Starting phenix.real_space_refine on Thu Jul 31 11:03:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a5a_15163/07_2025/8a5a_15163.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a5a_15163/07_2025/8a5a_15163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a5a_15163/07_2025/8a5a_15163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a5a_15163/07_2025/8a5a_15163.map" model { file = "/net/cci-nas-00/data/ceres_data/8a5a_15163/07_2025/8a5a_15163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a5a_15163/07_2025/8a5a_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.84, per 1000 atoms: 0.59 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: 3.48 Conformation dependent library (CDL) restraints added in 2.3 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: 2.07 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: 4.59 Time building geometry restraints manager: 4.04 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.780 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.550 ------------------------------------------------------------------------------- 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= 1.149 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 Details of bonding type rmsd hydrogen bonds : bond 0.19711 ( 630) hydrogen bonds : angle 8.19746 ( 1689) covalent geometry : bond 0.01587 (13475) covalent geometry : angle 2.07997 (18251) *********************** 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 : 1.466 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: 0.2879 time to fit residues: 130.3553 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 : 1.465 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111667 restraints weight = 16642.612| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.14 r_work: 0.3098 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13475 Z= 0.158 Angle : 0.657 16.259 18251 Z= 0.353 Chirality : 0.046 0.156 2010 Planarity : 0.005 0.045 2336 Dihedral : 9.868 69.300 1894 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.29 % Favored : 97.58 % Rotamer: Outliers : 2.61 % Allowed : 9.47 % Favored : 87.92 % 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: -0.14 (0.20), residues: 1613 helix: 0.10 (0.19), residues: 710 sheet: 0.09 (0.36), 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 0.003 0.001 HIS V 372 PHE 0.016 0.002 PHE U 546 TYR 0.021 0.002 TYR U 596 ARG 0.003 0.001 ARG U 674 Details of bonding type rmsd hydrogen bonds : bond 0.04851 ( 630) hydrogen bonds : angle 5.08498 ( 1689) covalent geometry : bond 0.00349 (13475) covalent geometry : angle 0.65656 (18251) *********************** 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 241 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 468 HIS cc_start: 0.7862 (t-90) cc_final: 0.7587 (t70) REVERT: G 479 ASP cc_start: 0.7311 (m-30) cc_final: 0.7070 (t0) REVERT: G 519 SER cc_start: 0.9092 (t) cc_final: 0.8573 (p) REVERT: G 539 MET cc_start: 0.8886 (tmm) cc_final: 0.8637 (tmm) REVERT: U 202 LYS cc_start: 0.8660 (mttt) cc_final: 0.8232 (mptt) REVERT: U 207 ASP cc_start: 0.8389 (t0) cc_final: 0.7310 (t0) REVERT: U 212 ASP cc_start: 0.7971 (m-30) cc_final: 0.7609 (t0) REVERT: U 222 LYS cc_start: 0.7549 (mmmt) cc_final: 0.7173 (mtpt) REVERT: U 316 GLN cc_start: 0.7587 (mp10) cc_final: 0.7305 (mp10) REVERT: U 573 GLN cc_start: 0.7938 (tt0) cc_final: 0.7701 (tp-100) REVERT: U 576 ASP cc_start: 0.7529 (m-30) cc_final: 0.7135 (p0) REVERT: U 586 ASN cc_start: 0.7624 (t0) cc_final: 0.7395 (t0) REVERT: U 631 GLU cc_start: 0.8470 (tt0) cc_final: 0.8213 (pt0) REVERT: U 687 ASP cc_start: 0.7135 (m-30) cc_final: 0.6652 (m-30) REVERT: U 690 GLU cc_start: 0.7607 (tt0) cc_final: 0.7072 (pt0) REVERT: U 806 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8297 (tm-30) REVERT: V 62 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7618 (ttm110) REVERT: V 325 MET cc_start: 0.8880 (tpp) cc_final: 0.8253 (tpp) REVERT: V 375 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6415 (m-80) REVERT: W 33 SER cc_start: 0.9094 (m) cc_final: 0.8868 (p) REVERT: W 174 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7419 (mtm) REVERT: W 182 ARG cc_start: 0.8250 (ptt180) cc_final: 0.8044 (ttp-110) REVERT: W 196 LYS cc_start: 0.7869 (tttt) cc_final: 0.7528 (ttmt) REVERT: W 206 LEU cc_start: 0.8937 (tt) cc_final: 0.8707 (tp) REVERT: W 219 LYS cc_start: 0.8355 (tttm) cc_final: 0.8078 (ttpt) REVERT: W 277 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7985 (tt0) REVERT: W 308 ASN cc_start: 0.7322 (t0) cc_final: 0.7022 (t0) REVERT: W 313 LYS cc_start: 0.7483 (tttt) cc_final: 0.7129 (tptt) REVERT: W 436 LYS cc_start: 0.7936 (mttt) cc_final: 0.7706 (pttp) REVERT: X 54 SER cc_start: 0.8556 (t) cc_final: 0.8111 (p) outliers start: 38 outliers final: 22 residues processed: 229 average time/residue: 0.3091 time to fit residues: 104.9406 Evaluate side-chains 184 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 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 8 VAL 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 174 MET Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 220 THR 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 111 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 142 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 161 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 319 GLN U 709 GLN U 713 ASN ** U 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.148983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113013 restraints weight = 16749.312| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.15 r_work: 0.3119 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13475 Z= 0.134 Angle : 0.554 8.859 18251 Z= 0.297 Chirality : 0.044 0.164 2010 Planarity : 0.004 0.041 2336 Dihedral : 8.681 65.237 1872 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 2.40 % Allowed : 10.98 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.43 (0.21), residues: 1613 helix: 0.72 (0.19), residues: 710 sheet: 0.30 (0.36), residues: 205 loop : -0.01 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 340 HIS 0.004 0.001 HIS W 162 PHE 0.022 0.001 PHE U 223 TYR 0.014 0.001 TYR U 596 ARG 0.004 0.000 ARG U 722 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 630) hydrogen bonds : angle 4.59742 ( 1689) covalent geometry : bond 0.00308 (13475) covalent geometry : angle 0.55400 (18251) *********************** 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 227 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 468 HIS cc_start: 0.7911 (t-90) cc_final: 0.7554 (t70) REVERT: G 479 ASP cc_start: 0.7064 (m-30) cc_final: 0.6844 (t0) REVERT: G 519 SER cc_start: 0.9044 (t) cc_final: 0.8488 (p) REVERT: U 202 LYS cc_start: 0.8608 (mttt) cc_final: 0.8191 (mptt) REVERT: U 207 ASP cc_start: 0.8287 (t0) cc_final: 0.7317 (t0) REVERT: U 212 ASP cc_start: 0.7931 (m-30) cc_final: 0.7523 (t0) REVERT: U 576 ASP cc_start: 0.7483 (m-30) cc_final: 0.6974 (p0) REVERT: U 586 ASN cc_start: 0.7508 (t0) cc_final: 0.7308 (t0) REVERT: U 598 PHE cc_start: 0.8095 (p90) cc_final: 0.7865 (p90) REVERT: U 605 MET cc_start: 0.8569 (tpt) cc_final: 0.7780 (tpt) REVERT: U 631 GLU cc_start: 0.8402 (tt0) cc_final: 0.8134 (pt0) REVERT: U 687 ASP cc_start: 0.7198 (m-30) cc_final: 0.6692 (m-30) REVERT: U 690 GLU cc_start: 0.7701 (tt0) cc_final: 0.7073 (pt0) REVERT: U 834 ARG cc_start: 0.7207 (mtm-85) cc_final: 0.6964 (mtm110) REVERT: V 62 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7642 (ttm110) REVERT: V 325 MET cc_start: 0.8762 (tpp) cc_final: 0.8145 (tpp) REVERT: V 360 GLN cc_start: 0.7558 (tt0) cc_final: 0.7336 (mm110) REVERT: W 33 SER cc_start: 0.9024 (m) cc_final: 0.8721 (p) REVERT: W 196 LYS cc_start: 0.7872 (tttt) cc_final: 0.7495 (ttmt) REVERT: W 206 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8527 (tt) REVERT: W 277 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7966 (tt0) REVERT: W 308 ASN cc_start: 0.7308 (t0) cc_final: 0.7004 (t0) REVERT: W 313 LYS cc_start: 0.7328 (tttt) cc_final: 0.6962 (tptt) REVERT: W 427 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7680 (mm-30) REVERT: X 54 SER cc_start: 0.8548 (t) cc_final: 0.8084 (p) outliers start: 35 outliers final: 23 residues processed: 216 average time/residue: 0.3144 time to fit residues: 98.8581 Evaluate side-chains 189 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 555 SER Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain V residue 144 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain 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 206 LEU Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113300 restraints weight = 16586.044| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.11 r_work: 0.3123 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13475 Z= 0.131 Angle : 0.523 7.206 18251 Z= 0.279 Chirality : 0.044 0.186 2010 Planarity : 0.004 0.040 2336 Dihedral : 8.083 64.814 1866 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.48 % Favored : 97.40 % Rotamer: Outliers : 2.61 % Allowed : 12.22 % Favored : 85.18 % 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: 0.58 (0.21), residues: 1613 helix: 0.87 (0.19), residues: 728 sheet: 0.55 (0.37), 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 0.005 0.001 HIS W 162 PHE 0.013 0.001 PHE U 766 TYR 0.015 0.001 TYR U 596 ARG 0.005 0.000 ARG G 548 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 630) hydrogen bonds : angle 4.39291 ( 1689) covalent geometry : bond 0.00307 (13475) covalent geometry : angle 0.52327 (18251) *********************** 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: 38 poor density : 180 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 468 HIS cc_start: 0.7885 (t-90) cc_final: 0.7372 (t-90) REVERT: G 519 SER cc_start: 0.8944 (t) cc_final: 0.8351 (p) REVERT: U 202 LYS cc_start: 0.8557 (mttt) cc_final: 0.8164 (mptt) REVERT: U 207 ASP cc_start: 0.8266 (t0) cc_final: 0.7323 (t0) REVERT: U 212 ASP cc_start: 0.7891 (m-30) cc_final: 0.7523 (t0) REVERT: U 332 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8279 (ttpt) REVERT: U 576 ASP cc_start: 0.7450 (m-30) cc_final: 0.6928 (p0) REVERT: U 605 MET cc_start: 0.8626 (tpt) cc_final: 0.7950 (tpt) REVERT: U 631 GLU cc_start: 0.8386 (tt0) cc_final: 0.8179 (pt0) REVERT: U 687 ASP cc_start: 0.7185 (m-30) cc_final: 0.6702 (m-30) REVERT: U 690 GLU cc_start: 0.7676 (tt0) cc_final: 0.7066 (pt0) REVERT: U 778 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: V 62 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7763 (ttm110) REVERT: V 325 MET cc_start: 0.8589 (tpp) cc_final: 0.8061 (tpp) REVERT: V 360 GLN cc_start: 0.7599 (tt0) cc_final: 0.7356 (mm110) REVERT: W 33 SER cc_start: 0.8993 (m) cc_final: 0.8673 (p) REVERT: W 196 LYS cc_start: 0.7861 (tttt) cc_final: 0.7486 (ttmt) REVERT: W 206 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8433 (tt) REVERT: W 277 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7778 (tt0) REVERT: W 308 ASN cc_start: 0.7276 (t0) cc_final: 0.6978 (t0) REVERT: W 313 LYS cc_start: 0.7253 (tttt) cc_final: 0.7043 (tttp) REVERT: X 54 SER cc_start: 0.8758 (t) cc_final: 0.8246 (p) outliers start: 38 outliers final: 27 residues processed: 204 average time/residue: 0.4007 time to fit residues: 123.3674 Evaluate side-chains 204 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 2.075 ------------------------------------------------------------------------------- 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 332 LYS Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 555 SER Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 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 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 206 LEU 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 W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 120 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 134 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 55 optimal weight: 0.0270 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 541 ASN V 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114610 restraints weight = 16523.019| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.93 r_work: 0.3144 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13475 Z= 0.132 Angle : 0.517 9.428 18251 Z= 0.273 Chirality : 0.044 0.187 2010 Planarity : 0.004 0.039 2336 Dihedral : 7.801 65.541 1864 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.11 % Favored : 97.77 % Rotamer: Outliers : 3.09 % Allowed : 12.42 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.68 (0.21), residues: 1613 helix: 1.01 (0.20), residues: 727 sheet: 0.36 (0.37), residues: 204 loop : 0.01 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 356 HIS 0.005 0.001 HIS W 162 PHE 0.020 0.001 PHE U 598 TYR 0.013 0.001 TYR U 596 ARG 0.007 0.000 ARG X 69 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 630) hydrogen bonds : angle 4.27376 ( 1689) covalent geometry : bond 0.00311 (13475) covalent geometry : angle 0.51678 (18251) *********************** 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 231 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 1.547 Fit side-chains revert: symmetry clash REVERT: G 468 HIS cc_start: 0.7891 (t-90) cc_final: 0.7380 (t-90) REVERT: G 519 SER cc_start: 0.8893 (t) cc_final: 0.8689 (t) REVERT: G 549 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7972 (tt0) REVERT: U 202 LYS cc_start: 0.8533 (mttt) cc_final: 0.8129 (mptt) REVERT: U 207 ASP cc_start: 0.8193 (t0) cc_final: 0.7307 (t0) REVERT: U 212 ASP cc_start: 0.7847 (m-30) cc_final: 0.7417 (t0) REVERT: U 332 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8232 (ttpt) REVERT: U 576 ASP cc_start: 0.7351 (m-30) cc_final: 0.6855 (p0) REVERT: U 605 MET cc_start: 0.8607 (tpt) cc_final: 0.7938 (tpt) REVERT: U 631 GLU cc_start: 0.8353 (tt0) cc_final: 0.8139 (pt0) REVERT: U 687 ASP cc_start: 0.7122 (m-30) cc_final: 0.6639 (m-30) REVERT: U 690 GLU cc_start: 0.7689 (tt0) cc_final: 0.7117 (pt0) REVERT: U 778 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: V 34 ILE cc_start: 0.8983 (mt) cc_final: 0.8686 (pt) REVERT: V 62 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7641 (ttm110) REVERT: V 82 MET cc_start: 0.8378 (tpt) cc_final: 0.7623 (tpt) REVERT: V 325 MET cc_start: 0.8607 (tpp) cc_final: 0.8143 (tpp) REVERT: V 360 GLN cc_start: 0.7579 (tt0) cc_final: 0.7330 (mm110) REVERT: W 196 LYS cc_start: 0.7770 (tttt) cc_final: 0.7410 (ttmt) REVERT: W 206 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8387 (tt) REVERT: W 277 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7741 (tt0) REVERT: W 292 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7914 (tt) REVERT: W 313 LYS cc_start: 0.7168 (tttt) cc_final: 0.6942 (tttp) REVERT: W 489 ARG cc_start: 0.7473 (ttm-80) cc_final: 0.6993 (ttm-80) REVERT: X 54 SER cc_start: 0.8647 (t) cc_final: 0.8185 (p) REVERT: X 64 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7686 (mt) outliers start: 45 outliers final: 35 residues processed: 215 average time/residue: 0.2581 time to fit residues: 80.7215 Evaluate side-chains 214 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 332 LYS Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 555 SER Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 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 144 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 142 THR Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 292 LEU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 446 ILE 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 1 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 81 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111337 restraints weight = 16924.072| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.26 r_work: 0.3096 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3405 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= 0.149 Angle : 0.523 6.018 18251 Z= 0.277 Chirality : 0.044 0.186 2010 Planarity : 0.004 0.038 2336 Dihedral : 7.716 66.832 1864 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.29 % Favored : 97.58 % Rotamer: Outliers : 3.57 % Allowed : 12.56 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.61 (0.21), residues: 1613 helix: 0.97 (0.20), residues: 731 sheet: 0.22 (0.36), residues: 206 loop : -0.01 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 356 HIS 0.005 0.001 HIS W 162 PHE 0.014 0.001 PHE W 207 TYR 0.015 0.001 TYR U 596 ARG 0.005 0.000 ARG X 69 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 630) hydrogen bonds : angle 4.26778 ( 1689) covalent geometry : bond 0.00357 (13475) covalent geometry : angle 0.52341 (18251) *********************** 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 224 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 468 HIS cc_start: 0.8000 (t-90) cc_final: 0.7453 (t-90) REVERT: G 519 SER cc_start: 0.8905 (t) cc_final: 0.8699 (t) REVERT: G 549 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7983 (tt0) REVERT: U 202 LYS cc_start: 0.8542 (mttt) cc_final: 0.8127 (mptt) REVERT: U 207 ASP cc_start: 0.8389 (t0) cc_final: 0.7451 (t0) REVERT: U 212 ASP cc_start: 0.7989 (m-30) cc_final: 0.7522 (t0) REVERT: U 332 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8158 (ttpt) REVERT: U 576 ASP cc_start: 0.7407 (m-30) cc_final: 0.6799 (p0) REVERT: U 605 MET cc_start: 0.8658 (tpt) cc_final: 0.8002 (tpt) REVERT: U 631 GLU cc_start: 0.8461 (tt0) cc_final: 0.8188 (pt0) REVERT: U 687 ASP cc_start: 0.7164 (m-30) cc_final: 0.6656 (m-30) REVERT: U 690 GLU cc_start: 0.7897 (tt0) cc_final: 0.7335 (pt0) REVERT: U 778 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: V 34 ILE cc_start: 0.9040 (mt) cc_final: 0.8790 (pt) REVERT: V 82 MET cc_start: 0.8377 (tpt) cc_final: 0.7592 (tpt) REVERT: V 325 MET cc_start: 0.8598 (tpp) cc_final: 0.8187 (tpp) REVERT: V 360 GLN cc_start: 0.7599 (tt0) cc_final: 0.7351 (mm110) REVERT: W 196 LYS cc_start: 0.7922 (tttt) cc_final: 0.7561 (ttmt) REVERT: W 277 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7820 (tt0) REVERT: W 313 LYS cc_start: 0.7158 (tttt) cc_final: 0.6938 (tttp) REVERT: W 446 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8252 (tp) REVERT: W 489 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.7232 (ttm-80) REVERT: X 54 SER cc_start: 0.8703 (t) cc_final: 0.8267 (p) REVERT: X 64 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7751 (mt) outliers start: 52 outliers final: 42 residues processed: 206 average time/residue: 0.2529 time to fit residues: 77.2422 Evaluate side-chains 210 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 332 LYS Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 555 SER Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 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 144 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 142 THR Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 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 W residue 441 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 103 optimal weight: 6.9990 chunk 56 optimal weight: 0.0170 chunk 138 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 111 optimal weight: 0.0050 chunk 25 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.8038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 372 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.146189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109547 restraints weight = 16821.313| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.24 r_work: 0.3070 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13475 Z= 0.194 Angle : 0.554 6.223 18251 Z= 0.292 Chirality : 0.045 0.184 2010 Planarity : 0.004 0.040 2336 Dihedral : 7.830 70.122 1864 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.67 % Favored : 97.21 % Rotamer: Outliers : 3.64 % Allowed : 13.38 % 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: 0.50 (0.21), residues: 1613 helix: 0.87 (0.19), residues: 730 sheet: 0.11 (0.36), residues: 208 loop : -0.03 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 356 HIS 0.005 0.001 HIS W 162 PHE 0.017 0.001 PHE W 207 TYR 0.018 0.002 TYR W 450 ARG 0.005 0.000 ARG X 69 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 630) hydrogen bonds : angle 4.35867 ( 1689) covalent geometry : bond 0.00473 (13475) covalent geometry : angle 0.55429 (18251) *********************** 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 218 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 165 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 519 SER cc_start: 0.8925 (t) cc_final: 0.8720 (t) REVERT: U 181 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7688 (ttpp) REVERT: U 202 LYS cc_start: 0.8576 (mttt) cc_final: 0.8148 (mptt) REVERT: U 207 ASP cc_start: 0.8465 (t0) cc_final: 0.7518 (t0) REVERT: U 212 ASP cc_start: 0.8007 (m-30) cc_final: 0.7527 (t0) REVERT: U 332 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8115 (ttpt) REVERT: U 576 ASP cc_start: 0.7393 (m-30) cc_final: 0.6794 (p0) REVERT: U 605 MET cc_start: 0.8647 (tpt) cc_final: 0.8003 (tpt) REVERT: U 631 GLU cc_start: 0.8491 (tt0) cc_final: 0.8233 (pt0) REVERT: U 687 ASP cc_start: 0.7217 (m-30) cc_final: 0.6710 (m-30) REVERT: U 778 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: V 34 ILE cc_start: 0.9034 (mt) cc_final: 0.8756 (pt) REVERT: V 325 MET cc_start: 0.8633 (tpp) cc_final: 0.8215 (tpp) REVERT: V 360 GLN cc_start: 0.7578 (tt0) cc_final: 0.7369 (mm110) REVERT: V 363 ASP cc_start: 0.8086 (m-30) cc_final: 0.7863 (m-30) REVERT: W 196 LYS cc_start: 0.7936 (tttt) cc_final: 0.7579 (ttmt) REVERT: W 277 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7790 (tt0) REVERT: W 308 ASN cc_start: 0.7140 (t0) cc_final: 0.6906 (t0) REVERT: W 313 LYS cc_start: 0.7162 (tttt) cc_final: 0.6871 (tmtm) REVERT: W 446 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8253 (tp) REVERT: W 448 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7843 (mtm180) REVERT: X 54 SER cc_start: 0.8743 (t) cc_final: 0.8320 (p) REVERT: X 64 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7791 (mt) outliers start: 53 outliers final: 44 residues processed: 200 average time/residue: 0.2514 time to fit residues: 73.6391 Evaluate side-chains 209 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 332 LYS Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 555 SER Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 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 144 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 142 THR Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 211 GLN Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 441 THR Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain W residue 448 ARG Chi-restraints excluded: chain X residue 58 VAL 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 26 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 0.0270 chunk 47 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.0044 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** V 372 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.148255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111743 restraints weight = 16790.311| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.26 r_work: 0.3099 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13475 Z= 0.128 Angle : 0.505 6.058 18251 Z= 0.267 Chirality : 0.043 0.192 2010 Planarity : 0.004 0.038 2336 Dihedral : 7.566 68.567 1864 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.36 % Favored : 97.52 % Rotamer: Outliers : 2.95 % Allowed : 14.21 % Favored : 82.84 % 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: 0.66 (0.21), residues: 1613 helix: 1.03 (0.20), residues: 731 sheet: 0.20 (0.37), residues: 207 loop : 0.01 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 543 HIS 0.005 0.001 HIS W 162 PHE 0.014 0.001 PHE U 378 TYR 0.014 0.001 TYR U 596 ARG 0.004 0.000 ARG X 69 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 630) hydrogen bonds : angle 4.19090 ( 1689) covalent geometry : bond 0.00304 (13475) covalent geometry : angle 0.50485 (18251) *********************** 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 211 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 181 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7717 (ttpp) REVERT: U 202 LYS cc_start: 0.8550 (mttt) cc_final: 0.8135 (mptt) REVERT: U 207 ASP cc_start: 0.8331 (t0) cc_final: 0.7420 (t0) REVERT: U 212 ASP cc_start: 0.7921 (m-30) cc_final: 0.7453 (t0) REVERT: U 361 LYS cc_start: 0.8189 (tptt) cc_final: 0.7693 (tmtt) REVERT: U 576 ASP cc_start: 0.7355 (m-30) cc_final: 0.6813 (p0) REVERT: U 580 GLN cc_start: 0.6767 (mt0) cc_final: 0.6334 (tp40) REVERT: U 605 MET cc_start: 0.8625 (tpt) cc_final: 0.8020 (tpt) REVERT: U 631 GLU cc_start: 0.8466 (tt0) cc_final: 0.8222 (pt0) REVERT: U 687 ASP cc_start: 0.7205 (m-30) cc_final: 0.6704 (m-30) REVERT: U 778 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: V 34 ILE cc_start: 0.9059 (mt) cc_final: 0.8818 (pt) REVERT: V 325 MET cc_start: 0.8570 (tpp) cc_final: 0.8188 (tpp) REVERT: V 360 GLN cc_start: 0.7636 (tt0) cc_final: 0.7426 (mm110) REVERT: V 363 ASP cc_start: 0.8027 (m-30) cc_final: 0.7787 (m-30) REVERT: W 196 LYS cc_start: 0.7927 (tttt) cc_final: 0.7572 (ttmt) REVERT: W 277 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7753 (tt0) REVERT: W 308 ASN cc_start: 0.7134 (t0) cc_final: 0.6870 (t0) REVERT: W 313 LYS cc_start: 0.7133 (tttt) cc_final: 0.6845 (tmtm) REVERT: W 446 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8283 (tp) REVERT: X 54 SER cc_start: 0.8723 (t) cc_final: 0.8279 (p) REVERT: X 64 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7771 (mt) outliers start: 43 outliers final: 36 residues processed: 195 average time/residue: 0.2545 time to fit residues: 73.0639 Evaluate side-chains 201 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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 290 VAL Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 555 SER Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 778 GLU Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 441 THR Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL 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 42 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 157 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 101 optimal weight: 0.0000 chunk 43 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 109 optimal weight: 0.0070 overall best weight: 0.4604 ------------------------------------------------------------------------------- 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 799 GLN V 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.149922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114521 restraints weight = 16555.473| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.06 r_work: 0.3163 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13475 Z= 0.099 Angle : 0.483 8.545 18251 Z= 0.254 Chirality : 0.042 0.202 2010 Planarity : 0.004 0.037 2336 Dihedral : 7.094 65.332 1862 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 1.51 % Allowed : 16.06 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.21), residues: 1613 helix: 1.19 (0.20), residues: 738 sheet: 0.46 (0.38), residues: 200 loop : 0.14 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 274 HIS 0.004 0.000 HIS W 162 PHE 0.013 0.001 PHE U 378 TYR 0.012 0.001 TYR U 596 ARG 0.007 0.000 ARG X 69 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 630) hydrogen bonds : angle 4.04791 ( 1689) covalent geometry : bond 0.00223 (13475) covalent geometry : angle 0.48274 (18251) *********************** 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 198 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 181 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7656 (ttpp) REVERT: U 202 LYS cc_start: 0.8542 (mttt) cc_final: 0.8150 (mptt) REVERT: U 207 ASP cc_start: 0.8106 (t0) cc_final: 0.7371 (t0) REVERT: U 361 LYS cc_start: 0.8143 (tptt) cc_final: 0.7796 (mppt) REVERT: U 576 ASP cc_start: 0.7328 (m-30) cc_final: 0.6752 (p0) REVERT: U 580 GLN cc_start: 0.6777 (mt0) cc_final: 0.6318 (tp40) REVERT: U 599 LYS cc_start: 0.8002 (tptt) cc_final: 0.7302 (tptp) REVERT: U 605 MET cc_start: 0.8622 (tpt) cc_final: 0.8024 (tpt) REVERT: U 631 GLU cc_start: 0.8428 (tt0) cc_final: 0.8177 (pt0) REVERT: U 687 ASP cc_start: 0.7176 (m-30) cc_final: 0.6831 (m-30) REVERT: U 778 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: V 34 ILE cc_start: 0.9013 (mt) cc_final: 0.8809 (pt) REVERT: V 325 MET cc_start: 0.8521 (tpp) cc_final: 0.8106 (tpp) REVERT: V 363 ASP cc_start: 0.7931 (m-30) cc_final: 0.7654 (m-30) REVERT: W 196 LYS cc_start: 0.7902 (tttt) cc_final: 0.7576 (ttmt) REVERT: W 277 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7667 (tt0) REVERT: W 308 ASN cc_start: 0.7112 (t0) cc_final: 0.6836 (t0) REVERT: W 313 LYS cc_start: 0.7138 (tttt) cc_final: 0.6860 (tmtm) REVERT: W 446 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8313 (tp) REVERT: W 489 ARG cc_start: 0.7530 (ttm-80) cc_final: 0.7261 (ttm-80) REVERT: X 54 SER cc_start: 0.8791 (t) cc_final: 0.8314 (p) outliers start: 22 outliers final: 17 residues processed: 189 average time/residue: 0.2614 time to fit residues: 72.7476 Evaluate side-chains 184 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 1.531 ------------------------------------------------------------------------------- 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 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 737 SER Chi-restraints excluded: chain U residue 778 GLU 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 W residue 17 VAL Chi-restraints excluded: chain W residue 183 ASN 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 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 125 optimal weight: 0.3980 chunk 101 optimal weight: 0.0970 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 475 GLN U 799 GLN V 228 GLN V 372 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.151517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115649 restraints weight = 16486.383| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.13 r_work: 0.3159 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13475 Z= 0.101 Angle : 0.493 9.784 18251 Z= 0.257 Chirality : 0.042 0.199 2010 Planarity : 0.004 0.036 2336 Dihedral : 6.907 66.281 1862 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 1.44 % Allowed : 16.33 % Favored : 82.22 % 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: 1.06 (0.21), residues: 1613 helix: 1.30 (0.20), residues: 739 sheet: 0.54 (0.38), residues: 199 loop : 0.22 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP U 551 HIS 0.004 0.000 HIS W 162 PHE 0.013 0.001 PHE U 378 TYR 0.016 0.001 TYR W 319 ARG 0.007 0.000 ARG X 69 Details of bonding type rmsd hydrogen bonds : bond 0.03011 ( 630) hydrogen bonds : angle 4.04966 ( 1689) covalent geometry : bond 0.00228 (13475) covalent geometry : angle 0.49303 (18251) ********************** 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 187 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 181 LYS cc_start: 0.7944 (ttmm) cc_final: 0.7621 (ttpp) REVERT: U 202 LYS cc_start: 0.8585 (mttt) cc_final: 0.8204 (mptt) REVERT: U 207 ASP cc_start: 0.8096 (t0) cc_final: 0.7384 (t0) REVERT: U 223 PHE cc_start: 0.7363 (t80) cc_final: 0.7137 (t80) REVERT: U 576 ASP cc_start: 0.7248 (m-30) cc_final: 0.6655 (p0) REVERT: U 580 GLN cc_start: 0.6721 (mt0) cc_final: 0.6250 (tp40) REVERT: U 599 LYS cc_start: 0.7983 (tptt) cc_final: 0.7275 (tptp) REVERT: U 605 MET cc_start: 0.8571 (tpt) cc_final: 0.7955 (tpt) REVERT: U 631 GLU cc_start: 0.8409 (tt0) cc_final: 0.8114 (pt0) REVERT: U 687 ASP cc_start: 0.7092 (m-30) cc_final: 0.6701 (m-30) REVERT: U 778 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: V 34 ILE cc_start: 0.9004 (mt) cc_final: 0.8788 (pt) REVERT: V 325 MET cc_start: 0.8477 (tpp) cc_final: 0.8046 (tpp) REVERT: V 363 ASP cc_start: 0.8000 (m-30) cc_final: 0.7788 (m-30) REVERT: W 196 LYS cc_start: 0.7889 (tttt) cc_final: 0.7561 (ttmt) REVERT: W 277 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7582 (tt0) REVERT: W 308 ASN cc_start: 0.7072 (t0) cc_final: 0.6800 (t0) REVERT: W 313 LYS cc_start: 0.7087 (tttt) cc_final: 0.6803 (tmtm) REVERT: W 446 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8270 (tp) REVERT: W 489 ARG cc_start: 0.7429 (ttm-80) cc_final: 0.7156 (ttm-80) REVERT: X 54 SER cc_start: 0.8769 (t) cc_final: 0.8277 (p) outliers start: 21 outliers final: 19 residues processed: 180 average time/residue: 0.2770 time to fit residues: 73.4789 Evaluate side-chains 183 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 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 737 SER Chi-restraints excluded: chain U residue 778 GLU 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 W residue 17 VAL Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 211 GLN 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 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 99 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 153 optimal weight: 0.0000 overall best weight: 1.0390 ------------------------------------------------------------------------------- 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 333 ASN U 799 GLN U 817 HIS ** U 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 372 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.149441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112951 restraints weight = 16751.372| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.20 r_work: 0.3133 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13475 Z= 0.133 Angle : 0.509 9.845 18251 Z= 0.266 Chirality : 0.043 0.190 2010 Planarity : 0.004 0.037 2336 Dihedral : 6.991 65.689 1862 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.60 % Favored : 97.27 % Rotamer: Outliers : 1.51 % Allowed : 16.33 % Favored : 82.16 % 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: 0.96 (0.21), residues: 1613 helix: 1.26 (0.20), residues: 737 sheet: 0.36 (0.37), residues: 204 loop : 0.18 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 551 HIS 0.005 0.001 HIS W 162 PHE 0.013 0.001 PHE U 378 TYR 0.021 0.001 TYR U 596 ARG 0.007 0.000 ARG X 69 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 630) hydrogen bonds : angle 4.09325 ( 1689) covalent geometry : bond 0.00317 (13475) covalent geometry : angle 0.50877 (18251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7945.87 seconds wall clock time: 140 minutes 41.16 seconds (8441.16 seconds total)