Starting phenix.real_space_refine on Fri Jul 3 09:28:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8a5a_15163/07_2026/8a5a_15163.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a5a_15163/07_2026/8a5a_15163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a5a_15163/07_2026/8a5a_15163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a5a_15163/07_2026/8a5a_15163.map" model { file = "/net/cci-nas-00/data/ceres_data/8a5a_15163/07_2026/8a5a_15163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a5a_15163/07_2026/8a5a_15163.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8a5a_15163/07_2026/8a5a_15163.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8a5a_15163/07_2026/8a5a_15163.cif" } resolution = 3.3 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= 0.006 sd= 0.157 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 3 5.21 5 S 49 5.16 5 C 8361 2.51 5 N 2238 2.21 5 O 2531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13191 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 938 Classifications: {'peptide': 110} Link IDs: {'TRANS': 109} Chain: "U" Number of atoms: 5582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5582 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 656} Chain breaks: 1 Chain: "V" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2830 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "W" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3398 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Chain: "X" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 347 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 2, 'TRANS': 37} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.94, per 1000 atoms: 0.22 Number of scatterers: 13191 At special positions: 0 Unit cell: (100.605, 99.546, 163.086, 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 49 16.00 P 9 15.00 Mg 3 11.99 O 2531 8.00 N 2238 7.00 C 8361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 618.4 milliseconds 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 20 sheets defined 51.9% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'G' and resid 458 through 482 Processing helix chain 'G' and resid 484 through 514 Processing helix chain 'G' and resid 515 through 519 Processing helix chain 'G' and resid 521 through 560 Processing helix chain 'U' and resid 166 through 178 removed outlier: 3.951A pdb=" N PHE U 170 " --> pdb=" O ALA U 166 " (cutoff:3.500A) Processing helix chain 'U' and resid 215 through 228 Processing helix chain 'U' and resid 300 through 302 No H-bonds generated for 'chain 'U' and resid 300 through 302' Processing helix chain 'U' and resid 320 through 341 Processing helix chain 'U' and resid 348 through 360 removed outlier: 3.668A pdb=" N ASN U 359 " --> pdb=" O SER U 355 " (cutoff:3.500A) Processing helix chain 'U' and resid 366 through 370 Processing helix chain 'U' and resid 387 through 392 Processing helix chain 'U' and resid 417 through 434 Processing helix chain 'U' and resid 444 through 448 Processing helix chain 'U' and resid 459 through 472 removed outlier: 3.610A pdb=" N ARG U 468 " --> pdb=" O GLU U 464 " (cutoff:3.500A) Processing helix chain 'U' and resid 484 through 493 Processing helix chain 'U' and resid 520 through 523 Processing helix chain 'U' and resid 529 through 544 Processing helix chain 'U' and resid 555 through 570 removed outlier: 4.180A pdb=" N LEU U 561 " --> pdb=" O HIS U 557 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG U 564 " --> pdb=" O LEU U 560 " (cutoff:3.500A) Processing helix chain 'U' and resid 573 through 577 Processing helix chain 'U' and resid 602 through 610 Proline residue: U 608 - end of helix Processing helix chain 'U' and resid 611 through 613 No H-bonds generated for 'chain 'U' and resid 611 through 613' Processing helix chain 'U' and resid 614 through 621 removed outlier: 3.715A pdb=" N LYS U 618 " --> pdb=" O PRO U 614 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU U 619 " --> pdb=" O GLN U 615 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG U 621 " --> pdb=" O PHE U 617 " (cutoff:3.500A) Processing helix chain 'U' and resid 629 through 633 Processing helix chain 'U' and resid 650 through 658 Processing helix chain 'U' and resid 661 through 665 Processing helix chain 'U' and resid 667 through 676 Processing helix chain 'U' and resid 677 through 688 Processing helix chain 'U' and resid 688 through 693 removed outlier: 3.602A pdb=" N GLY U 693 " --> pdb=" O PRO U 689 " (cutoff:3.500A) Processing helix chain 'U' and resid 702 through 716 removed outlier: 3.958A pdb=" N ASN U 713 " --> pdb=" O GLN U 709 " (cutoff:3.500A) Processing helix chain 'U' and resid 717 through 718 No H-bonds generated for 'chain 'U' and resid 717 through 718' Processing helix chain 'U' and resid 719 through 721 No H-bonds generated for 'chain 'U' and resid 719 through 721' Processing helix chain 'U' and resid 722 through 728 Processing helix chain 'U' and resid 734 through 739 Processing helix chain 'U' and resid 741 through 754 removed outlier: 3.518A pdb=" N ILE U 745 " --> pdb=" O ALA U 741 " (cutoff:3.500A) Processing helix chain 'U' and resid 755 through 760 removed outlier: 4.427A pdb=" N SER U 760 " --> pdb=" O SER U 756 " (cutoff:3.500A) Processing helix chain 'U' and resid 762 through 781 Processing helix chain 'U' and resid 788 through 816 Processing helix chain 'U' and resid 818 through 823 removed outlier: 3.838A pdb=" N ASN U 821 " --> pdb=" O GLN U 818 " (cutoff:3.500A) Processing helix chain 'U' and resid 840 through 851 removed outlier: 3.629A pdb=" N ALA U 846 " --> pdb=" O ILE U 842 " (cutoff:3.500A) Processing helix chain 'U' and resid 852 through 858 removed outlier: 3.560A pdb=" N GLU U 856 " --> pdb=" O LYS U 853 " (cutoff:3.500A) Processing helix chain 'U' and resid 862 through 869 removed outlier: 4.050A pdb=" N VAL U 867 " --> pdb=" O SER U 863 " (cutoff:3.500A) Processing helix chain 'U' and resid 870 through 875 Processing helix chain 'V' and resid 55 through 61 Processing helix chain 'V' and resid 78 through 92 removed outlier: 3.777A pdb=" N LYS V 84 " --> pdb=" O ASP V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 101 Processing helix chain 'V' and resid 112 through 128 removed outlier: 3.566A pdb=" N ARG V 116 " --> pdb=" O PRO V 112 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE V 124 " --> pdb=" O THR V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 137 through 144 Processing helix chain 'V' and resid 172 through 175 removed outlier: 3.553A pdb=" N ILE V 175 " --> pdb=" O PRO V 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 172 through 175' Processing helix chain 'V' and resid 181 through 195 Processing helix chain 'V' and resid 202 through 217 removed outlier: 3.754A pdb=" N GLU V 207 " --> pdb=" O THR V 203 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE V 208 " --> pdb=" O ALA V 204 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP V 211 " --> pdb=" O GLU V 207 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS V 217 " --> pdb=" O LYS V 213 " (cutoff:3.500A) Processing helix chain 'V' and resid 222 through 233 removed outlier: 3.568A pdb=" N GLU V 226 " --> pdb=" O ASP V 222 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER V 233 " --> pdb=" O THR V 229 " (cutoff:3.500A) Processing helix chain 'V' and resid 252 through 260 removed outlier: 3.541A pdb=" N ALA V 257 " --> pdb=" O GLU V 253 " (cutoff:3.500A) Proline residue: V 258 - end of helix Processing helix chain 'V' and resid 261 through 262 No H-bonds generated for 'chain 'V' and resid 261 through 262' Processing helix chain 'V' and resid 263 through 268 Processing helix chain 'V' and resid 273 through 283 Processing helix chain 'V' and resid 289 through 295 Processing helix chain 'V' and resid 301 through 306 removed outlier: 4.272A pdb=" N PHE V 306 " --> pdb=" O THR V 303 " (cutoff:3.500A) Processing helix chain 'V' and resid 308 through 321 Processing helix chain 'V' and resid 337 through 347 removed outlier: 3.508A pdb=" N GLY V 343 " --> pdb=" O VAL V 339 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 356 removed outlier: 3.598A pdb=" N MET V 355 " --> pdb=" O THR V 351 " (cutoff:3.500A) Processing helix chain 'V' and resid 359 through 366 Processing helix chain 'V' and resid 367 through 372 Processing helix chain 'W' and resid 82 through 97 Processing helix chain 'W' and resid 117 through 130 removed outlier: 3.936A pdb=" N LEU W 125 " --> pdb=" O ARG W 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 141 through 151 Processing helix chain 'W' and resid 186 through 197 Processing helix chain 'W' and resid 205 through 207 No H-bonds generated for 'chain 'W' and resid 205 through 207' Processing helix chain 'W' and resid 226 through 236 removed outlier: 3.837A pdb=" N TYR W 230 " --> pdb=" O ASP W 226 " (cutoff:3.500A) Processing helix chain 'W' and resid 237 through 246 Processing helix chain 'W' and resid 258 through 265 removed outlier: 3.772A pdb=" N SER W 264 " --> pdb=" O THR W 260 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR W 265 " --> pdb=" O GLU W 261 " (cutoff:3.500A) Processing helix chain 'W' and resid 281 through 291 removed outlier: 4.009A pdb=" N ALA W 289 " --> pdb=" O ARG W 285 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU W 291 " --> pdb=" O GLY W 287 " (cutoff:3.500A) Processing helix chain 'W' and resid 307 through 311 Processing helix chain 'W' and resid 384 through 396 removed outlier: 3.526A pdb=" N ILE W 393 " --> pdb=" O VAL W 389 " (cutoff:3.500A) Processing helix chain 'W' and resid 397 through 399 No H-bonds generated for 'chain 'W' and resid 397 through 399' Processing helix chain 'W' and resid 400 through 406 Processing helix chain 'W' and resid 419 through 432 Processing helix chain 'W' and resid 446 through 462 removed outlier: 4.036A pdb=" N TYR W 450 " --> pdb=" O ILE W 446 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER W 452 " --> pdb=" O ARG W 448 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TRP W 453 " --> pdb=" O GLN W 449 " (cutoff:3.500A) Processing helix chain 'W' and resid 464 through 469 removed outlier: 3.794A pdb=" N TRP W 469 " --> pdb=" O HIS W 466 " (cutoff:3.500A) Processing helix chain 'W' and resid 471 through 479 Processing helix chain 'W' and resid 479 through 487 removed outlier: 3.938A pdb=" N ASN W 485 " --> pdb=" O GLU W 481 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 73 removed outlier: 3.971A pdb=" N GLU X 71 " --> pdb=" O ASP X 67 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'U' and resid 289 through 292 Processing sheet with id=AA2, first strand: chain 'U' and resid 384 through 385 Processing sheet with id=AA3, first strand: chain 'U' and resid 363 through 365 removed outlier: 3.864A pdb=" N THR U 593 " --> pdb=" O ILE U 365 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE U 584 " --> pdb=" O TYR U 596 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'U' and resid 403 through 404 removed outlier: 3.678A pdb=" N SER U 407 " --> pdb=" O ARG U 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'U' and resid 517 through 518 Processing sheet with id=AA6, first strand: chain 'U' and resid 517 through 518 removed outlier: 6.192A pdb=" N CYS U 499 " --> pdb=" O LEU U 731 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE U 730 " --> pdb=" O ILE U 830 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'V' and resid 29 through 32 removed outlier: 6.420A pdb=" N LEU V 8 " --> pdb=" O LEU V 104 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N THR V 106 " --> pdb=" O LEU V 8 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE V 10 " --> pdb=" O THR V 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'V' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'V' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'V' and resid 169 through 170 removed outlier: 5.851A pdb=" N ILE V 151 " --> pdb=" O VAL V 298 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N SER V 300 " --> pdb=" O ILE V 151 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU V 153 " --> pdb=" O SER V 300 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE V 297 " --> pdb=" O ILE V 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'V' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'W' and resid 38 through 41 Processing sheet with id=AB5, first strand: chain 'W' and resid 55 through 56 Processing sheet with id=AB6, first strand: chain 'W' and resid 75 through 76 Processing sheet with id=AB7, first strand: chain 'W' and resid 174 through 175 Processing sheet with id=AB8, first strand: chain 'W' and resid 174 through 175 removed outlier: 3.578A pdb=" N VAL W 409 " --> pdb=" O LEU W 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 209 through 211 removed outlier: 6.825A pdb=" N ILE W 217 " --> pdb=" O LYS W 210 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 270 through 271 Processing sheet with id=AC2, first strand: chain 'X' and resid 41 through 51 removed outlier: 3.603A pdb=" N GLY X 62 " --> pdb=" O LYS X 44 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS X 46 " --> pdb=" O PHE X 60 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N PHE X 60 " --> pdb=" O LYS X 46 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE X 48 " --> pdb=" O VAL X 58 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL X 58 " --> pdb=" O ILE X 48 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1689 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: 2.40 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2212 1.29 - 1.44: 3516 1.44 - 1.58: 7658 1.58 - 1.72: 11 1.72 - 1.87: 78 Bond restraints: 13475 Sorted by residual: bond pdb=" C ALA W 136 " pdb=" O ALA W 136 " ideal model delta sigma weight residual 1.234 1.387 -0.152 1.10e-02 8.26e+03 1.92e+02 bond pdb=" C GLY W 11 " pdb=" O GLY W 11 " ideal model delta sigma weight residual 1.236 1.350 -0.114 1.15e-02 7.56e+03 9.89e+01 bond pdb=" C THR W 26 " pdb=" O THR W 26 " ideal model delta sigma weight residual 1.235 1.347 -0.112 1.22e-02 6.72e+03 8.46e+01 bond pdb=" C THR W 175 " pdb=" O THR W 175 " ideal model delta sigma weight residual 1.234 1.318 -0.084 1.23e-02 6.61e+03 4.65e+01 bond pdb=" C TRP G 477 " pdb=" O TRP G 477 " ideal model delta sigma weight residual 1.237 1.316 -0.079 1.19e-02 7.06e+03 4.42e+01 ... (remaining 13470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.53: 17621 4.53 - 9.06: 613 9.06 - 13.59: 11 13.59 - 18.12: 3 18.12 - 22.65: 3 Bond angle restraints: 18251 Sorted by residual: angle pdb=" PA ATP W 500 " pdb=" O3A ATP W 500 " pdb=" PB ATP W 500 " ideal model delta sigma weight residual 136.83 114.18 22.65 1.00e+00 1.00e+00 5.13e+02 angle pdb=" PA ATP V 500 " pdb=" O3A ATP V 500 " pdb=" PB ATP V 500 " ideal model delta sigma weight residual 136.83 116.16 20.67 1.00e+00 1.00e+00 4.27e+02 angle pdb=" PB ATP W 500 " pdb=" O3B ATP W 500 " pdb=" PG ATP W 500 " ideal model delta sigma weight residual 139.87 119.56 20.31 1.00e+00 1.00e+00 4.12e+02 angle pdb=" PB ATP V 500 " pdb=" O3B ATP V 500 " pdb=" PG ATP V 500 " ideal model delta sigma weight residual 139.87 124.18 15.69 1.00e+00 1.00e+00 2.46e+02 angle pdb=" N ILE U 454 " pdb=" CA ILE U 454 " pdb=" CB ILE U 454 " ideal model delta sigma weight residual 111.83 105.01 6.82 6.90e-01 2.10e+00 9.78e+01 ... (remaining 18246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 7272 17.45 - 34.89: 703 34.89 - 52.34: 122 52.34 - 69.79: 34 69.79 - 87.23: 10 Dihedral angle restraints: 8141 sinusoidal: 3369 harmonic: 4772 Sorted by residual: dihedral pdb=" CA THR U 184 " pdb=" C THR U 184 " pdb=" N THR U 185 " pdb=" CA THR U 185 " ideal model delta harmonic sigma weight residual -180.00 -139.56 -40.44 0 5.00e+00 4.00e-02 6.54e+01 dihedral pdb=" CA ASP U 207 " pdb=" C ASP U 207 " pdb=" N TYR U 208 " pdb=" CA TYR U 208 " ideal model delta harmonic sigma weight residual -180.00 -146.24 -33.76 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CA LEU U 696 " pdb=" C LEU U 696 " pdb=" N LYS U 697 " pdb=" CA LYS U 697 " ideal model delta harmonic sigma weight residual 180.00 -148.05 -31.95 0 5.00e+00 4.00e-02 4.08e+01 ... (remaining 8138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1095 0.074 - 0.147: 646 0.147 - 0.221: 207 0.221 - 0.294: 56 0.294 - 0.368: 6 Chirality restraints: 2010 Sorted by residual: chirality pdb=" CA ILE W 28 " pdb=" N ILE W 28 " pdb=" C ILE W 28 " pdb=" CB ILE W 28 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA ILE V 10 " pdb=" N ILE V 10 " pdb=" C ILE V 10 " pdb=" CB ILE V 10 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB VAL V 129 " pdb=" CA VAL V 129 " pdb=" CG1 VAL V 129 " pdb=" CG2 VAL V 129 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 2007 not shown) Planarity restraints: 2336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR U 490 " -0.098 2.00e-02 2.50e+03 6.14e-02 7.53e+01 pdb=" CG TYR U 490 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR U 490 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR U 490 " 0.105 2.00e-02 2.50e+03 pdb=" CE1 TYR U 490 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TYR U 490 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR U 490 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR U 490 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 362 " -0.099 2.00e-02 2.50e+03 5.66e-02 6.41e+01 pdb=" CG TYR V 362 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR V 362 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR V 362 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR V 362 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR V 362 " 0.053 2.00e-02 2.50e+03 pdb=" CZ TYR V 362 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR V 362 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP W 469 " -0.103 2.00e-02 2.50e+03 5.04e-02 6.35e+01 pdb=" CG TRP W 469 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP W 469 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP W 469 " 0.073 2.00e-02 2.50e+03 pdb=" NE1 TRP W 469 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP W 469 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP W 469 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP W 469 " -0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP W 469 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP W 469 " -0.015 2.00e-02 2.50e+03 ... (remaining 2333 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 17 2.45 - 3.06: 8450 3.06 - 3.68: 18401 3.68 - 4.29: 28675 4.29 - 4.90: 47848 Nonbonded interactions: 103391 Sorted by model distance: nonbonded pdb=" O2G ATP W 500 " pdb="MG MG W 501 " model vdw 1.838 2.170 nonbonded pdb=" O1B ATP W 500 " pdb="MG MG W 501 " model vdw 1.943 2.170 nonbonded pdb=" O2B ATP V 500 " pdb="MG MG V 501 " model vdw 2.036 2.170 nonbonded pdb=" O2G ATP V 500 " pdb="MG MG V 501 " model vdw 2.064 2.170 nonbonded pdb=" OH TYR G 473 " pdb=" OH TYR W 138 " model vdw 2.185 3.040 ... (remaining 103386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.940 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 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 : 0.016 0.152 13475 Z= 1.149 Angle : 2.080 22.655 18251 Z= 1.498 Chirality : 0.099 0.368 2010 Planarity : 0.011 0.061 2336 Dihedral : 14.658 87.233 5045 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.90 % Favored : 94.73 % Rotamer: Outliers : 2.26 % Allowed : 5.56 % Favored : 92.18 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -2.22 (0.18), residues: 1613 helix: -2.08 (0.16), residues: 702 sheet: -0.25 (0.38), residues: 171 loop : -0.96 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG G 482 TYR 0.106 0.015 TYR W 450 PHE 0.070 0.013 PHE W 207 TRP 0.103 0.018 TRP W 469 HIS 0.033 0.007 HIS W 162 Details of bonding type rmsd/Z covalent geometry : bond 0.01587 / 1.15 (13475) covalent geometry : angle 2.07997 / 1.50 (18251) hydrogen bonds : bond 0.19711 / 13.40 ( 630) hydrogen bonds : angle 8.19746 / 5.90 ( 1689) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 294 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 468 HIS cc_start: 0.6650 (t-90) cc_final: 0.6286 (t70) REVERT: G 479 ASP cc_start: 0.5701 (m-30) cc_final: 0.5402 (t0) REVERT: G 488 MET cc_start: 0.6004 (tpt) cc_final: 0.5753 (tpt) REVERT: G 519 SER cc_start: 0.7649 (t) cc_final: 0.7365 (p) REVERT: G 522 PHE cc_start: 0.6432 (t80) cc_final: 0.6192 (t80) REVERT: U 202 LYS cc_start: 0.7414 (mttt) cc_final: 0.7207 (mptt) REVERT: U 212 ASP cc_start: 0.7353 (m-30) cc_final: 0.6887 (t0) REVERT: U 283 PRO cc_start: 0.8440 (OUTLIER) cc_final: 0.8188 (Cg_exo) REVERT: U 316 GLN cc_start: 0.6451 (mp10) cc_final: 0.6251 (mp10) REVERT: U 338 MET cc_start: 0.7669 (mmt) cc_final: 0.7404 (mmt) REVERT: U 374 ILE cc_start: 0.8001 (mt) cc_final: 0.7604 (tt) REVERT: U 497 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.7547 (p) REVERT: U 546 PHE cc_start: 0.7435 (t80) cc_final: 0.7117 (t80) REVERT: U 556 LYS cc_start: 0.6848 (mtmm) cc_final: 0.6512 (mtpp) REVERT: U 576 ASP cc_start: 0.7103 (m-30) cc_final: 0.6613 (p0) REVERT: U 586 ASN cc_start: 0.7323 (t0) cc_final: 0.6990 (t0) REVERT: U 601 PHE cc_start: 0.6483 (t80) cc_final: 0.6208 (t80) REVERT: U 626 LYS cc_start: 0.8055 (mttt) cc_final: 0.7642 (mppt) REVERT: U 631 GLU cc_start: 0.7578 (tt0) cc_final: 0.7255 (pt0) REVERT: U 661 LEU cc_start: 0.7999 (mt) cc_final: 0.7627 (mp) REVERT: U 687 ASP cc_start: 0.7177 (m-30) cc_final: 0.6902 (t0) REVERT: U 690 GLU cc_start: 0.7826 (tt0) cc_final: 0.7216 (pt0) REVERT: U 694 ASN cc_start: 0.4841 (m-40) cc_final: 0.4579 (t0) REVERT: U 713 ASN cc_start: 0.7716 (m-40) cc_final: 0.7418 (m110) REVERT: U 723 MET cc_start: 0.7714 (ttm) cc_final: 0.7309 (ttp) REVERT: U 773 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7958 (tt0) REVERT: V 52 SER cc_start: 0.8695 (p) cc_final: 0.8277 (m) REVERT: V 53 TYR cc_start: 0.7810 (m-80) cc_final: 0.7524 (m-80) REVERT: V 62 ARG cc_start: 0.6617 (ttm-80) cc_final: 0.6302 (ttm110) REVERT: V 83 GLU cc_start: 0.6425 (tt0) cc_final: 0.6198 (tm-30) REVERT: V 241 GLU cc_start: 0.7297 (tt0) cc_final: 0.7085 (tt0) REVERT: V 305 MET cc_start: 0.7907 (mmm) cc_final: 0.7557 (mmm) REVERT: V 355 MET cc_start: 0.7689 (mtm) cc_final: 0.7473 (mtm) REVERT: V 360 GLN cc_start: 0.6659 (tt0) cc_final: 0.5990 (mm110) REVERT: V 364 GLU cc_start: 0.7121 (tt0) cc_final: 0.6534 (mm-30) REVERT: V 375 PHE cc_start: 0.6779 (OUTLIER) cc_final: 0.6072 (m-80) REVERT: W 13 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6744 (mp0) REVERT: W 33 SER cc_start: 0.7284 (m) cc_final: 0.6863 (p) REVERT: W 59 GLU cc_start: 0.7918 (tt0) cc_final: 0.7662 (tt0) REVERT: W 91 GLN cc_start: 0.6472 (tt0) cc_final: 0.6131 (tp-100) REVERT: W 132 MET cc_start: 0.5781 (mtm) cc_final: 0.5550 (mtp) REVERT: W 196 LYS cc_start: 0.6515 (tttt) cc_final: 0.6269 (mtmm) REVERT: W 219 LYS cc_start: 0.6215 (tttm) cc_final: 0.5971 (ttpt) REVERT: W 298 ASP cc_start: 0.8124 (m-30) cc_final: 0.7890 (p0) REVERT: W 313 LYS cc_start: 0.6270 (tttt) cc_final: 0.6010 (tptt) REVERT: W 436 LYS cc_start: 0.7270 (mttt) cc_final: 0.6959 (pttp) REVERT: W 454 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6492 (tt) REVERT: W 481 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7648 (pm20) REVERT: X 44 LYS cc_start: 0.6972 (mmtt) cc_final: 0.6721 (mmmm) REVERT: X 54 SER cc_start: 0.7738 (t) cc_final: 0.7459 (p) REVERT: X 56 TYR cc_start: 0.6868 (m-80) cc_final: 0.6650 (m-80) outliers start: 33 outliers final: 14 residues processed: 324 average time/residue: 0.1334 time to fit residues: 60.7334 Evaluate side-chains 219 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 451 PRO Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 283 PRO Chi-restraints excluded: chain U residue 497 SER Chi-restraints excluded: chain U residue 553 ILE Chi-restraints excluded: chain U residue 555 SER Chi-restraints excluded: chain V residue 113 LYS Chi-restraints excluded: chain V residue 293 LEU Chi-restraints excluded: chain V residue 375 PHE Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 142 THR Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 417 ILE Chi-restraints excluded: chain W residue 425 MET Chi-restraints excluded: chain W residue 454 LEU Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 541 ASN U 475 GLN U 660 ASN U 709 GLN U 792 ASN U 799 GLN U 862 ASN U 868 HIS V 92 ASN V 115 ASN V 228 GLN W 7 GLN W 53 ASN W 183 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.148594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112966 restraints weight = 16697.585| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.11 r_work: 0.3135 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13475 Z= 0.150 Angle : 0.648 17.081 18251 Z= 0.346 Chirality : 0.045 0.151 2010 Planarity : 0.005 0.043 2336 Dihedral : 7.314 67.414 1801 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.36 % Favored : 97.52 % Rotamer: Outliers : 2.06 % Allowed : 9.54 % Favored : 88.40 % 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 are not related in a simple way. whole: -0.10 (0.20), residues: 1613 helix: 0.14 (0.19), residues: 713 sheet: 0.10 (0.35), residues: 209 loop : -0.16 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 65 TYR 0.022 0.002 TYR U 596 PHE 0.017 0.002 PHE U 766 TRP 0.016 0.002 TRP V 340 HIS 0.003 0.001 HIS U 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (13475) covalent geometry : angle 0.64755 / 0.35 (18251) hydrogen bonds : bond 0.04602 / 3.11 ( 630) hydrogen bonds : angle 5.00932 / 3.54 ( 1689) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 468 HIS cc_start: 0.7823 (t-90) cc_final: 0.7530 (t70) REVERT: G 479 ASP cc_start: 0.7175 (m-30) cc_final: 0.6955 (t0) REVERT: G 494 GLN cc_start: 0.7366 (mt0) cc_final: 0.7149 (tt0) REVERT: G 519 SER cc_start: 0.9056 (t) cc_final: 0.8527 (p) REVERT: G 539 MET cc_start: 0.8835 (tmm) cc_final: 0.8607 (tmm) REVERT: U 202 LYS cc_start: 0.8622 (mttt) cc_final: 0.8179 (mptt) REVERT: U 207 ASP cc_start: 0.8314 (t0) cc_final: 0.7242 (t0) REVERT: U 212 ASP cc_start: 0.7889 (m-30) cc_final: 0.7474 (t0) REVERT: U 222 LYS cc_start: 0.7496 (mmmt) cc_final: 0.7121 (mtpt) REVERT: U 573 GLN cc_start: 0.7888 (tt0) cc_final: 0.7633 (tp-100) REVERT: U 576 ASP cc_start: 0.7554 (m-30) cc_final: 0.7072 (p0) REVERT: U 586 ASN cc_start: 0.7599 (t0) cc_final: 0.7379 (t0) REVERT: U 631 GLU cc_start: 0.8406 (tt0) cc_final: 0.8133 (pt0) REVERT: U 687 ASP cc_start: 0.7125 (m-30) cc_final: 0.6645 (m-30) REVERT: U 690 GLU cc_start: 0.7590 (tt0) cc_final: 0.7049 (pt0) REVERT: U 806 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8277 (tm-30) REVERT: V 62 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7502 (ttm110) REVERT: V 325 MET cc_start: 0.8869 (tpp) cc_final: 0.8271 (tpp) REVERT: V 375 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6379 (m-80) REVERT: W 33 SER cc_start: 0.9074 (m) cc_final: 0.8802 (p) REVERT: W 182 ARG cc_start: 0.8202 (ptt180) cc_final: 0.7981 (ttp-110) REVERT: W 196 LYS cc_start: 0.7807 (tttt) cc_final: 0.7422 (ttmt) REVERT: W 206 LEU cc_start: 0.8873 (tt) cc_final: 0.8664 (tp) REVERT: W 219 LYS cc_start: 0.8300 (tttm) cc_final: 0.7971 (ttpt) REVERT: W 277 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7930 (tt0) REVERT: W 308 ASN cc_start: 0.7286 (t0) cc_final: 0.6985 (t0) REVERT: W 313 LYS cc_start: 0.7368 (tttt) cc_final: 0.6945 (tptt) REVERT: W 436 LYS cc_start: 0.7903 (mttt) cc_final: 0.7673 (pttp) REVERT: X 54 SER cc_start: 0.8486 (t) cc_final: 0.8007 (p) REVERT: X 64 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8021 (mt) outliers start: 30 outliers final: 17 residues processed: 228 average time/residue: 0.1158 time to fit residues: 38.3237 Evaluate side-chains 182 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain U residue 553 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 375 PHE Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 142 THR Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 260 THR Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 319 GLN U 709 GLN U 713 ASN ** U 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113569 restraints weight = 16756.743| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.14 r_work: 0.3128 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13475 Z= 0.132 Angle : 0.545 6.790 18251 Z= 0.292 Chirality : 0.044 0.166 2010 Planarity : 0.004 0.040 2336 Dihedral : 5.961 56.874 1778 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 2.40 % Allowed : 11.19 % Favored : 86.41 % 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 are not related in a simple way. whole: 0.50 (0.21), residues: 1613 helix: 0.80 (0.20), residues: 710 sheet: 0.30 (0.36), residues: 205 loop : 0.00 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 722 TYR 0.018 0.001 TYR U 596 PHE 0.024 0.001 PHE U 223 TRP 0.013 0.001 TRP G 543 HIS 0.004 0.001 HIS W 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (13475) covalent geometry : angle 0.54486 / 0.29 (18251) hydrogen bonds : bond 0.03799 / 2.58 ( 630) hydrogen bonds : angle 4.56389 / 3.23 ( 1689) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 468 HIS cc_start: 0.7942 (t-90) cc_final: 0.7239 (t-90) REVERT: G 479 ASP cc_start: 0.7042 (m-30) cc_final: 0.6816 (t0) REVERT: G 519 SER cc_start: 0.9024 (t) cc_final: 0.8455 (p) REVERT: U 202 LYS cc_start: 0.8583 (mttt) cc_final: 0.8117 (mptt) REVERT: U 207 ASP cc_start: 0.8250 (t0) cc_final: 0.7302 (t0) REVERT: U 212 ASP cc_start: 0.7922 (m-30) cc_final: 0.7512 (t0) REVERT: U 576 ASP cc_start: 0.7454 (m-30) cc_final: 0.6961 (p0) REVERT: U 631 GLU cc_start: 0.8397 (tt0) cc_final: 0.8131 (pt0) REVERT: U 687 ASP cc_start: 0.7170 (m-30) cc_final: 0.6669 (m-30) REVERT: U 690 GLU cc_start: 0.7570 (tt0) cc_final: 0.7076 (pt0) REVERT: V 62 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7646 (ttm110) REVERT: V 157 ASP cc_start: 0.8937 (t0) cc_final: 0.8731 (t0) REVERT: V 325 MET cc_start: 0.8725 (tpp) cc_final: 0.8135 (tpp) REVERT: V 360 GLN cc_start: 0.7638 (tt0) cc_final: 0.7360 (mm-40) REVERT: W 33 SER cc_start: 0.9019 (m) cc_final: 0.8721 (p) REVERT: W 182 ARG cc_start: 0.8101 (ptt180) cc_final: 0.7893 (ttp-110) REVERT: W 196 LYS cc_start: 0.7845 (tttt) cc_final: 0.7495 (ttmt) REVERT: W 206 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8503 (tt) REVERT: W 277 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7931 (tt0) REVERT: W 308 ASN cc_start: 0.7289 (t0) cc_final: 0.6995 (t0) REVERT: W 313 LYS cc_start: 0.7323 (tttt) cc_final: 0.6932 (tptt) REVERT: W 427 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7695 (mm-30) REVERT: X 54 SER cc_start: 0.8530 (t) cc_final: 0.8067 (p) outliers start: 35 outliers final: 25 residues processed: 222 average time/residue: 0.1177 time to fit residues: 38.3082 Evaluate side-chains 196 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 555 SER Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain V residue 144 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 19 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 140 optimal weight: 0.0050 chunk 108 optimal weight: 0.8980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 541 ASN V 228 GLN V 372 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.150075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114611 restraints weight = 16693.514| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.13 r_work: 0.3139 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13475 Z= 0.114 Angle : 0.499 6.870 18251 Z= 0.265 Chirality : 0.043 0.191 2010 Planarity : 0.004 0.039 2336 Dihedral : 5.310 51.789 1771 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 2.20 % Allowed : 13.04 % Favored : 84.76 % 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 are not related in a simple way. whole: 0.72 (0.21), residues: 1613 helix: 0.97 (0.20), residues: 728 sheet: 0.67 (0.38), residues: 191 loop : 0.02 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 548 TYR 0.014 0.001 TYR U 596 PHE 0.011 0.001 PHE W 207 TRP 0.010 0.001 TRP V 340 HIS 0.004 0.001 HIS W 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (13475) covalent geometry : angle 0.49920 / 0.27 (18251) hydrogen bonds : bond 0.03392 / 2.30 ( 630) hydrogen bonds : angle 4.33131 / 3.07 ( 1689) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 468 HIS cc_start: 0.7917 (t-90) cc_final: 0.7354 (t-90) REVERT: U 202 LYS cc_start: 0.8538 (mttt) cc_final: 0.8073 (mptt) REVERT: U 207 ASP cc_start: 0.8185 (t0) cc_final: 0.7318 (t0) REVERT: U 212 ASP cc_start: 0.7834 (m-30) cc_final: 0.7473 (t0) REVERT: U 332 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8276 (ttpt) REVERT: U 576 ASP cc_start: 0.7424 (m-30) cc_final: 0.6899 (p0) REVERT: U 631 GLU cc_start: 0.8377 (tt0) cc_final: 0.8176 (pt0) REVERT: U 690 GLU cc_start: 0.7439 (tt0) cc_final: 0.7014 (pt0) REVERT: V 34 ILE cc_start: 0.8978 (mt) cc_final: 0.8715 (pt) REVERT: V 62 ARG cc_start: 0.8128 (ttm-80) cc_final: 0.7681 (ttm110) REVERT: V 325 MET cc_start: 0.8631 (tpp) cc_final: 0.8126 (tpp) REVERT: V 360 GLN cc_start: 0.7619 (tt0) cc_final: 0.7363 (mm110) REVERT: W 182 ARG cc_start: 0.8111 (ptt180) cc_final: 0.7885 (ttp-110) REVERT: W 196 LYS cc_start: 0.7822 (tttt) cc_final: 0.7477 (ttmt) REVERT: W 206 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8365 (tt) REVERT: W 277 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7752 (tt0) REVERT: W 308 ASN cc_start: 0.7213 (t0) cc_final: 0.6961 (t0) REVERT: W 313 LYS cc_start: 0.7313 (tttt) cc_final: 0.6920 (tptt) REVERT: X 54 SER cc_start: 0.8643 (t) cc_final: 0.8182 (p) outliers start: 32 outliers final: 23 residues processed: 195 average time/residue: 0.1103 time to fit residues: 31.8388 Evaluate side-chains 193 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 332 LYS Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 555 SER Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 823 HIS Chi-restraints excluded: chain U residue 841 ILE Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 41 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 228 GLN V 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.147518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111705 restraints weight = 16793.126| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.04 r_work: 0.3101 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13475 Z= 0.173 Angle : 0.545 8.512 18251 Z= 0.287 Chirality : 0.045 0.189 2010 Planarity : 0.004 0.041 2336 Dihedral : 5.396 50.334 1771 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.48 % Favored : 97.40 % Rotamer: Outliers : 3.02 % Allowed : 12.70 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1613 helix: 0.94 (0.20), residues: 725 sheet: 0.37 (0.37), residues: 199 loop : -0.01 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 69 TYR 0.018 0.002 TYR W 450 PHE 0.016 0.001 PHE W 207 TRP 0.011 0.001 TRP V 356 HIS 0.006 0.001 HIS W 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (13475) covalent geometry : angle 0.54514 / 0.29 (18251) hydrogen bonds : bond 0.03732 / 2.52 ( 630) hydrogen bonds : angle 4.37345 / 3.10 ( 1689) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: G 468 HIS cc_start: 0.7965 (t-90) cc_final: 0.7445 (t-90) REVERT: G 549 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7943 (tt0) REVERT: U 181 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7871 (ttpp) REVERT: U 202 LYS cc_start: 0.8564 (mttt) cc_final: 0.8164 (mptt) REVERT: U 207 ASP cc_start: 0.8315 (t0) cc_final: 0.7425 (t0) REVERT: U 212 ASP cc_start: 0.7896 (m-30) cc_final: 0.7461 (t0) REVERT: U 332 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8212 (ttpt) REVERT: U 576 ASP cc_start: 0.7377 (m-30) cc_final: 0.6872 (p0) REVERT: U 631 GLU cc_start: 0.8418 (tt0) cc_final: 0.8184 (pt0) REVERT: U 687 ASP cc_start: 0.7195 (m-30) cc_final: 0.6717 (m-30) REVERT: U 690 GLU cc_start: 0.7732 (tt0) cc_final: 0.7130 (pt0) REVERT: V 34 ILE cc_start: 0.9017 (mt) cc_final: 0.8761 (pt) REVERT: V 62 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7686 (ttm110) REVERT: V 82 MET cc_start: 0.8423 (tpt) cc_final: 0.7690 (tpt) REVERT: V 325 MET cc_start: 0.8616 (tpp) cc_final: 0.8112 (tpp) REVERT: V 360 GLN cc_start: 0.7679 (tt0) cc_final: 0.7428 (mm110) REVERT: W 182 ARG cc_start: 0.8156 (ptt180) cc_final: 0.7909 (ttp-110) REVERT: W 196 LYS cc_start: 0.7872 (tttt) cc_final: 0.7526 (ttmt) REVERT: W 277 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7785 (tt0) REVERT: W 292 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7860 (tt) REVERT: W 313 LYS cc_start: 0.7267 (tttt) cc_final: 0.6986 (tttp) REVERT: W 489 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7172 (ttm-80) REVERT: X 54 SER cc_start: 0.8704 (t) cc_final: 0.8268 (p) outliers start: 44 outliers final: 38 residues processed: 208 average time/residue: 0.1144 time to fit residues: 35.0464 Evaluate side-chains 212 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 332 LYS Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 555 SER Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 823 HIS Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 144 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 292 LEU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 441 THR Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 11 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 372 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.149426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113841 restraints weight = 16702.993| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.05 r_work: 0.3132 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13475 Z= 0.118 Angle : 0.497 6.490 18251 Z= 0.263 Chirality : 0.043 0.196 2010 Planarity : 0.004 0.038 2336 Dihedral : 5.143 49.720 1771 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.11 % Favored : 97.77 % Rotamer: Outliers : 2.54 % Allowed : 13.66 % Favored : 83.80 % 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 are not related in a simple way. whole: 0.73 (0.21), residues: 1613 helix: 1.04 (0.20), residues: 732 sheet: 0.29 (0.37), residues: 201 loop : 0.08 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 69 TYR 0.016 0.001 TYR U 596 PHE 0.012 0.001 PHE U 378 TRP 0.009 0.001 TRP V 340 HIS 0.004 0.001 HIS W 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (13475) covalent geometry : angle 0.49688 / 0.26 (18251) hydrogen bonds : bond 0.03279 / 2.21 ( 630) hydrogen bonds : angle 4.21257 / 2.99 ( 1689) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 468 HIS cc_start: 0.7952 (t-90) cc_final: 0.7413 (t-90) REVERT: U 181 LYS cc_start: 0.8120 (mtpp) cc_final: 0.7858 (ttpp) REVERT: U 202 LYS cc_start: 0.8536 (mttt) cc_final: 0.8146 (mptt) REVERT: U 207 ASP cc_start: 0.8277 (t0) cc_final: 0.7359 (t0) REVERT: U 212 ASP cc_start: 0.7907 (m-30) cc_final: 0.7465 (t0) REVERT: U 332 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8169 (ttpt) REVERT: U 576 ASP cc_start: 0.7388 (m-30) cc_final: 0.6805 (p0) REVERT: U 605 MET cc_start: 0.8633 (tpt) cc_final: 0.7968 (tpt) REVERT: U 631 GLU cc_start: 0.8398 (tt0) cc_final: 0.8186 (pt0) REVERT: U 687 ASP cc_start: 0.7128 (m-30) cc_final: 0.6634 (m-30) REVERT: U 690 GLU cc_start: 0.7833 (tt0) cc_final: 0.7316 (pt0) REVERT: V 34 ILE cc_start: 0.8982 (mt) cc_final: 0.8750 (pt) REVERT: V 325 MET cc_start: 0.8574 (tpp) cc_final: 0.8128 (tpp) REVERT: V 360 GLN cc_start: 0.7554 (tt0) cc_final: 0.7327 (mm110) REVERT: W 182 ARG cc_start: 0.8158 (ptt180) cc_final: 0.7870 (ttp-110) REVERT: W 196 LYS cc_start: 0.7834 (tttt) cc_final: 0.7487 (ttmt) REVERT: W 277 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7768 (tt0) REVERT: W 313 LYS cc_start: 0.7245 (tttt) cc_final: 0.6961 (tttp) REVERT: W 446 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8256 (tp) REVERT: W 489 ARG cc_start: 0.7537 (ttm-80) cc_final: 0.7141 (ttm-80) REVERT: X 54 SER cc_start: 0.8653 (t) cc_final: 0.8195 (p) outliers start: 37 outliers final: 31 residues processed: 198 average time/residue: 0.1046 time to fit residues: 30.9734 Evaluate side-chains 201 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 332 LYS Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 555 SER Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 823 HIS Chi-restraints excluded: chain U residue 835 ASP Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 13 optimal weight: 0.0270 chunk 70 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 228 GLN V 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112707 restraints weight = 16693.751| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.04 r_work: 0.3117 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13475 Z= 0.142 Angle : 0.507 6.021 18251 Z= 0.268 Chirality : 0.044 0.192 2010 Planarity : 0.004 0.038 2336 Dihedral : 5.141 52.567 1771 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.23 % Favored : 97.64 % Rotamer: Outliers : 2.81 % Allowed : 13.93 % Favored : 83.25 % 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 are not related in a simple way. whole: 0.74 (0.21), residues: 1613 helix: 1.05 (0.20), residues: 734 sheet: 0.29 (0.37), residues: 203 loop : 0.08 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 69 TYR 0.015 0.001 TYR U 596 PHE 0.017 0.001 PHE U 378 TRP 0.010 0.001 TRP V 356 HIS 0.005 0.001 HIS W 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (13475) covalent geometry : angle 0.50694 / 0.27 (18251) hydrogen bonds : bond 0.03408 / 2.30 ( 630) hydrogen bonds : angle 4.22535 / 2.99 ( 1689) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 181 LYS cc_start: 0.8160 (mtpp) cc_final: 0.7925 (ttpp) REVERT: U 202 LYS cc_start: 0.8548 (mttt) cc_final: 0.8126 (mptt) REVERT: U 207 ASP cc_start: 0.8309 (t0) cc_final: 0.7378 (t0) REVERT: U 212 ASP cc_start: 0.7957 (m-30) cc_final: 0.7486 (t0) REVERT: U 332 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8073 (ttpt) REVERT: U 361 LYS cc_start: 0.8147 (tptt) cc_final: 0.7637 (tmtt) REVERT: U 576 ASP cc_start: 0.7315 (m-30) cc_final: 0.6803 (p0) REVERT: U 580 GLN cc_start: 0.6754 (mt0) cc_final: 0.6354 (tp40) REVERT: U 605 MET cc_start: 0.8645 (tpt) cc_final: 0.7975 (tpt) REVERT: U 631 GLU cc_start: 0.8408 (tt0) cc_final: 0.8198 (pt0) REVERT: U 687 ASP cc_start: 0.7147 (m-30) cc_final: 0.6654 (m-30) REVERT: U 690 GLU cc_start: 0.7872 (tt0) cc_final: 0.7259 (pt0) REVERT: V 34 ILE cc_start: 0.8992 (mt) cc_final: 0.8745 (pt) REVERT: V 325 MET cc_start: 0.8571 (tpp) cc_final: 0.8169 (tpp) REVERT: V 360 GLN cc_start: 0.7573 (tt0) cc_final: 0.7358 (mm110) REVERT: V 363 ASP cc_start: 0.8045 (m-30) cc_final: 0.7823 (m-30) REVERT: W 182 ARG cc_start: 0.8172 (ptt180) cc_final: 0.7882 (ttp-110) REVERT: W 196 LYS cc_start: 0.7907 (tttt) cc_final: 0.7562 (ttmt) REVERT: W 277 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7748 (tt0) REVERT: W 292 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7945 (tt) REVERT: W 313 LYS cc_start: 0.7210 (tttt) cc_final: 0.6927 (tttp) REVERT: W 446 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8285 (tp) REVERT: W 489 ARG cc_start: 0.7581 (ttm-80) cc_final: 0.7259 (ttm-80) REVERT: X 54 SER cc_start: 0.8674 (t) cc_final: 0.8238 (p) outliers start: 41 outliers final: 37 residues processed: 193 average time/residue: 0.0980 time to fit residues: 28.1762 Evaluate side-chains 203 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 332 LYS Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 555 SER Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 823 HIS Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 144 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 292 LEU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 441 THR Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 131 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 372 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.147352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111440 restraints weight = 16570.532| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.07 r_work: 0.3110 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13475 Z= 0.185 Angle : 0.538 5.877 18251 Z= 0.283 Chirality : 0.045 0.186 2010 Planarity : 0.004 0.040 2336 Dihedral : 5.192 54.718 1769 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 3.36 % Allowed : 14.00 % Favored : 82.64 % 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 are not related in a simple way. whole: 0.63 (0.21), residues: 1613 helix: 0.97 (0.20), residues: 730 sheet: 0.20 (0.37), residues: 203 loop : 0.03 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 69 TYR 0.017 0.001 TYR U 596 PHE 0.017 0.001 PHE U 378 TRP 0.010 0.001 TRP V 356 HIS 0.005 0.001 HIS W 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (13475) covalent geometry : angle 0.53764 / 0.28 (18251) hydrogen bonds : bond 0.03652 / 2.46 ( 630) hydrogen bonds : angle 4.31038 / 3.05 ( 1689) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 181 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7900 (ttpp) REVERT: U 202 LYS cc_start: 0.8548 (mttt) cc_final: 0.8131 (mptt) REVERT: U 207 ASP cc_start: 0.8401 (t0) cc_final: 0.7443 (t0) REVERT: U 212 ASP cc_start: 0.7881 (m-30) cc_final: 0.7422 (t0) REVERT: U 361 LYS cc_start: 0.8112 (tptt) cc_final: 0.7648 (tmtt) REVERT: U 552 LYS cc_start: 0.8329 (mttm) cc_final: 0.8054 (mttm) REVERT: U 576 ASP cc_start: 0.7308 (m-30) cc_final: 0.6776 (p0) REVERT: U 580 GLN cc_start: 0.6920 (mt0) cc_final: 0.6578 (tp40) REVERT: U 605 MET cc_start: 0.8651 (tpt) cc_final: 0.7977 (tpt) REVERT: U 631 GLU cc_start: 0.8434 (tt0) cc_final: 0.8144 (pt0) REVERT: U 687 ASP cc_start: 0.7137 (m-30) cc_final: 0.6636 (m-30) REVERT: V 34 ILE cc_start: 0.9035 (mt) cc_final: 0.8778 (pt) REVERT: V 325 MET cc_start: 0.8585 (tpp) cc_final: 0.8168 (tpp) REVERT: V 360 GLN cc_start: 0.7605 (tt0) cc_final: 0.7390 (mm110) REVERT: V 363 ASP cc_start: 0.8045 (m-30) cc_final: 0.7820 (m-30) REVERT: W 182 ARG cc_start: 0.8192 (ptt180) cc_final: 0.7876 (ttp-110) REVERT: W 196 LYS cc_start: 0.7901 (tttt) cc_final: 0.7547 (ttmt) REVERT: W 277 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7731 (tt0) REVERT: W 292 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7849 (tt) REVERT: W 313 LYS cc_start: 0.7190 (tttt) cc_final: 0.6841 (tmtm) REVERT: W 446 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8250 (tp) REVERT: W 448 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.7863 (mtm180) REVERT: W 489 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7291 (ttm-80) REVERT: X 54 SER cc_start: 0.8678 (t) cc_final: 0.8249 (p) outliers start: 49 outliers final: 42 residues processed: 198 average time/residue: 0.1043 time to fit residues: 30.5576 Evaluate side-chains 205 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 555 SER Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 823 HIS Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 144 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 142 THR Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 211 GLN Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 292 LEU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 441 THR Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain W residue 448 ARG Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 112 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 75 optimal weight: 0.0570 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 372 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114198 restraints weight = 16764.558| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.18 r_work: 0.3132 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13475 Z= 0.106 Angle : 0.484 6.374 18251 Z= 0.255 Chirality : 0.043 0.202 2010 Planarity : 0.004 0.037 2336 Dihedral : 4.933 57.121 1769 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.29 % Favored : 97.58 % Rotamer: Outliers : 2.26 % Allowed : 15.31 % Favored : 82.43 % 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 are not related in a simple way. whole: 0.83 (0.21), residues: 1613 helix: 1.13 (0.20), residues: 735 sheet: 0.32 (0.37), residues: 201 loop : 0.13 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 69 TYR 0.015 0.001 TYR U 596 PHE 0.016 0.001 PHE U 378 TRP 0.010 0.001 TRP V 340 HIS 0.004 0.000 HIS W 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (13475) covalent geometry : angle 0.48446 / 0.26 (18251) hydrogen bonds : bond 0.03142 / 2.11 ( 630) hydrogen bonds : angle 4.11247 / 2.92 ( 1689) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 181 LYS cc_start: 0.8185 (mtpp) cc_final: 0.7932 (ttpp) REVERT: U 202 LYS cc_start: 0.8516 (mttt) cc_final: 0.8093 (mptt) REVERT: U 207 ASP cc_start: 0.8202 (t0) cc_final: 0.7356 (t0) REVERT: U 212 ASP cc_start: 0.7865 (m-30) cc_final: 0.7399 (t0) REVERT: U 576 ASP cc_start: 0.7351 (m-30) cc_final: 0.6736 (p0) REVERT: U 580 GLN cc_start: 0.6943 (mt0) cc_final: 0.6596 (tp40) REVERT: U 605 MET cc_start: 0.8609 (tpt) cc_final: 0.7962 (tpt) REVERT: U 631 GLU cc_start: 0.8447 (tt0) cc_final: 0.8193 (pt0) REVERT: V 34 ILE cc_start: 0.8994 (mt) cc_final: 0.8775 (pt) REVERT: V 325 MET cc_start: 0.8509 (tpp) cc_final: 0.8129 (tpp) REVERT: V 360 GLN cc_start: 0.7587 (tt0) cc_final: 0.7360 (mm110) REVERT: V 363 ASP cc_start: 0.7967 (m-30) cc_final: 0.7709 (m-30) REVERT: W 182 ARG cc_start: 0.8217 (ptt180) cc_final: 0.7902 (ttp-110) REVERT: W 196 LYS cc_start: 0.7899 (tttt) cc_final: 0.7547 (ttmt) REVERT: W 277 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7771 (tt0) REVERT: W 313 LYS cc_start: 0.7167 (tttt) cc_final: 0.6877 (tttp) REVERT: W 446 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8301 (tp) REVERT: W 489 ARG cc_start: 0.7579 (ttm-80) cc_final: 0.7129 (ttm-80) REVERT: X 54 SER cc_start: 0.8616 (t) cc_final: 0.8218 (p) outliers start: 33 outliers final: 27 residues processed: 194 average time/residue: 0.1051 time to fit residues: 30.4234 Evaluate side-chains 190 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 142 THR Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 441 THR Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 117 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 799 GLN V 228 GLN V 372 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112057 restraints weight = 16810.721| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.04 r_work: 0.3112 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13475 Z= 0.161 Angle : 0.529 8.910 18251 Z= 0.277 Chirality : 0.044 0.195 2010 Planarity : 0.004 0.037 2336 Dihedral : 5.050 57.908 1769 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.91 % Favored : 96.96 % Rotamer: Outliers : 2.06 % Allowed : 15.85 % Favored : 82.09 % 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 are not related in a simple way. whole: 0.74 (0.21), residues: 1613 helix: 1.06 (0.20), residues: 735 sheet: 0.23 (0.37), residues: 201 loop : 0.09 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 69 TYR 0.023 0.001 TYR W 319 PHE 0.016 0.001 PHE U 378 TRP 0.010 0.001 TRP V 356 HIS 0.004 0.001 HIS W 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (13475) covalent geometry : angle 0.52909 / 0.28 (18251) hydrogen bonds : bond 0.03441 / 2.32 ( 630) hydrogen bonds : angle 4.20584 / 2.98 ( 1689) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 181 LYS cc_start: 0.8192 (mtpp) cc_final: 0.7984 (pttm) REVERT: U 202 LYS cc_start: 0.8525 (mttt) cc_final: 0.8115 (mptt) REVERT: U 207 ASP cc_start: 0.8322 (t0) cc_final: 0.7423 (t0) REVERT: U 212 ASP cc_start: 0.7884 (m-30) cc_final: 0.7426 (t0) REVERT: U 576 ASP cc_start: 0.7320 (m-30) cc_final: 0.6726 (p0) REVERT: U 580 GLN cc_start: 0.6932 (mt0) cc_final: 0.6550 (tp40) REVERT: U 599 LYS cc_start: 0.8016 (tptt) cc_final: 0.7310 (tptp) REVERT: U 605 MET cc_start: 0.8629 (tpt) cc_final: 0.7984 (tpt) REVERT: U 631 GLU cc_start: 0.8454 (tt0) cc_final: 0.8161 (pt0) REVERT: V 34 ILE cc_start: 0.9047 (mt) cc_final: 0.8806 (pt) REVERT: V 325 MET cc_start: 0.8545 (tpp) cc_final: 0.8123 (tpp) REVERT: V 360 GLN cc_start: 0.7607 (tt0) cc_final: 0.7399 (mm110) REVERT: V 363 ASP cc_start: 0.8008 (m-30) cc_final: 0.7753 (m-30) REVERT: W 182 ARG cc_start: 0.8221 (ptt180) cc_final: 0.7897 (ttp-110) REVERT: W 196 LYS cc_start: 0.7909 (tttt) cc_final: 0.7560 (ttmt) REVERT: W 277 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7673 (tt0) REVERT: W 313 LYS cc_start: 0.7142 (tttt) cc_final: 0.6797 (tmtm) REVERT: W 446 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8299 (tp) REVERT: W 489 ARG cc_start: 0.7726 (ttm-80) cc_final: 0.7347 (ttm-80) REVERT: X 54 SER cc_start: 0.8676 (t) cc_final: 0.8255 (p) outliers start: 30 outliers final: 27 residues processed: 181 average time/residue: 0.1001 time to fit residues: 26.9269 Evaluate side-chains 186 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 142 THR Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 441 THR Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 13 optimal weight: 0.0980 chunk 102 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 17 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 799 GLN U 817 HIS V 372 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.150034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114367 restraints weight = 16569.312| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.05 r_work: 0.3139 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13475 Z= 0.107 Angle : 0.500 9.871 18251 Z= 0.259 Chirality : 0.043 0.199 2010 Planarity : 0.004 0.036 2336 Dihedral : 4.861 59.826 1769 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 1.99 % Allowed : 15.92 % Favored : 82.09 % 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 are not related in a simple way. whole: 0.92 (0.21), residues: 1613 helix: 1.21 (0.20), residues: 736 sheet: 0.33 (0.38), residues: 201 loop : 0.18 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 339 TYR 0.026 0.001 TYR W 319 PHE 0.015 0.001 PHE U 378 TRP 0.010 0.001 TRP V 340 HIS 0.004 0.000 HIS W 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (13475) covalent geometry : angle 0.50008 / 0.26 (18251) hydrogen bonds : bond 0.03088 / 2.08 ( 630) hydrogen bonds : angle 4.09250 / 2.90 ( 1689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3142.72 seconds wall clock time: 54 minutes 40.27 seconds (3280.27 seconds total)