Starting phenix.real_space_refine on Thu May 15 17:22:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a5a_15163/05_2025/8a5a_15163.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a5a_15163/05_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_15163/05_2025/8a5a_15163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a5a_15163/05_2025/8a5a_15163.map" model { file = "/net/cci-nas-00/data/ceres_data/8a5a_15163/05_2025/8a5a_15163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a5a_15163/05_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-5687/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: 7.61, per 1000 atoms: 0.58 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: 3.31 Conformation dependent library (CDL) restraints added in 1.7 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: 1.82 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: 4.51 Time building geometry restraints manager: 3.86 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: 0.910 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.750 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.290 ------------------------------------------------------------------------------- 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 : 1.483 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: 0.2970 time to fit residues: 134.1589 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 : 1.518 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.147967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112365 restraints weight = 16576.942| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.09 r_work: 0.3117 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13475 Z= 0.165 Angle : 0.656 15.900 18251 Z= 0.354 Chirality : 0.046 0.155 2010 Planarity : 0.005 0.044 2336 Dihedral : 9.831 68.992 1894 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.29 % Favored : 97.58 % Rotamer: Outliers : 2.40 % Allowed : 9.54 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1613 helix: 0.11 (0.19), residues: 710 sheet: 0.09 (0.35), residues: 209 loop : -0.16 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP V 340 HIS 0.004 0.001 HIS V 372 PHE 0.016 0.002 PHE U 546 TYR 0.021 0.002 TYR U 596 ARG 0.004 0.001 ARG U 674 Details of bonding type rmsd hydrogen bonds : bond 0.04833 ( 630) hydrogen bonds : angle 5.07032 ( 1689) covalent geometry : bond 0.00353 (13475) covalent geometry : angle 0.65567 (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 237 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 468 HIS cc_start: 0.7851 (t-90) cc_final: 0.7571 (t70) REVERT: G 479 ASP cc_start: 0.7280 (m-30) cc_final: 0.7037 (t0) REVERT: G 494 GLN cc_start: 0.7421 (mt0) cc_final: 0.7220 (tt0) REVERT: G 519 SER cc_start: 0.9128 (t) cc_final: 0.8591 (p) REVERT: G 539 MET cc_start: 0.8878 (tmm) cc_final: 0.8636 (tmm) REVERT: U 202 LYS cc_start: 0.8646 (mttt) cc_final: 0.8220 (mptt) REVERT: U 207 ASP cc_start: 0.8381 (t0) cc_final: 0.7310 (t0) REVERT: U 212 ASP cc_start: 0.7937 (m-30) cc_final: 0.7537 (t0) REVERT: U 222 LYS cc_start: 0.7554 (mmmt) cc_final: 0.7168 (mtpt) REVERT: U 316 GLN cc_start: 0.7592 (mp10) cc_final: 0.7309 (mp10) REVERT: U 573 GLN cc_start: 0.7924 (tt0) cc_final: 0.7687 (tp-100) REVERT: U 576 ASP cc_start: 0.7515 (m-30) cc_final: 0.7142 (p0) REVERT: U 586 ASN cc_start: 0.7621 (t0) cc_final: 0.7398 (t0) REVERT: U 631 GLU cc_start: 0.8442 (tt0) cc_final: 0.8188 (pt0) REVERT: U 687 ASP cc_start: 0.7137 (m-30) cc_final: 0.6673 (m-30) REVERT: U 690 GLU cc_start: 0.7588 (tt0) cc_final: 0.7057 (pt0) REVERT: U 806 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8270 (tm-30) REVERT: V 62 ARG cc_start: 0.8096 (ttm-80) cc_final: 0.7626 (ttm110) REVERT: V 325 MET cc_start: 0.8881 (tpp) cc_final: 0.8261 (tpp) REVERT: V 375 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6401 (m-80) REVERT: W 33 SER cc_start: 0.9093 (m) cc_final: 0.8835 (p) REVERT: W 174 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7446 (mtm) REVERT: W 182 ARG cc_start: 0.8235 (ptt180) cc_final: 0.8018 (ttp-110) REVERT: W 196 LYS cc_start: 0.7840 (tttt) cc_final: 0.7492 (ttmt) REVERT: W 206 LEU cc_start: 0.8928 (tt) cc_final: 0.8699 (tp) REVERT: W 219 LYS cc_start: 0.8341 (tttm) cc_final: 0.8057 (ttpt) REVERT: W 277 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7967 (tt0) REVERT: W 308 ASN cc_start: 0.7312 (t0) cc_final: 0.7016 (t0) REVERT: W 313 LYS cc_start: 0.7467 (tttt) cc_final: 0.7106 (tptt) REVERT: W 436 LYS cc_start: 0.7913 (mttt) cc_final: 0.7699 (pttp) REVERT: X 54 SER cc_start: 0.8529 (t) cc_final: 0.8079 (p) outliers start: 35 outliers final: 21 residues processed: 228 average time/residue: 0.2699 time to fit residues: 89.4640 Evaluate side-chains 185 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 553 ILE Chi-restraints excluded: chain U residue 555 SER Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 375 PHE Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 142 THR Chi-restraints excluded: chain W residue 174 MET Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 260 THR Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain W residue 425 MET Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 111 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.148575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112636 restraints weight = 16769.423| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.09 r_work: 0.3114 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13475 Z= 0.139 Angle : 0.564 9.639 18251 Z= 0.302 Chirality : 0.044 0.163 2010 Planarity : 0.004 0.041 2336 Dihedral : 8.783 65.983 1873 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 2.33 % Allowed : 11.26 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.40 (0.21), residues: 1613 helix: 0.68 (0.19), residues: 710 sheet: 0.29 (0.36), residues: 205 loop : -0.03 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 340 HIS 0.004 0.001 HIS W 162 PHE 0.022 0.001 PHE U 223 TYR 0.015 0.001 TYR U 596 ARG 0.004 0.000 ARG U 722 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 630) hydrogen bonds : angle 4.64026 ( 1689) covalent geometry : bond 0.00318 (13475) covalent geometry : angle 0.56358 (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 220 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 468 HIS cc_start: 0.7918 (t-90) cc_final: 0.7579 (t70) REVERT: G 479 ASP cc_start: 0.7049 (m-30) cc_final: 0.6831 (t0) REVERT: G 519 SER cc_start: 0.9036 (t) cc_final: 0.8483 (p) REVERT: U 202 LYS cc_start: 0.8614 (mttt) cc_final: 0.8202 (mptt) REVERT: U 207 ASP cc_start: 0.8352 (t0) cc_final: 0.7315 (t0) REVERT: U 212 ASP cc_start: 0.7928 (m-30) cc_final: 0.7524 (t0) REVERT: U 573 GLN cc_start: 0.7740 (tt0) cc_final: 0.7476 (tp-100) REVERT: U 576 ASP cc_start: 0.7488 (m-30) cc_final: 0.6959 (p0) REVERT: U 586 ASN cc_start: 0.7535 (t0) cc_final: 0.7322 (t0) REVERT: U 605 MET cc_start: 0.8570 (tpt) cc_final: 0.7783 (tpt) REVERT: U 631 GLU cc_start: 0.8400 (tt0) cc_final: 0.8135 (pt0) REVERT: U 687 ASP cc_start: 0.7196 (m-30) cc_final: 0.6684 (m-30) REVERT: U 690 GLU cc_start: 0.7558 (tt0) cc_final: 0.7087 (pt0) REVERT: V 62 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7638 (ttm110) REVERT: V 325 MET cc_start: 0.8768 (tpp) cc_final: 0.8140 (tpp) REVERT: V 375 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.6499 (m-80) REVERT: W 33 SER cc_start: 0.9049 (m) cc_final: 0.8753 (p) REVERT: W 196 LYS cc_start: 0.7872 (tttt) cc_final: 0.7490 (ttmt) REVERT: W 206 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8545 (tt) REVERT: W 219 LYS cc_start: 0.8337 (tttm) cc_final: 0.8050 (ttpt) REVERT: W 277 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7932 (tt0) REVERT: W 308 ASN cc_start: 0.7307 (t0) cc_final: 0.6986 (t0) REVERT: W 313 LYS cc_start: 0.7337 (tttt) cc_final: 0.6988 (tptt) REVERT: W 427 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7716 (mm-30) REVERT: X 54 SER cc_start: 0.8532 (t) cc_final: 0.8073 (p) outliers start: 34 outliers final: 21 residues processed: 208 average time/residue: 0.2868 time to fit residues: 86.2031 Evaluate side-chains 189 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 553 ILE Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 375 PHE Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 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: 0.7980 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 160 optimal weight: 0.0370 chunk 56 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 137 optimal weight: 0.0670 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.151293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115599 restraints weight = 16524.394| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.11 r_work: 0.3151 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13475 Z= 0.104 Angle : 0.502 7.128 18251 Z= 0.268 Chirality : 0.043 0.187 2010 Planarity : 0.004 0.040 2336 Dihedral : 8.010 67.661 1868 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.29 % Favored : 97.58 % Rotamer: Outliers : 1.92 % Allowed : 12.49 % Favored : 85.59 % 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: 0.74 (0.21), residues: 1613 helix: 0.97 (0.20), residues: 722 sheet: 0.65 (0.37), residues: 205 loop : 0.07 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 543 HIS 0.003 0.000 HIS W 162 PHE 0.010 0.001 PHE W 207 TYR 0.014 0.001 TYR U 596 ARG 0.004 0.000 ARG W 212 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 630) hydrogen bonds : angle 4.31612 ( 1689) covalent geometry : bond 0.00227 (13475) covalent geometry : angle 0.50186 (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 215 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 468 HIS cc_start: 0.7889 (t-90) cc_final: 0.7278 (t-90) REVERT: G 519 SER cc_start: 0.8931 (t) cc_final: 0.8329 (p) REVERT: U 202 LYS cc_start: 0.8545 (mttt) cc_final: 0.8092 (mptt) REVERT: U 207 ASP cc_start: 0.8136 (t0) cc_final: 0.7253 (t0) REVERT: U 212 ASP cc_start: 0.7877 (m-30) cc_final: 0.7504 (t0) REVERT: U 332 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8244 (ttpt) REVERT: U 576 ASP cc_start: 0.7458 (m-30) cc_final: 0.6921 (p0) REVERT: U 631 GLU cc_start: 0.8382 (tt0) cc_final: 0.8110 (pt0) REVERT: U 687 ASP cc_start: 0.7136 (m-30) cc_final: 0.6635 (m-30) REVERT: U 690 GLU cc_start: 0.7389 (tt0) cc_final: 0.7019 (pt0) REVERT: U 778 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: V 62 ARG cc_start: 0.8103 (ttm-80) cc_final: 0.7657 (ttm110) REVERT: V 325 MET cc_start: 0.8616 (tpp) cc_final: 0.8070 (tpp) REVERT: V 360 GLN cc_start: 0.7609 (tt0) cc_final: 0.7348 (mm110) REVERT: W 182 ARG cc_start: 0.8188 (ptt180) cc_final: 0.7882 (ttp-110) REVERT: W 196 LYS cc_start: 0.7805 (tttt) cc_final: 0.7453 (ttmt) REVERT: W 206 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8375 (tt) REVERT: W 277 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7741 (tt0) REVERT: W 308 ASN cc_start: 0.7255 (t0) cc_final: 0.7023 (t0) REVERT: W 313 LYS cc_start: 0.7281 (tttt) cc_final: 0.6925 (tptt) REVERT: X 54 SER cc_start: 0.8709 (t) cc_final: 0.8192 (p) outliers start: 28 outliers final: 18 residues processed: 203 average time/residue: 0.2595 time to fit residues: 75.9104 Evaluate side-chains 191 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 332 LYS Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 778 GLU Chi-restraints excluded: chain U residue 823 HIS Chi-restraints excluded: chain U residue 841 ILE Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 120 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 134 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 55 optimal weight: 0.0170 chunk 60 optimal weight: 0.0980 chunk 107 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 541 ASN V 228 GLN V 372 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115635 restraints weight = 16622.411| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.09 r_work: 0.3154 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3396 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= 0.104 Angle : 0.489 5.639 18251 Z= 0.259 Chirality : 0.042 0.194 2010 Planarity : 0.004 0.039 2336 Dihedral : 7.541 70.507 1864 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.11 % Favored : 97.77 % Rotamer: Outliers : 2.20 % Allowed : 13.86 % Favored : 83.94 % 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: 0.92 (0.21), residues: 1613 helix: 1.17 (0.20), residues: 728 sheet: 0.63 (0.37), residues: 199 loop : 0.13 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 356 HIS 0.004 0.001 HIS W 162 PHE 0.019 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 0.03200 ( 630) hydrogen bonds : angle 4.18141 ( 1689) covalent geometry : bond 0.00235 (13475) covalent geometry : angle 0.48861 (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 211 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 1.548 Fit side-chains revert: symmetry clash REVERT: G 468 HIS cc_start: 0.7930 (t-90) cc_final: 0.7350 (t-90) REVERT: G 519 SER cc_start: 0.8900 (t) cc_final: 0.8696 (t) REVERT: U 202 LYS cc_start: 0.8519 (mttt) cc_final: 0.8062 (mptt) REVERT: U 207 ASP cc_start: 0.8227 (t0) cc_final: 0.7324 (t0) REVERT: U 212 ASP cc_start: 0.7821 (m-30) cc_final: 0.7461 (t0) REVERT: U 576 ASP cc_start: 0.7362 (m-30) cc_final: 0.6865 (p0) REVERT: U 687 ASP cc_start: 0.7140 (m-30) cc_final: 0.6655 (m-30) REVERT: U 690 GLU cc_start: 0.7491 (tt0) cc_final: 0.7039 (pt0) REVERT: V 34 ILE cc_start: 0.8954 (mt) cc_final: 0.8727 (pt) REVERT: V 62 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7718 (ttm110) REVERT: V 82 MET cc_start: 0.8279 (tpt) cc_final: 0.7552 (tpt) REVERT: V 325 MET cc_start: 0.8567 (tpp) cc_final: 0.8104 (tpp) REVERT: V 360 GLN cc_start: 0.7538 (tt0) cc_final: 0.7278 (mm110) REVERT: W 182 ARG cc_start: 0.8152 (ptt180) cc_final: 0.7940 (ttp-110) REVERT: W 196 LYS cc_start: 0.7815 (tttt) cc_final: 0.7479 (ttmt) REVERT: W 206 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8314 (tt) REVERT: W 277 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7786 (tt0) REVERT: W 308 ASN cc_start: 0.7178 (t0) cc_final: 0.6886 (t0) REVERT: W 313 LYS cc_start: 0.7269 (tttt) cc_final: 0.6885 (tptt) REVERT: W 446 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8189 (tp) REVERT: X 54 SER cc_start: 0.8728 (t) cc_final: 0.8225 (p) outliers start: 32 outliers final: 25 residues processed: 200 average time/residue: 0.2527 time to fit residues: 73.8342 Evaluate side-chains 199 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 823 HIS Chi-restraints excluded: chain U residue 841 ILE Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 1 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 372 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113642 restraints weight = 16842.909| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.10 r_work: 0.3131 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3453 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= 0.133 Angle : 0.509 9.635 18251 Z= 0.269 Chirality : 0.043 0.191 2010 Planarity : 0.004 0.038 2336 Dihedral : 7.479 68.930 1864 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.05 % Favored : 97.83 % Rotamer: Outliers : 2.75 % Allowed : 13.38 % 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: 0.86 (0.21), residues: 1613 helix: 1.14 (0.20), residues: 730 sheet: 0.40 (0.37), residues: 205 loop : 0.14 (0.24), residues: 678 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 0.025 0.001 PHE U 223 TYR 0.014 0.001 TYR W 450 ARG 0.004 0.000 ARG X 69 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 630) hydrogen bonds : angle 4.19881 ( 1689) covalent geometry : bond 0.00315 (13475) covalent geometry : angle 0.50886 (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 218 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 519 SER cc_start: 0.8884 (t) cc_final: 0.8673 (t) REVERT: U 181 LYS cc_start: 0.7545 (pttm) cc_final: 0.7138 (pttm) REVERT: U 202 LYS cc_start: 0.8526 (mttt) cc_final: 0.8121 (mptt) REVERT: U 207 ASP cc_start: 0.8286 (t0) cc_final: 0.7359 (t0) REVERT: U 212 ASP cc_start: 0.7905 (m-30) cc_final: 0.7518 (t0) REVERT: U 576 ASP cc_start: 0.7336 (m-30) cc_final: 0.6880 (p0) REVERT: U 687 ASP cc_start: 0.7115 (m-30) cc_final: 0.6634 (m-30) REVERT: U 690 GLU cc_start: 0.7777 (tt0) cc_final: 0.7217 (pt0) REVERT: V 34 ILE cc_start: 0.8959 (mt) cc_final: 0.8722 (pt) REVERT: V 269 LEU cc_start: 0.8547 (tp) cc_final: 0.8291 (tp) REVERT: V 325 MET cc_start: 0.8586 (tpp) cc_final: 0.8090 (tpp) REVERT: V 360 GLN cc_start: 0.7548 (tt0) cc_final: 0.7297 (mm110) REVERT: W 182 ARG cc_start: 0.8187 (ptt180) cc_final: 0.7956 (ttp-110) REVERT: W 196 LYS cc_start: 0.7869 (tttt) cc_final: 0.7521 (ttmt) REVERT: W 206 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8380 (tt) REVERT: W 277 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7774 (tt0) REVERT: W 292 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7889 (tt) REVERT: W 313 LYS cc_start: 0.7239 (tttt) cc_final: 0.6951 (tttp) REVERT: W 446 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8226 (tp) REVERT: W 489 ARG cc_start: 0.7286 (ttm-80) cc_final: 0.6859 (ttm-80) REVERT: X 54 SER cc_start: 0.8732 (t) cc_final: 0.8229 (p) outliers start: 40 outliers final: 32 residues processed: 204 average time/residue: 0.2673 time to fit residues: 81.2123 Evaluate side-chains 200 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 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 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 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 292 LEU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 103 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 372 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.149590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113557 restraints weight = 16660.966| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.12 r_work: 0.3130 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3559 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= 0.132 Angle : 0.505 6.266 18251 Z= 0.267 Chirality : 0.043 0.193 2010 Planarity : 0.004 0.037 2336 Dihedral : 7.398 67.731 1864 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.11 % Favored : 97.77 % Rotamer: Outliers : 2.61 % Allowed : 14.41 % 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: 0.87 (0.21), residues: 1613 helix: 1.13 (0.20), residues: 733 sheet: 0.42 (0.37), residues: 200 loop : 0.16 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 356 HIS 0.005 0.001 HIS W 162 PHE 0.035 0.001 PHE U 223 TYR 0.013 0.001 TYR W 450 ARG 0.006 0.000 ARG X 69 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 630) hydrogen bonds : angle 4.18655 ( 1689) covalent geometry : bond 0.00312 (13475) covalent geometry : angle 0.50476 (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 211 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 519 SER cc_start: 0.8883 (t) cc_final: 0.8675 (t) REVERT: U 181 LYS cc_start: 0.7539 (pttm) cc_final: 0.7222 (pttm) REVERT: U 202 LYS cc_start: 0.8524 (mttt) cc_final: 0.8124 (mptt) REVERT: U 207 ASP cc_start: 0.8275 (t0) cc_final: 0.7390 (t0) REVERT: U 212 ASP cc_start: 0.7931 (m-30) cc_final: 0.7488 (t0) REVERT: U 576 ASP cc_start: 0.7358 (m-30) cc_final: 0.6810 (p0) REVERT: U 580 GLN cc_start: 0.6744 (mt0) cc_final: 0.6313 (tp40) REVERT: U 605 MET cc_start: 0.8626 (tpt) cc_final: 0.7925 (tpt) REVERT: U 690 GLU cc_start: 0.7885 (tt0) cc_final: 0.7349 (pt0) REVERT: V 34 ILE cc_start: 0.8975 (mt) cc_final: 0.8749 (pt) REVERT: V 325 MET cc_start: 0.8568 (tpp) cc_final: 0.8085 (tpp) REVERT: V 360 GLN cc_start: 0.7565 (tt0) cc_final: 0.7308 (mm110) REVERT: W 182 ARG cc_start: 0.8188 (ptt180) cc_final: 0.7964 (ttp-110) REVERT: W 196 LYS cc_start: 0.7898 (tttt) cc_final: 0.7547 (ttmt) REVERT: W 277 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7753 (tt0) REVERT: W 292 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7836 (tt) REVERT: W 313 LYS cc_start: 0.7211 (tttt) cc_final: 0.6924 (tttp) REVERT: W 446 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8247 (tp) REVERT: W 489 ARG cc_start: 0.7348 (ttm-80) cc_final: 0.6959 (ttm-80) REVERT: X 54 SER cc_start: 0.8748 (t) cc_final: 0.8246 (p) outliers start: 38 outliers final: 33 residues processed: 197 average time/residue: 0.2515 time to fit residues: 72.9650 Evaluate side-chains 199 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 778 GLU Chi-restraints excluded: chain U residue 823 HIS Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 110 MET Chi-restraints excluded: chain V residue 144 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 12 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 292 LEU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 26 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 0.0270 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 50 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 868 HIS V 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115944 restraints weight = 16637.438| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.12 r_work: 0.3180 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3747 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= 0.100 Angle : 0.479 6.619 18251 Z= 0.253 Chirality : 0.042 0.199 2010 Planarity : 0.004 0.036 2336 Dihedral : 7.082 69.438 1864 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 2.40 % Allowed : 14.76 % 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: 1.07 (0.21), residues: 1613 helix: 1.27 (0.20), residues: 735 sheet: 0.69 (0.38), residues: 199 loop : 0.23 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 543 HIS 0.004 0.000 HIS W 162 PHE 0.031 0.001 PHE U 223 TYR 0.017 0.001 TYR U 596 ARG 0.005 0.000 ARG X 69 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 630) hydrogen bonds : angle 4.05038 ( 1689) covalent geometry : bond 0.00226 (13475) covalent geometry : angle 0.47893 (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 207 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 519 SER cc_start: 0.8819 (t) cc_final: 0.8609 (t) REVERT: U 181 LYS cc_start: 0.7579 (pttm) cc_final: 0.7171 (pttm) REVERT: U 202 LYS cc_start: 0.8529 (mttt) cc_final: 0.8115 (mptt) REVERT: U 207 ASP cc_start: 0.8114 (t0) cc_final: 0.7304 (t0) REVERT: U 212 ASP cc_start: 0.7884 (m-30) cc_final: 0.7415 (t0) REVERT: U 576 ASP cc_start: 0.7312 (m-30) cc_final: 0.6716 (p0) REVERT: U 580 GLN cc_start: 0.6704 (mt0) cc_final: 0.6226 (tp40) REVERT: U 599 LYS cc_start: 0.7960 (tptt) cc_final: 0.7279 (tptp) REVERT: U 605 MET cc_start: 0.8573 (tpt) cc_final: 0.7856 (tpt) REVERT: U 834 ARG cc_start: 0.7310 (mpp-170) cc_final: 0.7062 (mtt90) REVERT: V 34 ILE cc_start: 0.8977 (mt) cc_final: 0.8766 (pt) REVERT: V 269 LEU cc_start: 0.8387 (tp) cc_final: 0.8124 (tp) REVERT: V 325 MET cc_start: 0.8509 (tpp) cc_final: 0.8066 (tpp) REVERT: V 360 GLN cc_start: 0.7512 (tt0) cc_final: 0.7248 (mm110) REVERT: W 182 ARG cc_start: 0.8138 (ptt180) cc_final: 0.7851 (ttp-110) REVERT: W 196 LYS cc_start: 0.7841 (tttt) cc_final: 0.7490 (ttmt) REVERT: W 277 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7562 (tt0) REVERT: W 292 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7767 (tt) REVERT: W 313 LYS cc_start: 0.7193 (tttt) cc_final: 0.6917 (tttp) REVERT: W 446 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8207 (tp) REVERT: X 54 SER cc_start: 0.8724 (t) cc_final: 0.8161 (p) outliers start: 35 outliers final: 28 residues processed: 195 average time/residue: 0.2271 time to fit residues: 66.2744 Evaluate side-chains 191 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 435 SER Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 778 GLU Chi-restraints excluded: chain U residue 868 HIS Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 110 MET Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 292 LEU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 42 optimal weight: 1.9990 chunk 122 optimal weight: 0.0170 chunk 157 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 15 optimal weight: 0.0470 chunk 109 optimal weight: 0.5980 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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 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 = 0.3747 r_free = 0.3747 target = 0.152762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116816 restraints weight = 16551.667| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.16 r_work: 0.3170 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13475 Z= 0.095 Angle : 0.483 8.679 18251 Z= 0.253 Chirality : 0.042 0.204 2010 Planarity : 0.004 0.035 2336 Dihedral : 6.913 70.377 1864 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.23 % Favored : 97.64 % Rotamer: Outliers : 1.72 % Allowed : 15.85 % 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: 1.17 (0.22), residues: 1613 helix: 1.34 (0.20), residues: 736 sheet: 0.70 (0.38), residues: 200 loop : 0.31 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 340 HIS 0.006 0.000 HIS U 868 PHE 0.014 0.001 PHE U 378 TYR 0.025 0.001 TYR U 596 ARG 0.005 0.000 ARG X 69 Details of bonding type rmsd hydrogen bonds : bond 0.02977 ( 630) hydrogen bonds : angle 4.00801 ( 1689) covalent geometry : bond 0.00208 (13475) covalent geometry : angle 0.48327 (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 197 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 519 SER cc_start: 0.8837 (t) cc_final: 0.8624 (t) REVERT: U 181 LYS cc_start: 0.7682 (pttm) cc_final: 0.7257 (pttm) REVERT: U 202 LYS cc_start: 0.8604 (mttt) cc_final: 0.8206 (mptt) REVERT: U 207 ASP cc_start: 0.8079 (t0) cc_final: 0.7344 (t0) REVERT: U 212 ASP cc_start: 0.7871 (m-30) cc_final: 0.7439 (t0) REVERT: U 576 ASP cc_start: 0.7320 (m-30) cc_final: 0.6746 (p0) REVERT: U 580 GLN cc_start: 0.6737 (mt0) cc_final: 0.6252 (tp40) REVERT: U 599 LYS cc_start: 0.7990 (tptt) cc_final: 0.7290 (tptp) REVERT: U 605 MET cc_start: 0.8604 (tpt) cc_final: 0.7900 (tpt) REVERT: U 834 ARG cc_start: 0.7375 (mpp-170) cc_final: 0.7048 (mtt90) REVERT: V 325 MET cc_start: 0.8477 (tpp) cc_final: 0.8027 (tpp) REVERT: V 360 GLN cc_start: 0.7601 (tt0) cc_final: 0.7334 (mm110) REVERT: W 182 ARG cc_start: 0.8153 (ptt180) cc_final: 0.7906 (ttp-110) REVERT: W 196 LYS cc_start: 0.7879 (tttt) cc_final: 0.7545 (ttmt) REVERT: W 277 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7636 (tt0) REVERT: W 292 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7765 (tt) REVERT: W 313 LYS cc_start: 0.7202 (tttt) cc_final: 0.6938 (tttp) REVERT: W 446 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8240 (tp) REVERT: X 54 SER cc_start: 0.8676 (t) cc_final: 0.8178 (p) outliers start: 25 outliers final: 22 residues processed: 187 average time/residue: 0.2323 time to fit residues: 64.9099 Evaluate side-chains 185 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 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 V residue 110 MET 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 165 CYS Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 292 LEU 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: 0.9990 chunk 40 optimal weight: 0.6980 chunk 73 optimal weight: 30.0000 chunk 140 optimal weight: 0.0770 chunk 6 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 125 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 333 ASN U 475 GLN ** U 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 372 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116680 restraints weight = 16431.942| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.17 r_work: 0.3170 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13475 Z= 0.102 Angle : 0.486 10.098 18251 Z= 0.256 Chirality : 0.042 0.204 2010 Planarity : 0.004 0.035 2336 Dihedral : 6.771 70.333 1862 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 1.92 % Allowed : 15.79 % Favored : 82.29 % 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: 1.23 (0.22), residues: 1613 helix: 1.39 (0.20), residues: 737 sheet: 0.75 (0.38), residues: 199 loop : 0.34 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 551 HIS 0.005 0.000 HIS W 162 PHE 0.023 0.001 PHE U 223 TYR 0.026 0.001 TYR W 319 ARG 0.005 0.000 ARG U 339 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 630) hydrogen bonds : angle 4.03162 ( 1689) covalent geometry : bond 0.00230 (13475) covalent geometry : angle 0.48578 (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 193 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 202 LYS cc_start: 0.8601 (mttt) cc_final: 0.8109 (mptt) REVERT: U 207 ASP cc_start: 0.8087 (t0) cc_final: 0.7368 (t0) REVERT: U 576 ASP cc_start: 0.7230 (m-30) cc_final: 0.6669 (p0) REVERT: U 580 GLN cc_start: 0.6747 (mt0) cc_final: 0.6358 (tp40) REVERT: U 599 LYS cc_start: 0.7983 (tptt) cc_final: 0.7781 (mmtp) REVERT: U 605 MET cc_start: 0.8590 (tpt) cc_final: 0.7902 (tpt) REVERT: U 687 ASP cc_start: 0.7105 (m-30) cc_final: 0.6736 (m-30) REVERT: V 227 MET cc_start: 0.8530 (mmm) cc_final: 0.8298 (tpt) REVERT: V 269 LEU cc_start: 0.8373 (tp) cc_final: 0.8132 (tp) REVERT: V 325 MET cc_start: 0.8468 (tpp) cc_final: 0.8004 (tpp) REVERT: V 360 GLN cc_start: 0.7579 (tt0) cc_final: 0.7334 (mm110) REVERT: V 363 ASP cc_start: 0.8039 (m-30) cc_final: 0.7745 (m-30) REVERT: W 182 ARG cc_start: 0.8172 (ptt180) cc_final: 0.7907 (ttp-110) REVERT: W 196 LYS cc_start: 0.7858 (tttt) cc_final: 0.7520 (ttmt) REVERT: W 277 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7586 (tt0) REVERT: W 292 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7809 (tt) REVERT: W 313 LYS cc_start: 0.7200 (tttt) cc_final: 0.6764 (tptt) REVERT: W 446 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8248 (tp) REVERT: X 54 SER cc_start: 0.8664 (t) cc_final: 0.8176 (p) outliers start: 28 outliers final: 25 residues processed: 183 average time/residue: 0.2432 time to fit residues: 66.7973 Evaluate side-chains 189 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 534 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 778 GLU Chi-restraints excluded: chain V residue 110 MET Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 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 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 292 LEU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 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: 0.7980 chunk 87 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 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: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 799 GLN U 817 HIS V 372 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.151147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.115098 restraints weight = 16663.649| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.25 r_work: 0.3157 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13475 Z= 0.130 Angle : 0.508 10.429 18251 Z= 0.268 Chirality : 0.043 0.196 2010 Planarity : 0.004 0.037 2336 Dihedral : 6.870 68.089 1862 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.67 % Favored : 97.21 % Rotamer: Outliers : 2.06 % Allowed : 15.65 % Favored : 82.29 % 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: 1.13 (0.22), residues: 1613 helix: 1.34 (0.20), residues: 736 sheet: 0.57 (0.38), residues: 203 loop : 0.30 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP U 551 HIS 0.005 0.001 HIS W 162 PHE 0.017 0.001 PHE U 378 TYR 0.033 0.001 TYR W 319 ARG 0.005 0.000 ARG X 69 Details of bonding type rmsd hydrogen bonds : bond 0.03204 ( 630) hydrogen bonds : angle 4.08637 ( 1689) covalent geometry : bond 0.00309 (13475) covalent geometry : angle 0.50845 (18251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6928.14 seconds wall clock time: 121 minutes 18.04 seconds (7278.04 seconds total)