Starting phenix.real_space_refine on Mon Dec 30 15:16:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a5a_15163/12_2024/8a5a_15163.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a5a_15163/12_2024/8a5a_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_15163/12_2024/8a5a_15163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a5a_15163/12_2024/8a5a_15163.map" model { file = "/net/cci-nas-00/data/ceres_data/8a5a_15163/12_2024/8a5a_15163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a5a_15163/12_2024/8a5a_15163.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 8.06, per 1000 atoms: 0.61 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: 3.80 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.24 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: 5.79 Time building geometry restraints manager: 4.37 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: 7299 17.45 - 34.89: 722 34.89 - 52.34: 151 52.34 - 69.79: 49 69.79 - 87.23: 13 Dihedral angle restraints: 8234 sinusoidal: 3462 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 8231 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 34.790 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 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= 1.036 Angle : 2.080 22.655 18251 Z= 1.498 Chirality : 0.099 0.368 2010 Planarity : 0.011 0.061 2336 Dihedral : 15.440 87.233 5138 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.103 0.018 TRP W 469 HIS 0.033 0.007 HIS W 162 PHE 0.070 0.013 PHE W 207 TYR 0.106 0.015 TYR W 450 ARG 0.023 0.003 ARG G 482 *********************** 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 : 1.668 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: 0.7366 (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: 0.6780 (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: 0.3135 time to fit residues: 141.5426 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 : 1.632 ------------------------------------------------------------------------------- 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 136 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13475 Z= 0.233 Angle : 0.656 15.900 18251 Z= 0.354 Chirality : 0.046 0.155 2010 Planarity : 0.005 0.044 2336 Dihedral : 9.831 68.992 1894 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.29 % Favored : 97.58 % Rotamer: Outliers : 2.40 % Allowed : 9.54 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1613 helix: 0.11 (0.19), residues: 710 sheet: 0.09 (0.35), residues: 209 loop : -0.16 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP V 340 HIS 0.004 0.001 HIS V 372 PHE 0.016 0.002 PHE U 546 TYR 0.021 0.002 TYR U 596 ARG 0.004 0.001 ARG U 674 *********************** 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 237 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 519 SER cc_start: 0.7592 (t) cc_final: 0.7298 (p) REVERT: U 202 LYS cc_start: 0.7183 (mttt) cc_final: 0.6919 (mptt) REVERT: U 207 ASP cc_start: 0.6805 (t0) cc_final: 0.6027 (t0) REVERT: U 212 ASP cc_start: 0.7120 (m-30) cc_final: 0.6555 (t0) REVERT: U 316 GLN cc_start: 0.6341 (mp10) cc_final: 0.6118 (mp10) REVERT: U 338 MET cc_start: 0.7622 (mmt) cc_final: 0.7384 (mmt) REVERT: U 374 ILE cc_start: 0.7898 (mt) cc_final: 0.7621 (tt) REVERT: U 573 GLN cc_start: 0.6731 (tt0) cc_final: 0.6497 (tp-100) REVERT: U 576 ASP cc_start: 0.7073 (m-30) cc_final: 0.6556 (p0) REVERT: U 586 ASN cc_start: 0.7179 (t0) cc_final: 0.6868 (t0) REVERT: U 626 LYS cc_start: 0.7881 (mttt) cc_final: 0.7531 (mppt) REVERT: U 631 GLU cc_start: 0.7467 (tt0) cc_final: 0.7142 (pt0) REVERT: U 687 ASP cc_start: 0.6344 (m-30) cc_final: 0.6065 (m-30) REVERT: U 690 GLU cc_start: 0.7840 (tt0) cc_final: 0.7280 (pt0) REVERT: U 694 ASN cc_start: 0.5076 (m-40) cc_final: 0.4846 (t0) REVERT: U 719 ASP cc_start: 0.8539 (m-30) cc_final: 0.8313 (p0) REVERT: U 778 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7381 (mp0) REVERT: V 62 ARG cc_start: 0.6636 (ttm-80) cc_final: 0.6328 (ttm110) REVERT: V 364 GLU cc_start: 0.6980 (tt0) cc_final: 0.6396 (mm-30) REVERT: V 375 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.5860 (m-80) REVERT: W 9 TYR cc_start: 0.6374 (t80) cc_final: 0.6172 (t80) REVERT: W 33 SER cc_start: 0.7351 (m) cc_final: 0.6871 (p) REVERT: W 91 GLN cc_start: 0.5839 (tt0) cc_final: 0.5621 (tp40) REVERT: W 182 ARG cc_start: 0.7032 (ptt180) cc_final: 0.6519 (ttp-110) REVERT: W 219 LYS cc_start: 0.6223 (tttm) cc_final: 0.5973 (ttpt) REVERT: W 277 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7522 (tt0) REVERT: W 313 LYS cc_start: 0.5957 (tttt) cc_final: 0.5671 (tptt) REVERT: W 436 LYS cc_start: 0.6998 (mttt) cc_final: 0.6755 (pttp) REVERT: W 481 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7828 (pm20) REVERT: X 45 ASN cc_start: 0.7725 (m110) cc_final: 0.7300 (t0) REVERT: X 54 SER cc_start: 0.7573 (t) cc_final: 0.7158 (p) REVERT: X 56 TYR cc_start: 0.7105 (m-80) cc_final: 0.6739 (m-80) outliers start: 35 outliers final: 21 residues processed: 228 average time/residue: 0.2817 time to fit residues: 92.2936 Evaluate side-chains 189 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 1.659 ------------------------------------------------------------------------------- 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 435 SER Chi-restraints excluded: chain U residue 553 ILE Chi-restraints excluded: chain U residue 555 SER 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 299 MET 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 425 MET Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 159 optimal weight: 0.4980 chunk 131 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 468 HIS U 319 GLN U 709 GLN U 713 ASN ** U 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13475 Z= 0.214 Angle : 0.557 9.100 18251 Z= 0.298 Chirality : 0.044 0.161 2010 Planarity : 0.004 0.041 2336 Dihedral : 8.717 65.633 1873 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.48 % Favored : 97.40 % Rotamer: Outliers : 2.26 % Allowed : 11.19 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1613 helix: 0.70 (0.19), residues: 710 sheet: 0.29 (0.36), residues: 205 loop : -0.03 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 543 HIS 0.004 0.001 HIS W 162 PHE 0.022 0.001 PHE U 223 TYR 0.014 0.001 TYR W 69 ARG 0.003 0.000 ARG V 95 *********************** 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 220 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 519 SER cc_start: 0.7331 (t) cc_final: 0.7023 (p) REVERT: U 183 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6881 (mm-30) REVERT: U 202 LYS cc_start: 0.7183 (mttt) cc_final: 0.6943 (mptt) REVERT: U 207 ASP cc_start: 0.6803 (t0) cc_final: 0.6018 (t0) REVERT: U 212 ASP cc_start: 0.7143 (m-30) cc_final: 0.6592 (t0) REVERT: U 318 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8036 (pp20) REVERT: U 338 MET cc_start: 0.7626 (mmt) cc_final: 0.7417 (mmt) REVERT: U 341 TYR cc_start: 0.7422 (m-80) cc_final: 0.7186 (m-80) REVERT: U 374 ILE cc_start: 0.7857 (mt) cc_final: 0.7604 (tt) REVERT: U 576 ASP cc_start: 0.7007 (m-30) cc_final: 0.6438 (p0) REVERT: U 586 ASN cc_start: 0.7205 (t0) cc_final: 0.6920 (t0) REVERT: U 605 MET cc_start: 0.6717 (tpt) cc_final: 0.6304 (tpt) REVERT: U 626 LYS cc_start: 0.7950 (mttt) cc_final: 0.7606 (mppt) REVERT: U 631 GLU cc_start: 0.7431 (tt0) cc_final: 0.7076 (pt0) REVERT: U 687 ASP cc_start: 0.6340 (m-30) cc_final: 0.6051 (m-30) REVERT: U 690 GLU cc_start: 0.7886 (tt0) cc_final: 0.7325 (pt0) REVERT: V 62 ARG cc_start: 0.6582 (ttm-80) cc_final: 0.6303 (ttm110) REVERT: V 364 GLU cc_start: 0.7020 (tt0) cc_final: 0.6465 (mm-30) REVERT: V 375 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.6072 (m-80) REVERT: W 33 SER cc_start: 0.7230 (m) cc_final: 0.6734 (p) REVERT: W 91 GLN cc_start: 0.5654 (tt0) cc_final: 0.5339 (tp-100) REVERT: W 219 LYS cc_start: 0.6293 (tttm) cc_final: 0.6043 (ttpt) REVERT: W 277 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7606 (tt0) REVERT: W 313 LYS cc_start: 0.5609 (tttt) cc_final: 0.5356 (tptt) REVERT: W 436 LYS cc_start: 0.7081 (mttt) cc_final: 0.6870 (pttp) REVERT: W 481 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7844 (pm20) REVERT: X 45 ASN cc_start: 0.7740 (m110) cc_final: 0.7344 (t0) REVERT: X 54 SER cc_start: 0.7686 (t) cc_final: 0.7274 (p) REVERT: X 56 TYR cc_start: 0.7161 (m-80) cc_final: 0.6778 (m-80) outliers start: 33 outliers final: 21 residues processed: 210 average time/residue: 0.3012 time to fit residues: 92.7435 Evaluate side-chains 191 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 1.690 ------------------------------------------------------------------------------- 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 479 VAL Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 553 ILE 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 375 PHE 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 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 145 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 0.0000 chunk 98 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 156 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 228 GLN V 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.3128 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= 0.154 Angle : 0.504 7.015 18251 Z= 0.269 Chirality : 0.043 0.191 2010 Planarity : 0.004 0.040 2336 Dihedral : 7.991 67.606 1868 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.36 % Favored : 97.52 % Rotamer: Outliers : 1.99 % Allowed : 12.63 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1613 helix: 0.98 (0.20), residues: 728 sheet: 0.60 (0.38), residues: 198 loop : 0.05 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 356 HIS 0.004 0.001 HIS W 162 PHE 0.019 0.001 PHE U 598 TYR 0.014 0.001 TYR U 596 ARG 0.005 0.000 ARG G 548 *********************** 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 218 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 519 SER cc_start: 0.7223 (t) cc_final: 0.6910 (p) REVERT: U 183 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7065 (mm-30) REVERT: U 202 LYS cc_start: 0.7124 (mttt) cc_final: 0.6845 (mptt) REVERT: U 207 ASP cc_start: 0.6842 (t0) cc_final: 0.6102 (t0) REVERT: U 212 ASP cc_start: 0.7049 (m-30) cc_final: 0.6496 (t0) REVERT: U 318 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8026 (pp20) REVERT: U 338 MET cc_start: 0.7595 (mmt) cc_final: 0.7367 (mmt) REVERT: U 341 TYR cc_start: 0.7530 (m-80) cc_final: 0.7228 (m-80) REVERT: U 374 ILE cc_start: 0.7905 (mt) cc_final: 0.7681 (tt) REVERT: U 576 ASP cc_start: 0.6929 (m-30) cc_final: 0.6377 (p0) REVERT: U 586 ASN cc_start: 0.7216 (t0) cc_final: 0.6968 (t0) REVERT: U 605 MET cc_start: 0.6913 (tpt) cc_final: 0.6496 (tpt) REVERT: U 626 LYS cc_start: 0.7865 (mttt) cc_final: 0.7560 (mppt) REVERT: U 631 GLU cc_start: 0.7436 (tt0) cc_final: 0.7078 (pt0) REVERT: U 687 ASP cc_start: 0.6333 (m-30) cc_final: 0.6043 (m-30) REVERT: U 690 GLU cc_start: 0.7729 (tt0) cc_final: 0.7284 (pt0) REVERT: V 62 ARG cc_start: 0.6584 (ttm-80) cc_final: 0.6328 (ttm110) REVERT: V 363 ASP cc_start: 0.7457 (m-30) cc_final: 0.7187 (m-30) REVERT: V 364 GLU cc_start: 0.7003 (tt0) cc_final: 0.6459 (mm-30) REVERT: W 91 GLN cc_start: 0.5509 (tt0) cc_final: 0.5210 (tp-100) REVERT: W 277 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7682 (tt0) REVERT: W 313 LYS cc_start: 0.5590 (tttt) cc_final: 0.5344 (tptt) REVERT: W 436 LYS cc_start: 0.6877 (mttt) cc_final: 0.6670 (pttp) REVERT: W 481 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7864 (pm20) REVERT: X 45 ASN cc_start: 0.7713 (m110) cc_final: 0.7413 (t0) REVERT: X 54 SER cc_start: 0.7769 (t) cc_final: 0.7361 (p) REVERT: X 56 TYR cc_start: 0.7030 (m-80) cc_final: 0.6802 (m-80) REVERT: X 64 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7285 (mt) outliers start: 29 outliers final: 18 residues processed: 207 average time/residue: 0.2814 time to fit residues: 84.2736 Evaluate side-chains 193 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 364 ILE 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 U residue 870 SER Chi-restraints excluded: chain V residue 179 ASP 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 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 Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 chunk 140 optimal weight: 0.0980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 468 HIS G 541 ASN V 228 GLN V 372 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13475 Z= 0.166 Angle : 0.495 6.475 18251 Z= 0.262 Chirality : 0.043 0.190 2010 Planarity : 0.004 0.039 2336 Dihedral : 7.572 69.387 1864 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.05 % Favored : 97.83 % Rotamer: Outliers : 2.20 % Allowed : 13.59 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.21), residues: 1613 helix: 1.15 (0.20), residues: 728 sheet: 0.59 (0.37), residues: 200 loop : 0.14 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 356 HIS 0.005 0.001 HIS G 468 PHE 0.013 0.001 PHE U 766 TYR 0.012 0.001 TYR U 596 ARG 0.007 0.000 ARG X 69 *********************** 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 214 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 2.192 Fit side-chains revert: symmetry clash REVERT: G 549 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7702 (tt0) REVERT: U 183 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6906 (mm-30) REVERT: U 202 LYS cc_start: 0.7074 (mttt) cc_final: 0.6785 (mptt) REVERT: U 207 ASP cc_start: 0.6980 (t0) cc_final: 0.6197 (t0) REVERT: U 212 ASP cc_start: 0.7159 (m-30) cc_final: 0.6582 (t0) REVERT: U 318 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8051 (pp20) REVERT: U 338 MET cc_start: 0.7606 (mmt) cc_final: 0.7405 (mmt) REVERT: U 341 TYR cc_start: 0.7547 (m-80) cc_final: 0.7321 (m-80) REVERT: U 374 ILE cc_start: 0.7906 (mt) cc_final: 0.7571 (tt) REVERT: U 576 ASP cc_start: 0.6908 (m-30) cc_final: 0.6382 (p0) REVERT: U 586 ASN cc_start: 0.7262 (t0) cc_final: 0.7023 (t0) REVERT: U 626 LYS cc_start: 0.7883 (mttt) cc_final: 0.7625 (mppt) REVERT: U 631 GLU cc_start: 0.7513 (tt0) cc_final: 0.7075 (pt0) REVERT: U 687 ASP cc_start: 0.6333 (m-30) cc_final: 0.6044 (m-30) REVERT: U 690 GLU cc_start: 0.7737 (tt0) cc_final: 0.7317 (pt0) REVERT: V 34 ILE cc_start: 0.8098 (mt) cc_final: 0.7805 (pt) REVERT: V 62 ARG cc_start: 0.6642 (ttm-80) cc_final: 0.6415 (ttm110) REVERT: V 83 GLU cc_start: 0.6329 (tt0) cc_final: 0.6123 (tm-30) REVERT: V 364 GLU cc_start: 0.7059 (tt0) cc_final: 0.6588 (mm-30) REVERT: W 9 TYR cc_start: 0.6847 (t80) cc_final: 0.6636 (t80) REVERT: W 91 GLN cc_start: 0.5651 (tt0) cc_final: 0.5374 (tp-100) REVERT: W 277 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7719 (tt0) REVERT: W 481 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7924 (pm20) REVERT: X 45 ASN cc_start: 0.7686 (m110) cc_final: 0.7361 (t0) REVERT: X 54 SER cc_start: 0.7552 (t) cc_final: 0.7132 (p) REVERT: X 56 TYR cc_start: 0.6982 (m-80) cc_final: 0.6763 (m-80) REVERT: X 64 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7288 (mt) outliers start: 32 outliers final: 26 residues processed: 204 average time/residue: 0.2670 time to fit residues: 80.2638 Evaluate side-chains 202 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 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 U residue 870 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 165 CYS Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 220 THR 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 X residue 58 VAL Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 372 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13475 Z= 0.241 Angle : 0.521 5.938 18251 Z= 0.276 Chirality : 0.044 0.186 2010 Planarity : 0.004 0.039 2336 Dihedral : 7.581 66.681 1864 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.36 % Favored : 97.52 % Rotamer: Outliers : 2.81 % Allowed : 13.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1613 helix: 1.05 (0.20), residues: 731 sheet: 0.27 (0.36), residues: 206 loop : 0.07 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 356 HIS 0.006 0.001 HIS W 162 PHE 0.018 0.001 PHE U 598 TYR 0.016 0.001 TYR W 450 ARG 0.005 0.000 ARG X 69 *********************** 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 214 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 549 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7708 (tt0) REVERT: U 183 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6904 (mm-30) REVERT: U 202 LYS cc_start: 0.7077 (mttt) cc_final: 0.6829 (mptt) REVERT: U 207 ASP cc_start: 0.6996 (t0) cc_final: 0.6176 (t0) REVERT: U 212 ASP cc_start: 0.7239 (m-30) cc_final: 0.6622 (t0) REVERT: U 341 TYR cc_start: 0.7437 (m-80) cc_final: 0.7176 (m-80) REVERT: U 374 ILE cc_start: 0.7920 (mt) cc_final: 0.7590 (tt) REVERT: U 576 ASP cc_start: 0.6835 (m-30) cc_final: 0.6240 (p0) REVERT: U 586 ASN cc_start: 0.7264 (t0) cc_final: 0.7034 (t0) REVERT: U 626 LYS cc_start: 0.7827 (mttt) cc_final: 0.7572 (mppt) REVERT: U 631 GLU cc_start: 0.7441 (tt0) cc_final: 0.6980 (pt0) REVERT: U 687 ASP cc_start: 0.6305 (m-30) cc_final: 0.6015 (m-30) REVERT: U 690 GLU cc_start: 0.7866 (tt0) cc_final: 0.7441 (pt0) REVERT: V 34 ILE cc_start: 0.8106 (mt) cc_final: 0.7812 (pt) REVERT: V 83 GLU cc_start: 0.6357 (tt0) cc_final: 0.6141 (tm-30) REVERT: V 363 ASP cc_start: 0.7332 (m-30) cc_final: 0.7119 (m-30) REVERT: V 364 GLU cc_start: 0.7076 (tt0) cc_final: 0.6660 (mm-30) REVERT: W 91 GLN cc_start: 0.5679 (tt0) cc_final: 0.5411 (tp-100) REVERT: W 277 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7708 (tt0) REVERT: W 481 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7932 (pm20) REVERT: W 489 ARG cc_start: 0.6197 (ttm-80) cc_final: 0.5747 (ttm-80) REVERT: X 45 ASN cc_start: 0.7719 (m110) cc_final: 0.7404 (t0) REVERT: X 54 SER cc_start: 0.7637 (t) cc_final: 0.7234 (p) REVERT: X 57 LYS cc_start: 0.7884 (mttt) cc_final: 0.7655 (ttmm) REVERT: X 64 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7326 (mt) outliers start: 41 outliers final: 36 residues processed: 200 average time/residue: 0.2547 time to fit residues: 75.9694 Evaluate side-chains 203 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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 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 711 ILE Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 778 GLU Chi-restraints excluded: chain U residue 823 HIS Chi-restraints excluded: chain U residue 841 ILE Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 110 MET 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 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 400 LEU Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 88 optimal weight: 0.0570 chunk 131 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 156 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 372 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13475 Z= 0.157 Angle : 0.488 5.373 18251 Z= 0.257 Chirality : 0.042 0.193 2010 Planarity : 0.004 0.037 2336 Dihedral : 7.282 68.461 1864 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.98 % Favored : 97.89 % Rotamer: Outliers : 2.13 % Allowed : 14.69 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.21), residues: 1613 helix: 1.16 (0.20), residues: 736 sheet: 0.46 (0.37), residues: 200 loop : 0.15 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 543 HIS 0.004 0.000 HIS W 162 PHE 0.014 0.001 PHE U 598 TYR 0.014 0.001 TYR U 596 ARG 0.005 0.000 ARG X 69 *********************** 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 207 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 549 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7685 (tt0) REVERT: U 183 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6892 (mm-30) REVERT: U 202 LYS cc_start: 0.7058 (mttt) cc_final: 0.6817 (mptt) REVERT: U 207 ASP cc_start: 0.6939 (t0) cc_final: 0.6210 (t0) REVERT: U 212 ASP cc_start: 0.7215 (m-30) cc_final: 0.6601 (t0) REVERT: U 341 TYR cc_start: 0.7486 (m-80) cc_final: 0.7072 (m-80) REVERT: U 374 ILE cc_start: 0.8040 (mt) cc_final: 0.7710 (tt) REVERT: U 576 ASP cc_start: 0.6845 (m-30) cc_final: 0.6335 (p0) REVERT: U 586 ASN cc_start: 0.7313 (t0) cc_final: 0.7097 (t0) REVERT: U 605 MET cc_start: 0.6942 (tpt) cc_final: 0.6551 (tpt) REVERT: U 626 LYS cc_start: 0.7650 (mttt) cc_final: 0.7381 (mppt) REVERT: U 631 GLU cc_start: 0.7452 (tt0) cc_final: 0.6986 (pt0) REVERT: U 690 GLU cc_start: 0.7901 (tt0) cc_final: 0.7440 (pt0) REVERT: V 34 ILE cc_start: 0.8129 (mt) cc_final: 0.7866 (pt) REVERT: V 300 SER cc_start: 0.8373 (m) cc_final: 0.8050 (p) REVERT: V 360 GLN cc_start: 0.6165 (tt0) cc_final: 0.5559 (mm-40) REVERT: V 364 GLU cc_start: 0.7142 (tt0) cc_final: 0.6631 (mm-30) REVERT: W 9 TYR cc_start: 0.6845 (t80) cc_final: 0.6627 (t80) REVERT: W 91 GLN cc_start: 0.5515 (tt0) cc_final: 0.5280 (tp-100) REVERT: W 277 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7721 (tt0) REVERT: W 481 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7920 (pm20) REVERT: W 489 ARG cc_start: 0.6085 (ttm-80) cc_final: 0.5655 (ttm-80) REVERT: X 45 ASN cc_start: 0.7660 (m110) cc_final: 0.7353 (t0) REVERT: X 54 SER cc_start: 0.7541 (t) cc_final: 0.7118 (p) REVERT: X 57 LYS cc_start: 0.7896 (mttt) cc_final: 0.7677 (mttm) REVERT: X 64 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7146 (mt) outliers start: 31 outliers final: 28 residues processed: 198 average time/residue: 0.2587 time to fit residues: 76.6795 Evaluate side-chains 198 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 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 778 GLU Chi-restraints excluded: chain U residue 823 HIS 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 338 SER Chi-restraints excluded: chain W residue 17 VAL 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 X residue 58 VAL Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 868 HIS V 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.3649 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= 0.165 Angle : 0.483 5.373 18251 Z= 0.255 Chirality : 0.043 0.195 2010 Planarity : 0.004 0.036 2336 Dihedral : 7.068 68.428 1862 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.54 % Favored : 97.40 % Rotamer: Outliers : 2.33 % Allowed : 14.62 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.21), residues: 1613 helix: 1.22 (0.20), residues: 736 sheet: 0.41 (0.37), residues: 204 loop : 0.23 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 543 HIS 0.005 0.001 HIS W 162 PHE 0.015 0.001 PHE U 598 TYR 0.016 0.001 TYR U 596 ARG 0.004 0.000 ARG X 69 *********************** 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 206 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 549 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7756 (tt0) REVERT: U 183 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6905 (mm-30) REVERT: U 202 LYS cc_start: 0.7061 (mttt) cc_final: 0.6818 (mptt) REVERT: U 207 ASP cc_start: 0.6937 (t0) cc_final: 0.6224 (t0) REVERT: U 212 ASP cc_start: 0.7227 (m-30) cc_final: 0.6609 (t0) REVERT: U 374 ILE cc_start: 0.8050 (mt) cc_final: 0.7724 (tt) REVERT: U 576 ASP cc_start: 0.6931 (m-30) cc_final: 0.6331 (p0) REVERT: U 626 LYS cc_start: 0.7641 (mttt) cc_final: 0.7331 (mppt) REVERT: U 631 GLU cc_start: 0.7440 (tt0) cc_final: 0.6967 (pt0) REVERT: U 690 GLU cc_start: 0.7819 (tt0) cc_final: 0.7366 (pt0) REVERT: V 34 ILE cc_start: 0.8139 (mt) cc_final: 0.7877 (pt) REVERT: V 300 SER cc_start: 0.8384 (m) cc_final: 0.8082 (p) REVERT: V 360 GLN cc_start: 0.6167 (tt0) cc_final: 0.5608 (mm110) REVERT: V 364 GLU cc_start: 0.7135 (tt0) cc_final: 0.6631 (mm-30) REVERT: W 9 TYR cc_start: 0.6849 (t80) cc_final: 0.6622 (t80) REVERT: W 91 GLN cc_start: 0.5519 (tt0) cc_final: 0.5288 (tp-100) REVERT: W 277 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7552 (tt0) REVERT: W 481 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7923 (pm20) REVERT: W 489 ARG cc_start: 0.5987 (ttm-80) cc_final: 0.5586 (ttm-80) REVERT: X 45 ASN cc_start: 0.7722 (m110) cc_final: 0.7410 (t0) REVERT: X 54 SER cc_start: 0.7538 (t) cc_final: 0.7118 (p) REVERT: X 57 LYS cc_start: 0.7877 (mttt) cc_final: 0.7662 (mttm) REVERT: X 64 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7180 (mt) outliers start: 34 outliers final: 29 residues processed: 196 average time/residue: 0.2603 time to fit residues: 75.2553 Evaluate side-chains 199 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 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 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 737 SER Chi-restraints excluded: chain U residue 778 GLU Chi-restraints excluded: chain U residue 868 HIS 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 W residue 17 VAL 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 X residue 58 VAL Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 0.0770 chunk 44 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 137 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 95 optimal weight: 0.0980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 580 GLN U 868 HIS V 372 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.3689 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= 0.161 Angle : 0.487 10.619 18251 Z= 0.255 Chirality : 0.042 0.200 2010 Planarity : 0.004 0.036 2336 Dihedral : 6.991 68.633 1862 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.29 % Favored : 97.58 % Rotamer: Outliers : 2.20 % Allowed : 14.62 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.21), residues: 1613 helix: 1.23 (0.20), residues: 737 sheet: 0.60 (0.38), residues: 194 loop : 0.27 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 477 HIS 0.004 0.001 HIS W 162 PHE 0.016 0.001 PHE U 598 TYR 0.021 0.001 TYR W 319 ARG 0.004 0.000 ARG U 834 *********************** 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: 32 poor density : 172 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 549 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7780 (tt0) REVERT: U 183 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6880 (mm-30) REVERT: U 202 LYS cc_start: 0.7052 (mttt) cc_final: 0.6812 (mptt) REVERT: U 207 ASP cc_start: 0.6921 (t0) cc_final: 0.6217 (t0) REVERT: U 212 ASP cc_start: 0.7228 (m-30) cc_final: 0.6610 (t0) REVERT: U 374 ILE cc_start: 0.8041 (mt) cc_final: 0.7731 (tt) REVERT: U 576 ASP cc_start: 0.6881 (m-30) cc_final: 0.6277 (p0) REVERT: U 605 MET cc_start: 0.6963 (tpt) cc_final: 0.6546 (tpt) REVERT: U 626 LYS cc_start: 0.7597 (mttt) cc_final: 0.7315 (mppt) REVERT: U 631 GLU cc_start: 0.7443 (tt0) cc_final: 0.6968 (pt0) REVERT: U 690 GLU cc_start: 0.7836 (tt0) cc_final: 0.7390 (pt0) REVERT: V 34 ILE cc_start: 0.8161 (mt) cc_final: 0.7907 (pt) REVERT: V 300 SER cc_start: 0.8369 (m) cc_final: 0.8080 (p) REVERT: V 360 GLN cc_start: 0.6167 (tt0) cc_final: 0.5608 (mm110) REVERT: V 364 GLU cc_start: 0.7141 (tt0) cc_final: 0.6636 (mm-30) REVERT: W 91 GLN cc_start: 0.5531 (tt0) cc_final: 0.5306 (tp-100) REVERT: W 277 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7544 (tt0) REVERT: W 481 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7923 (pm20) REVERT: X 45 ASN cc_start: 0.7717 (m110) cc_final: 0.7409 (t0) REVERT: X 54 SER cc_start: 0.7499 (t) cc_final: 0.7073 (p) REVERT: X 57 LYS cc_start: 0.7874 (mttt) cc_final: 0.7643 (ttmm) REVERT: X 64 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7196 (tt) outliers start: 32 outliers final: 30 residues processed: 195 average time/residue: 0.2539 time to fit residues: 73.7582 Evaluate side-chains 199 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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 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 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 737 SER Chi-restraints excluded: chain U residue 778 GLU Chi-restraints excluded: chain U residue 868 HIS Chi-restraints excluded: chain V residue 110 MET 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 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 X residue 58 VAL Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 5.9990 chunk 93 optimal weight: 0.0870 chunk 72 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 161 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 868 HIS V 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.3708 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= 0.185 Angle : 0.494 7.024 18251 Z= 0.260 Chirality : 0.043 0.200 2010 Planarity : 0.004 0.036 2336 Dihedral : 6.978 68.033 1862 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.60 % Favored : 97.27 % Rotamer: Outliers : 2.13 % Allowed : 14.89 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1613 helix: 1.29 (0.20), residues: 729 sheet: 0.47 (0.38), residues: 204 loop : 0.30 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 551 HIS 0.007 0.001 HIS U 868 PHE 0.015 0.001 PHE U 598 TYR 0.016 0.001 TYR W 319 ARG 0.007 0.000 ARG X 69 ********************** 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 201 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 549 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7781 (tt0) REVERT: U 183 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6911 (mm-30) REVERT: U 202 LYS cc_start: 0.7067 (mttt) cc_final: 0.6831 (mptt) REVERT: U 207 ASP cc_start: 0.6936 (t0) cc_final: 0.6236 (t0) REVERT: U 212 ASP cc_start: 0.7207 (m-30) cc_final: 0.6592 (t0) REVERT: U 374 ILE cc_start: 0.8081 (mt) cc_final: 0.7772 (tt) REVERT: U 576 ASP cc_start: 0.6838 (m-30) cc_final: 0.6239 (p0) REVERT: U 599 LYS cc_start: 0.7146 (tptt) cc_final: 0.6869 (tptp) REVERT: U 626 LYS cc_start: 0.7589 (mttt) cc_final: 0.7319 (mppt) REVERT: U 631 GLU cc_start: 0.7449 (tt0) cc_final: 0.6980 (pt0) REVERT: U 690 GLU cc_start: 0.7781 (tt0) cc_final: 0.7342 (pt0) REVERT: V 34 ILE cc_start: 0.8162 (mt) cc_final: 0.7906 (pt) REVERT: V 83 GLU cc_start: 0.6306 (tt0) cc_final: 0.6103 (tm-30) REVERT: V 300 SER cc_start: 0.8407 (m) cc_final: 0.8108 (p) REVERT: V 360 GLN cc_start: 0.6166 (tt0) cc_final: 0.5611 (mm110) REVERT: V 364 GLU cc_start: 0.7146 (tt0) cc_final: 0.6648 (mm-30) REVERT: W 9 TYR cc_start: 0.6885 (t80) cc_final: 0.6660 (t80) REVERT: W 91 GLN cc_start: 0.5411 (tt0) cc_final: 0.5179 (tp-100) REVERT: W 174 MET cc_start: 0.3965 (mtm) cc_final: 0.3573 (mtm) REVERT: W 277 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7540 (tt0) REVERT: W 481 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7926 (pm20) REVERT: X 45 ASN cc_start: 0.7731 (m110) cc_final: 0.7421 (t0) REVERT: X 54 SER cc_start: 0.7501 (t) cc_final: 0.7076 (p) REVERT: X 57 LYS cc_start: 0.7896 (mttt) cc_final: 0.7676 (ttmm) REVERT: X 64 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7179 (mt) outliers start: 31 outliers final: 29 residues processed: 193 average time/residue: 0.2854 time to fit residues: 81.5581 Evaluate side-chains 196 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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 711 ILE Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 778 GLU Chi-restraints excluded: chain U residue 868 HIS Chi-restraints excluded: chain V residue 110 MET 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 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 X residue 58 VAL Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 868 HIS V 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.151032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115291 restraints weight = 16566.811| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.13 r_work: 0.3170 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13475 Z= 0.167 Angle : 0.491 9.225 18251 Z= 0.258 Chirality : 0.043 0.198 2010 Planarity : 0.004 0.042 2336 Dihedral : 6.926 68.041 1862 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.48 % Favored : 97.40 % Rotamer: Outliers : 2.13 % Allowed : 15.10 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1613 helix: 1.28 (0.20), residues: 736 sheet: 0.53 (0.38), residues: 204 loop : 0.28 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 551 HIS 0.004 0.001 HIS W 162 PHE 0.016 0.001 PHE U 598 TYR 0.015 0.001 TYR U 596 ARG 0.007 0.000 ARG X 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3044.20 seconds wall clock time: 57 minutes 5.98 seconds (3425.98 seconds total)