) REVERT: B 351 SER cc_start: 0.7363 (p) cc_final: 0.6469 (p) REVERT: B 353 PHE cc_start: 0.8329 (t80) cc_final: 0.8015 (t80) REVERT: B 357 TRP cc_start: 0.6889 (m-10) cc_final: 0.6627 (m-10) REVERT: B 360 LYS cc_start: 0.8252 (tptp) cc_final: 0.7455 (tptp) REVERT: B 362 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8279 (tm-30) REVERT: B 364 ASP cc_start: 0.7875 (m-30) cc_final: 0.7234 (m-30) REVERT: B 370 ILE cc_start: 0.8448 (tp) cc_final: 0.7689 (tp) REVERT: B 372 HIS cc_start: 0.7965 (m-70) cc_final: 0.7342 (m90) REVERT: C 44 MET cc_start: 0.8407 (ppp) cc_final: 0.7946 (ppp) REVERT: C 50 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8512 (mtmt) REVERT: C 76 ILE cc_start: 0.7306 (mm) cc_final: 0.6982 (tp) REVERT: C 82 MET cc_start: 0.7622 (tpp) cc_final: 0.6863 (tpp) REVERT: C 84 LYS cc_start: 0.9096 (ttmm) cc_final: 0.8665 (ttmm) REVERT: C 87 HIS cc_start: 0.8337 (t70) cc_final: 0.7629 (t-90) REVERT: C 90 PHE cc_start: 0.7762 (m-10) cc_final: 0.7264 (m-80) REVERT: C 91 TYR cc_start: 0.7985 (m-80) cc_final: 0.7500 (m-80) REVERT: C 105 LEU cc_start: 0.8021 (mm) cc_final: 0.7778 (mm) REVERT: C 111 ASN cc_start: 0.8623 (t0) cc_final: 0.7960 (t0) REVERT: C 113 LYS cc_start: 0.8553 (mttp) cc_final: 0.7827 (mttp) REVERT: C 115 ASN cc_start: 0.8513 (t0) cc_final: 0.8235 (t0) REVERT: C 116 ARG cc_start: 0.8457 (ttm110) cc_final: 0.8035 (ttm110) REVERT: C 117 GLU cc_start: 0.8383 (pp20) cc_final: 0.8075 (pp20) REVERT: C 119 MET cc_start: 0.8372 (ttm) cc_final: 0.8100 (ttm) REVERT: C 121 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8613 (tm-30) REVERT: C 123 MET cc_start: 0.8220 (tpp) cc_final: 0.7282 (tpp) REVERT: C 127 PHE cc_start: 0.8046 (m-80) cc_final: 0.7349 (m-80) REVERT: C 140 LEU cc_start: 0.8856 (mt) cc_final: 0.8583 (mt) REVERT: C 151 ILE cc_start: 0.7892 (tt) cc_final: 0.7085 (tp) REVERT: C 164 PRO cc_start: 0.7654 (Cg_endo) cc_final: 0.7384 (Cg_exo) REVERT: C 167 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8049 (mm-30) REVERT: C 187 ASP cc_start: 0.8792 (m-30) cc_final: 0.8555 (m-30) REVERT: C 196 ARG cc_start: 0.8097 (ttp-170) cc_final: 0.7607 (ttm170) REVERT: C 200 PHE cc_start: 0.8170 (m-10) cc_final: 0.7953 (m-10) REVERT: C 207 GLU cc_start: 0.8131 (pp20) cc_final: 0.7752 (pp20) REVERT: C 211 ASP cc_start: 0.8313 (m-30) cc_final: 0.7903 (m-30) REVERT: C 213 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8360 (ttpt) REVERT: C 216 LEU cc_start: 0.8491 (mp) cc_final: 0.8192 (mp) REVERT: C 223 PHE cc_start: 0.7692 (t80) cc_final: 0.7451 (t80) REVERT: C 240 TYR cc_start: 0.7948 (t80) cc_final: 0.7601 (t80) REVERT: C 242 LEU cc_start: 0.8301 (mp) cc_final: 0.8098 (mp) REVERT: C 254 ARG cc_start: 0.7652 (mtp85) cc_final: 0.7275 (ttp80) REVERT: C 280 ASN cc_start: 0.8728 (m110) cc_final: 0.8242 (m-40) REVERT: C 282 ILE cc_start: 0.8677 (mt) cc_final: 0.8337 (pt) REVERT: C 283 MET cc_start: 0.8382 (mmm) cc_final: 0.7944 (mmm) REVERT: C 284 LYS cc_start: 0.8819 (mtpt) cc_final: 0.8443 (mtpt) REVERT: C 286 ASP cc_start: 0.8484 (t70) cc_final: 0.7728 (p0) REVERT: C 289 ILE cc_start: 0.8164 (pt) cc_final: 0.7816 (pt) REVERT: C 294 TYR cc_start: 0.7798 (m-80) cc_final: 0.7260 (m-80) REVERT: C 296 ASN cc_start: 0.7430 (p0) cc_final: 0.6753 (p0) REVERT: C 305 MET cc_start: 0.7153 (mmm) cc_final: 0.6810 (mmm) REVERT: C 313 MET cc_start: 0.8170 (tpp) cc_final: 0.5348 (tpp) REVERT: C 314 GLN cc_start: 0.8463 (tt0) cc_final: 0.8039 (mt0) REVERT: C 317 ILE cc_start: 0.8814 (mm) cc_final: 0.7082 (mm) REVERT: C 361 GLU cc_start: 0.8575 (tp30) cc_final: 0.8051 (tp30) REVERT: C 371 HIS cc_start: 0.7341 (m90) cc_final: 0.6909 (m-70) REVERT: D 24 ASP cc_start: 0.6766 (t0) cc_final: 0.6478 (t0) REVERT: D 34 ILE cc_start: 0.8156 (mt) cc_final: 0.7467 (tp) REVERT: D 41 GLN cc_start: 0.8037 (tp40) cc_final: 0.7586 (tm-30) REVERT: D 50 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7637 (mtmm) REVERT: D 66 THR cc_start: 0.6818 (t) cc_final: 0.6239 (p) REVERT: D 68 LYS cc_start: 0.7712 (mmtt) cc_final: 0.7478 (mmtt) REVERT: D 72 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7764 (tm-30) REVERT: D 81 ASP cc_start: 0.8072 (m-30) cc_final: 0.7771 (m-30) REVERT: D 87 HIS cc_start: 0.8555 (t-90) cc_final: 0.7980 (t-90) REVERT: D 91 TYR cc_start: 0.8310 (m-80) cc_final: 0.7614 (m-80) REVERT: D 92 ASN cc_start: 0.7766 (m110) cc_final: 0.7464 (m110) REVERT: D 111 ASN cc_start: 0.8394 (m-40) cc_final: 0.8126 (m-40) REVERT: D 116 ARG cc_start: 0.8356 (mtt-85) cc_final: 0.8018 (mtt-85) REVERT: D 119 MET cc_start: 0.8866 (ttm) cc_final: 0.8460 (ttm) REVERT: D 121 GLN cc_start: 0.8875 (pp30) cc_final: 0.8557 (pp30) REVERT: D 124 PHE cc_start: 0.7959 (m-80) cc_final: 0.7402 (m-80) REVERT: D 128 ASN cc_start: 0.8757 (m110) cc_final: 0.8494 (m110) REVERT: D 132 MET cc_start: 0.7253 (tpt) cc_final: 0.6729 (tpt) REVERT: D 137 GLN cc_start: 0.8026 (mt0) cc_final: 0.7507 (mt0) REVERT: D 175 ILE cc_start: 0.8591 (pt) cc_final: 0.8081 (pt) REVERT: D 176 MET cc_start: 0.6993 (mmm) cc_final: 0.6709 (mmm) REVERT: D 187 ASP cc_start: 0.8762 (m-30) cc_final: 0.8445 (m-30) REVERT: D 191 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8539 (ttpt) REVERT: D 192 ILE cc_start: 0.8257 (tp) cc_final: 0.7717 (tp) REVERT: D 195 GLU cc_start: 0.6660 (mp0) cc_final: 0.6306 (mp0) REVERT: D 196 ARG cc_start: 0.7888 (tpp80) cc_final: 0.7424 (tpp80) REVERT: D 205 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8295 (mt-10) REVERT: D 207 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7046 (mm-30) REVERT: D 210 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7614 (ttp-110) REVERT: D 211 ASP cc_start: 0.8139 (m-30) cc_final: 0.7926 (m-30) REVERT: D 213 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8437 (ttpt) REVERT: D 214 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7820 (tt0) REVERT: D 215 LYS cc_start: 0.8967 (mmpt) cc_final: 0.8736 (mmmt) REVERT: D 225 ASN cc_start: 0.8800 (m110) cc_final: 0.8426 (m110) REVERT: D 240 TYR cc_start: 0.7635 (t80) cc_final: 0.7379 (t80) REVERT: D 243 PRO cc_start: 0.8476 (Cg_exo) cc_final: 0.7540 (Cg_endo) REVERT: D 246 GLN cc_start: 0.8335 (pt0) cc_final: 0.7773 (pt0) REVERT: D 256 ARG cc_start: 0.7869 (mtm-85) cc_final: 0.7359 (mtm-85) REVERT: D 259 GLU cc_start: 0.8294 (tp30) cc_final: 0.7858 (tp30) REVERT: D 266 PHE cc_start: 0.8313 (m-80) cc_final: 0.7555 (m-80) REVERT: D 283 MET cc_start: 0.8377 (mmp) cc_final: 0.7917 (mmp) REVERT: D 286 ASP cc_start: 0.8482 (t0) cc_final: 0.8031 (t0) REVERT: D 288 ASP cc_start: 0.8146 (m-30) cc_final: 0.7586 (m-30) REVERT: D 289 ILE cc_start: 0.7938 (pt) cc_final: 0.7655 (mt) REVERT: D 290 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7008 (mtt180) REVERT: D 294 TYR cc_start: 0.8324 (m-80) cc_final: 0.7644 (m-80) REVERT: D 298 VAL cc_start: 0.8409 (t) cc_final: 0.8105 (t) REVERT: D 305 MET cc_start: 0.6923 (mmp) cc_final: 0.6646 (mmt) REVERT: D 309 ILE cc_start: 0.8671 (pt) cc_final: 0.8290 (mt) REVERT: D 312 ARG cc_start: 0.8835 (tpt-90) cc_final: 0.7824 (tpt-90) REVERT: D 314 GLN cc_start: 0.9036 (mt0) cc_final: 0.8599 (mm110) REVERT: D 316 GLU cc_start: 0.8765 (mm-30) cc_final: 0.7975 (mm-30) REVERT: D 325 MET cc_start: 0.8271 (tpt) cc_final: 0.7906 (tpp) REVERT: D 329 ILE cc_start: 0.8686 (mm) cc_final: 0.7482 (mm) REVERT: D 340 TRP cc_start: 0.7683 (t60) cc_final: 0.6746 (t60) REVERT: D 345 ILE cc_start: 0.8359 (tp) cc_final: 0.7983 (pt) REVERT: D 346 LEU cc_start: 0.8284 (tp) cc_final: 0.7899 (tp) REVERT: D 361 GLU cc_start: 0.8796 (mp0) cc_final: 0.8522 (pm20) REVERT: D 371 HIS cc_start: 0.7512 (p90) cc_final: 0.7064 (p90) outliers start: 0 outliers final: 0 residues processed: 741 average time/residue: 0.1239 time to fit residues: 127.8803 Evaluate side-chains 700 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 700 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 74 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 118 optimal weight: 0.0370 chunk 167 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 61 HIS A 200 ASN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 GLN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS C 40 HIS C 128 ASN C 263 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.106670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.082010 restraints weight = 44256.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.085552 restraints weight = 26349.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.088061 restraints weight = 17745.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.089870 restraints weight = 12964.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.091201 restraints weight = 10077.736| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.8529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.160 15178 Z= 0.350 Angle : 0.870 10.242 20547 Z= 0.468 Chirality : 0.050 0.226 2251 Planarity : 0.007 0.091 2631 Dihedral : 9.725 169.450 2071 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.49 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.19), residues: 1847 helix: 0.20 (0.17), residues: 827 sheet: -1.31 (0.28), residues: 283 loop : -0.52 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A 691 TYR 0.029 0.003 TYR A 439 PHE 0.022 0.002 PHE B 256 TRP 0.029 0.003 TRP C 79 HIS 0.011 0.002 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00656 (15177) covalent geometry : angle 0.87028 (20547) hydrogen bonds : bond 0.05453 ( 724) hydrogen bonds : angle 5.95056 ( 2007) Misc. bond : bond 0.00137 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 782 time to evaluate : 0.463 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 5 GLU cc_start: 0.8241 (mp0) cc_final: 0.7896 (mp0) REVERT: A 20 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7652 (mm-30) REVERT: A 59 LEU cc_start: 0.7926 (mt) cc_final: 0.7535 (mt) REVERT: A 73 ASP cc_start: 0.7533 (t0) cc_final: 0.6948 (t0) REVERT: A 92 ARG cc_start: 0.8529 (mmp80) cc_final: 0.7770 (mtt90) REVERT: A 138 HIS cc_start: 0.5971 (t-170) cc_final: 0.5518 (t-90) REVERT: A 174 LYS cc_start: 0.8736 (ptpp) cc_final: 0.8190 (pttm) REVERT: A 177 MET cc_start: 0.8200 (mtp) cc_final: 0.7799 (mtp) REVERT: A 179 TYR cc_start: 0.8283 (t80) cc_final: 0.8052 (t80) REVERT: A 180 PHE cc_start: 0.8666 (m-80) cc_final: 0.8293 (m-80) REVERT: A 204 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8138 (mm-30) REVERT: A 219 ARG cc_start: 0.7393 (mmm160) cc_final: 0.6482 (mmm160) REVERT: A 223 TYR cc_start: 0.8183 (t80) cc_final: 0.6744 (t80) REVERT: A 224 ILE cc_start: 0.8820 (pt) cc_final: 0.8290 (pt) REVERT: A 225 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7283 (mp0) REVERT: A 240 ARG cc_start: 0.8027 (ttm170) cc_final: 0.6862 (ttm170) REVERT: A 259 TYR cc_start: 0.7968 (m-80) cc_final: 0.7144 (m-10) REVERT: A 262 PHE cc_start: 0.8528 (m-80) cc_final: 0.7901 (m-80) REVERT: A 286 HIS cc_start: 0.7461 (t70) cc_final: 0.7158 (t-90) REVERT: A 307 HIS cc_start: 0.8873 (m90) cc_final: 0.8605 (m90) REVERT: A 327 ARG cc_start: 0.8548 (mmt-90) cc_final: 0.8244 (mmt180) REVERT: A 329 LEU cc_start: 0.8508 (mt) cc_final: 0.8099 (pp) REVERT: A 370 GLU cc_start: 0.8412 (tt0) cc_final: 0.7812 (tm-30) REVERT: A 371 MET cc_start: 0.9174 (mtm) cc_final: 0.8429 (mtp) REVERT: A 373 HIS cc_start: 0.8533 (t70) cc_final: 0.8126 (t70) REVERT: A 395 GLN cc_start: 0.8251 (mt0) cc_final: 0.7703 (mt0) REVERT: A 400 ARG cc_start: 0.8507 (ptt90) cc_final: 0.8001 (ttp-110) REVERT: A 401 ASP cc_start: 0.8450 (p0) cc_final: 0.8204 (p0) REVERT: A 408 TYR cc_start: 0.8823 (t80) cc_final: 0.7859 (t80) REVERT: A 410 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8449 (mmtm) REVERT: A 423 LEU cc_start: 0.7489 (mt) cc_final: 0.6844 (mt) REVERT: A 433 ILE cc_start: 0.8266 (tp) cc_final: 0.8051 (tp) REVERT: A 451 GLN cc_start: 0.8922 (mp10) cc_final: 0.8584 (mp10) REVERT: A 452 PHE cc_start: 0.8590 (t80) cc_final: 0.8035 (t80) REVERT: A 456 TYR cc_start: 0.8820 (t80) cc_final: 0.8364 (t80) REVERT: A 466 ASN cc_start: 0.8518 (m-40) cc_final: 0.8125 (t0) REVERT: A 468 HIS cc_start: 0.8408 (t-90) cc_final: 0.7833 (t-90) REVERT: A 472 LEU cc_start: 0.8695 (mt) cc_final: 0.8355 (mt) REVERT: A 473 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8456 (mp0) REVERT: A 475 GLU cc_start: 0.8500 (mp0) cc_final: 0.8152 (pm20) REVERT: A 478 MET cc_start: 0.8678 (mtm) cc_final: 0.8364 (mtm) REVERT: A 498 LEU cc_start: 0.9060 (mp) cc_final: 0.8415 (tt) REVERT: A 512 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7800 (mm-30) REVERT: A 521 ASP cc_start: 0.8685 (p0) cc_final: 0.8455 (p0) REVERT: A 522 THR cc_start: 0.8507 (p) cc_final: 0.7692 (p) REVERT: A 525 GLN cc_start: 0.8535 (tp40) cc_final: 0.8009 (pp30) REVERT: A 528 TYR cc_start: 0.8711 (m-80) cc_final: 0.8412 (m-80) REVERT: A 529 ASN cc_start: 0.8690 (m-40) cc_final: 0.8421 (m-40) REVERT: A 532 LEU cc_start: 0.7994 (mt) cc_final: 0.7529 (mt) REVERT: A 534 LYS cc_start: 0.8370 (pttt) cc_final: 0.8127 (pttt) REVERT: A 537 LEU cc_start: 0.9021 (mp) cc_final: 0.8734 (mp) REVERT: A 538 PHE cc_start: 0.8120 (t80) cc_final: 0.7390 (t80) REVERT: A 543 MET cc_start: 0.7690 (mmt) cc_final: 0.7299 (mmt) REVERT: A 545 ASN cc_start: 0.8122 (t0) cc_final: 0.7710 (t0) REVERT: A 556 LYS cc_start: 0.8666 (mttt) cc_final: 0.8144 (mttp) REVERT: A 558 GLU cc_start: 0.7954 (tt0) cc_final: 0.7604 (tm-30) REVERT: A 559 TYR cc_start: 0.7397 (m-80) cc_final: 0.7113 (m-80) REVERT: A 568 ASN cc_start: 0.8454 (t0) cc_final: 0.8135 (t0) REVERT: A 633 LYS cc_start: 0.7214 (mmtt) cc_final: 0.6742 (mmtm) REVERT: A 637 HIS cc_start: 0.8325 (t-90) cc_final: 0.7704 (t-90) REVERT: A 638 GLN cc_start: 0.9014 (pt0) cc_final: 0.8603 (pt0) REVERT: A 641 ASN cc_start: 0.9196 (m110) cc_final: 0.8687 (m-40) REVERT: A 643 LEU cc_start: 0.8871 (tp) cc_final: 0.8252 (tp) REVERT: A 647 MET cc_start: 0.8950 (mmm) cc_final: 0.8389 (mmm) REVERT: A 657 TYR cc_start: 0.6296 (m-80) cc_final: 0.5844 (m-80) REVERT: A 666 PHE cc_start: 0.8491 (m-10) cc_final: 0.8119 (m-10) REVERT: A 688 GLU cc_start: 0.8813 (tp30) cc_final: 0.8364 (tp30) REVERT: A 706 PHE cc_start: 0.8414 (t80) cc_final: 0.8210 (t80) REVERT: A 741 TYR cc_start: 0.8671 (p90) cc_final: 0.8068 (p90) REVERT: A 750 PHE cc_start: 0.8862 (m-10) cc_final: 0.8465 (m-10) REVERT: A 757 TYR cc_start: 0.8989 (t80) cc_final: 0.8594 (t80) REVERT: B 32 PHE cc_start: 0.8147 (p90) cc_final: 0.7904 (p90) REVERT: B 35 ILE cc_start: 0.8478 (mt) cc_final: 0.7874 (tp) REVERT: B 48 MET cc_start: 0.7582 (mmt) cc_final: 0.7203 (tpp) REVERT: B 51 LYS cc_start: 0.8164 (mppt) cc_final: 0.7901 (mmtm) REVERT: B 54 TYR cc_start: 0.8256 (m-80) cc_final: 0.7902 (m-80) REVERT: B 58 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8160 (pt0) REVERT: B 62 LYS cc_start: 0.8939 (mmtp) cc_final: 0.8694 (mmtp) REVERT: B 76 ILE cc_start: 0.8547 (pt) cc_final: 0.8235 (tp) REVERT: B 83 MET cc_start: 0.8209 (tpp) cc_final: 0.7932 (tpp) REVERT: B 84 GLU cc_start: 0.8848 (tt0) cc_final: 0.8373 (tm-30) REVERT: B 85 LYS cc_start: 0.9276 (mttm) cc_final: 0.8926 (mttm) REVERT: B 100 GLU cc_start: 0.8448 (mp0) cc_final: 0.8092 (mp0) REVERT: B 101 GLU cc_start: 0.8278 (pm20) cc_final: 0.7972 (pm20) REVERT: B 114 LYS cc_start: 0.8483 (ptmm) cc_final: 0.7992 (ptmm) REVERT: B 118 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7203 (mm-30) REVERT: B 120 MET cc_start: 0.8502 (ttm) cc_final: 0.8138 (tmm) REVERT: B 123 ILE cc_start: 0.8509 (mt) cc_final: 0.8231 (mt) REVERT: B 124 MET cc_start: 0.8389 (tpp) cc_final: 0.7868 (tpp) REVERT: B 128 PHE cc_start: 0.8167 (m-80) cc_final: 0.7411 (m-80) REVERT: B 133 MET cc_start: 0.7663 (ttp) cc_final: 0.7097 (ttp) REVERT: B 134 TYR cc_start: 0.7226 (t80) cc_final: 0.6761 (t80) REVERT: B 144 TYR cc_start: 0.8593 (m-10) cc_final: 0.8358 (m-80) REVERT: B 163 ASN cc_start: 0.7755 (t0) cc_final: 0.7337 (t0) REVERT: B 168 GLU cc_start: 0.8221 (tp30) cc_final: 0.7933 (tp30) REVERT: B 184 ARG cc_start: 0.8315 (ttm170) cc_final: 0.7753 (ttm110) REVERT: B 192 LYS cc_start: 0.8291 (ptmt) cc_final: 0.7966 (ptmt) REVERT: B 199 TYR cc_start: 0.7905 (m-80) cc_final: 0.7553 (m-80) REVERT: B 201 PHE cc_start: 0.7589 (m-10) cc_final: 0.7207 (m-80) REVERT: B 207 ARG cc_start: 0.8602 (mtt90) cc_final: 0.8169 (mtt-85) REVERT: B 208 GLU cc_start: 0.7985 (pp20) cc_final: 0.7689 (pm20) REVERT: B 209 ILE cc_start: 0.8677 (mm) cc_final: 0.8285 (mm) REVERT: B 211 ARG cc_start: 0.8746 (ppt170) cc_final: 0.8460 (ttp80) REVERT: B 212 ASP cc_start: 0.8671 (m-30) cc_final: 0.8323 (m-30) REVERT: B 214 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8821 (ttpt) REVERT: B 225 GLU cc_start: 0.8486 (mp0) cc_final: 0.8284 (pm20) REVERT: B 226 ASN cc_start: 0.8619 (t0) cc_final: 0.8352 (t0) REVERT: B 230 THR cc_start: 0.8474 (m) cc_final: 0.8142 (p) REVERT: B 249 ILE cc_start: 0.8956 (pt) cc_final: 0.8743 (pt) REVERT: B 260 GLU cc_start: 0.8310 (tp30) cc_final: 0.8091 (tp30) REVERT: B 263 PHE cc_start: 0.8552 (m-80) cc_final: 0.8023 (m-80) REVERT: B 267 PHE cc_start: 0.8140 (m-10) cc_final: 0.7730 (m-10) REVERT: B 277 GLU cc_start: 0.8443 (tp30) cc_final: 0.8207 (tp30) REVERT: B 287 ASP cc_start: 0.8196 (t70) cc_final: 0.7889 (t70) REVERT: B 292 LYS cc_start: 0.8750 (pttm) cc_final: 0.8313 (pttm) REVERT: B 293 ASP cc_start: 0.8585 (m-30) cc_final: 0.8384 (m-30) REVERT: B 298 ASN cc_start: 0.7125 (m-40) cc_final: 0.6675 (m-40) REVERT: B 300 MET cc_start: 0.7903 (mmm) cc_final: 0.7354 (mmm) REVERT: B 306 MET cc_start: 0.7547 (mmt) cc_final: 0.7281 (mmt) REVERT: B 310 ILE cc_start: 0.8875 (tt) cc_final: 0.7707 (mm) REVERT: B 313 ARG cc_start: 0.8779 (tpt-90) cc_final: 0.8377 (tpp-160) REVERT: B 314 MET cc_start: 0.8614 (tpt) cc_final: 0.8021 (mmm) REVERT: B 315 GLN cc_start: 0.8377 (mm110) cc_final: 0.8160 (mm110) REVERT: B 316 LYS cc_start: 0.8842 (ptpt) cc_final: 0.8537 (ptpt) REVERT: B 330 ILE cc_start: 0.8482 (mm) cc_final: 0.8279 (mm) REVERT: B 335 GLU cc_start: 0.7834 (mm-30) cc_final: 0.6600 (mm-30) REVERT: B 338 TYR cc_start: 0.8096 (m-80) cc_final: 0.7286 (m-80) REVERT: B 355 GLN cc_start: 0.8606 (pp30) cc_final: 0.7646 (pp30) REVERT: B 356 MET cc_start: 0.8764 (mtm) cc_final: 0.7937 (mmm) REVERT: B 358 ILE cc_start: 0.8079 (mp) cc_final: 0.7874 (mm) REVERT: B 360 LYS cc_start: 0.8364 (tptp) cc_final: 0.7779 (tptp) REVERT: B 362 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8394 (tm-30) REVERT: B 364 ASP cc_start: 0.8004 (m-30) cc_final: 0.7336 (m-30) REVERT: B 370 ILE cc_start: 0.8611 (tp) cc_final: 0.8015 (tp) REVERT: B 372 HIS cc_start: 0.8217 (m-70) cc_final: 0.7621 (m90) REVERT: C 34 ILE cc_start: 0.8206 (mp) cc_final: 0.7789 (tt) REVERT: C 37 ARG cc_start: 0.7724 (mmm-85) cc_final: 0.7168 (mmm-85) REVERT: C 44 MET cc_start: 0.8458 (ppp) cc_final: 0.7684 (ppp) REVERT: C 50 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8391 (mtmt) REVERT: C 61 LYS cc_start: 0.8716 (mmtm) cc_final: 0.8282 (mmtm) REVERT: C 82 MET cc_start: 0.7817 (tpp) cc_final: 0.7167 (tpp) REVERT: C 84 LYS cc_start: 0.9052 (ttmm) cc_final: 0.8692 (ttmm) REVERT: C 87 HIS cc_start: 0.8319 (t70) cc_final: 0.7549 (t-90) REVERT: C 90 PHE cc_start: 0.7934 (m-10) cc_final: 0.7288 (m-80) REVERT: C 91 TYR cc_start: 0.8054 (m-80) cc_final: 0.7604 (m-80) REVERT: C 92 ASN cc_start: 0.7622 (m-40) cc_final: 0.7323 (m110) REVERT: C 105 LEU cc_start: 0.8115 (mm) cc_final: 0.7727 (mm) REVERT: C 107 GLU cc_start: 0.7241 (pm20) cc_final: 0.6930 (pm20) REVERT: C 111 ASN cc_start: 0.9094 (t0) cc_final: 0.8670 (t0) REVERT: C 113 LYS cc_start: 0.8472 (mttp) cc_final: 0.7641 (mttp) REVERT: C 116 ARG cc_start: 0.8491 (ttm110) cc_final: 0.8070 (ttm110) REVERT: C 118 LYS cc_start: 0.8189 (tptt) cc_final: 0.7594 (tptt) REVERT: C 119 MET cc_start: 0.8401 (ttm) cc_final: 0.8180 (ttm) REVERT: C 121 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8439 (tm-30) REVERT: C 123 MET cc_start: 0.8470 (tpp) cc_final: 0.7697 (tpp) REVERT: C 127 PHE cc_start: 0.8217 (m-80) cc_final: 0.7443 (m-80) REVERT: C 136 ILE cc_start: 0.8747 (mm) cc_final: 0.8328 (pt) REVERT: C 153 LEU cc_start: 0.8389 (tp) cc_final: 0.7958 (tp) REVERT: C 157 ASP cc_start: 0.7080 (t0) cc_final: 0.6365 (t0) REVERT: C 163 VAL cc_start: 0.7909 (t) cc_final: 0.7698 (t) REVERT: C 164 PRO cc_start: 0.7539 (Cg_endo) cc_final: 0.7254 (Cg_exo) REVERT: C 176 MET cc_start: 0.7142 (mtt) cc_final: 0.6643 (mtt) REVERT: C 183 ARG cc_start: 0.8332 (ttm-80) cc_final: 0.8008 (ttm-80) REVERT: C 187 ASP cc_start: 0.8942 (m-30) cc_final: 0.8736 (m-30) REVERT: C 207 GLU cc_start: 0.8274 (pp20) cc_final: 0.7605 (pp20) REVERT: C 211 ASP cc_start: 0.8331 (m-30) cc_final: 0.7620 (m-30) REVERT: C 213 LYS cc_start: 0.9029 (ttpt) cc_final: 0.8588 (ttpt) REVERT: C 216 LEU cc_start: 0.8463 (mp) cc_final: 0.8223 (mp) REVERT: C 218 TYR cc_start: 0.6642 (p90) cc_final: 0.6092 (p90) REVERT: C 240 TYR cc_start: 0.8007 (t80) cc_final: 0.7667 (t80) REVERT: C 242 LEU cc_start: 0.8709 (mp) cc_final: 0.8181 (mp) REVERT: C 253 GLU cc_start: 0.8412 (mp0) cc_final: 0.8184 (mp0) REVERT: C 262 PHE cc_start: 0.8631 (m-10) cc_final: 0.8403 (m-10) REVERT: C 279 TYR cc_start: 0.8678 (t80) cc_final: 0.8399 (t80) REVERT: C 283 MET cc_start: 0.8401 (mmm) cc_final: 0.8075 (mmm) REVERT: C 284 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8402 (mtpt) REVERT: C 294 TYR cc_start: 0.7945 (m-80) cc_final: 0.7439 (m-80) REVERT: C 296 ASN cc_start: 0.7495 (p0) cc_final: 0.6817 (p0) REVERT: C 299 MET cc_start: 0.7722 (mmm) cc_final: 0.7144 (mmm) REVERT: C 361 GLU cc_start: 0.8774 (tp30) cc_final: 0.8039 (tp30) REVERT: C 371 HIS cc_start: 0.7597 (m90) cc_final: 0.7205 (m90) REVERT: D 8 LEU cc_start: 0.7827 (mt) cc_final: 0.7522 (mt) REVERT: D 24 ASP cc_start: 0.6804 (t0) cc_final: 0.6560 (t0) REVERT: D 41 GLN cc_start: 0.7937 (tp40) cc_final: 0.7560 (tm-30) REVERT: D 52 SER cc_start: 0.7925 (t) cc_final: 0.7706 (m) REVERT: D 65 LEU cc_start: 0.8499 (mt) cc_final: 0.8254 (mt) REVERT: D 67 LEU cc_start: 0.8053 (mt) cc_final: 0.7729 (mt) REVERT: D 72 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7513 (tm-30) REVERT: D 84 LYS cc_start: 0.8633 (mmtp) cc_final: 0.8285 (mmtt) REVERT: D 87 HIS cc_start: 0.8604 (t-90) cc_final: 0.8077 (t70) REVERT: D 91 TYR cc_start: 0.8679 (m-80) cc_final: 0.8109 (m-80) REVERT: D 99 GLU cc_start: 0.7156 (mp0) cc_final: 0.6846 (mp0) REVERT: D 111 ASN cc_start: 0.8411 (m-40) cc_final: 0.8151 (m-40) REVERT: D 116 ARG cc_start: 0.8388 (mtt-85) cc_final: 0.7921 (mtt-85) REVERT: D 117 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8121 (mt-10) REVERT: D 119 MET cc_start: 0.8921 (ttm) cc_final: 0.8549 (ttm) REVERT: D 121 GLN cc_start: 0.8835 (pp30) cc_final: 0.8567 (pp30) REVERT: D 124 PHE cc_start: 0.8169 (m-80) cc_final: 0.7658 (m-80) REVERT: D 137 GLN cc_start: 0.8280 (mt0) cc_final: 0.7834 (mt0) REVERT: D 143 TYR cc_start: 0.7284 (m-80) cc_final: 0.6774 (m-80) REVERT: D 175 ILE cc_start: 0.8638 (pt) cc_final: 0.8041 (pt) REVERT: D 176 MET cc_start: 0.7025 (mmm) cc_final: 0.6769 (mmm) REVERT: D 191 LYS cc_start: 0.8851 (ttpt) cc_final: 0.8566 (ttpt) REVERT: D 192 ILE cc_start: 0.8228 (tp) cc_final: 0.7641 (tp) REVERT: D 195 GLU cc_start: 0.6566 (mp0) cc_final: 0.6325 (mp0) REVERT: D 207 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7015 (mm-30) REVERT: D 210 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7515 (ttp-110) REVERT: D 214 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8007 (tt0) REVERT: D 240 TYR cc_start: 0.7893 (t80) cc_final: 0.7630 (t80) REVERT: D 243 PRO cc_start: 0.8688 (Cg_exo) cc_final: 0.7778 (Cg_endo) REVERT: D 254 ARG cc_start: 0.7748 (ptm-80) cc_final: 0.7465 (ptm-80) REVERT: D 256 ARG cc_start: 0.8030 (mtm-85) cc_final: 0.7442 (mtm-85) REVERT: D 259 GLU cc_start: 0.8385 (tp30) cc_final: 0.8099 (tp30) REVERT: D 266 PHE cc_start: 0.8895 (m-80) cc_final: 0.8506 (m-80) REVERT: D 279 TYR cc_start: 0.8034 (t80) cc_final: 0.7531 (t80) REVERT: D 283 MET cc_start: 0.8574 (mmp) cc_final: 0.8102 (mmp) REVERT: D 286 ASP cc_start: 0.8290 (t0) cc_final: 0.7693 (t0) REVERT: D 288 ASP cc_start: 0.8258 (m-30) cc_final: 0.7675 (m-30) REVERT: D 289 ILE cc_start: 0.8370 (pt) cc_final: 0.7732 (mt) REVERT: D 293 LEU cc_start: 0.9005 (mt) cc_final: 0.8606 (mt) REVERT: D 294 TYR cc_start: 0.8241 (m-80) cc_final: 0.7684 (m-80) REVERT: D 296 ASN cc_start: 0.7670 (p0) cc_final: 0.7088 (p0) REVERT: D 297 ASN cc_start: 0.8147 (p0) cc_final: 0.7652 (p0) REVERT: D 298 VAL cc_start: 0.8159 (t) cc_final: 0.7917 (t) REVERT: D 299 MET cc_start: 0.7917 (mmm) cc_final: 0.7400 (mmm) REVERT: D 305 MET cc_start: 0.7387 (mmp) cc_final: 0.7088 (mmm) REVERT: D 312 ARG cc_start: 0.8863 (tpt-90) cc_final: 0.7680 (tpp80) REVERT: D 314 GLN cc_start: 0.9073 (mt0) cc_final: 0.8636 (mm110) REVERT: D 316 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8129 (mm-30) REVERT: D 320 LEU cc_start: 0.8883 (mt) cc_final: 0.8562 (mt) REVERT: D 325 MET cc_start: 0.8352 (tpt) cc_final: 0.8108 (tpp) REVERT: D 326 LYS cc_start: 0.8317 (mmtt) cc_final: 0.8082 (mmtt) REVERT: D 329 ILE cc_start: 0.8532 (mm) cc_final: 0.6872 (mm) REVERT: D 340 TRP cc_start: 0.7681 (t60) cc_final: 0.6880 (t60) REVERT: D 345 ILE cc_start: 0.8388 (tp) cc_final: 0.8043 (pt) REVERT: D 361 GLU cc_start: 0.8919 (mp0) cc_final: 0.8601 (pm20) REVERT: D 373 LYS cc_start: 0.8745 (mmtt) cc_final: 0.8324 (mmtt) outliers start: 0 outliers final: 0 residues processed: 782 average time/residue: 0.1138 time to fit residues: 124.4709 Evaluate side-chains 714 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 714 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 179 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 398 ASN A 458 ASN A 679 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 HIS B 174 HIS C 12 ASN C 128 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.110669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.085545 restraints weight = 42620.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.089236 restraints weight = 25391.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.091850 restraints weight = 17113.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.093732 restraints weight = 12487.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.095099 restraints weight = 9663.347| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.8630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15178 Z= 0.163 Angle : 0.751 9.435 20547 Z= 0.385 Chirality : 0.047 0.257 2251 Planarity : 0.007 0.177 2631 Dihedral : 9.280 173.562 2071 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 0.06 % Allowed : 0.13 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.19), residues: 1847 helix: 0.43 (0.18), residues: 837 sheet: -1.38 (0.29), residues: 270 loop : -0.46 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 691 TYR 0.025 0.002 TYR A 439 PHE 0.029 0.002 PHE B 353 TRP 0.045 0.003 TRP C 79 HIS 0.006 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00356 (15177) covalent geometry : angle 0.75123 (20547) hydrogen bonds : bond 0.04214 ( 724) hydrogen bonds : angle 5.39761 ( 2007) Misc. bond : bond 0.00073 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3204.17 seconds wall clock time: 55 minutes 50.91 seconds (3350.91 seconds total)