Starting phenix.real_space_refine on Thu Jul 2 18:52:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mid_23847/07_2026/7mid_23847.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mid_23847/07_2026/7mid_23847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mid_23847/07_2026/7mid_23847.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mid_23847/07_2026/7mid_23847.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mid_23847/07_2026/7mid_23847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mid_23847/07_2026/7mid_23847.map" model { file = "/net/cci-nas-00/data/ceres_data/7mid_23847/07_2026/7mid_23847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mid_23847/07_2026/7mid_23847.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.027 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: 7 Type Number sf(0) Gaussians Mn 5 7.51 5 Fe 4 7.16 5 P 57 5.49 5 S 55 5.16 5 C 5994 2.51 5 N 1799 2.21 5 O 1875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9789 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4355 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 35, 'TRANS': 518} Chain: "B" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2711 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "C" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 786 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 758 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "E" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 488 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "F" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 678 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 142 SG CYS A 22 67.781 52.551 83.007 1.00 50.21 S ATOM 1468 SG CYS A 196 64.162 56.883 83.234 1.00 54.73 S ATOM 1429 SG CYS A 190 63.083 53.528 78.591 1.00 55.03 S ATOM 1405 SG CYS A 187 67.882 56.088 79.078 1.00 56.92 S Time building chain proxies: 1.84, per 1000 atoms: 0.19 Number of scatterers: 9789 At special positions: 0 Unit cell: (89.8242, 114.062, 135.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Mn 5 24.99 S 55 16.00 P 57 15.00 O 1875 8.00 N 1799 7.00 C 5994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 232.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 601 " pdb="FE4 SF4 A 601 " - pdb=" SG CYS A 187 " pdb="FE3 SF4 A 601 " - pdb=" SG CYS A 190 " pdb="FE2 SF4 A 601 " - pdb=" SG CYS A 196 " pdb="FE1 SF4 A 601 " - pdb=" SG CYS A 22 " Number of angles added : 12 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 11 sheets defined 48.3% alpha, 15.3% beta 16 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.564A pdb=" N VAL A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.895A pdb=" N ARG A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 131 Processing helix chain 'A' and resid 154 through 175 removed outlier: 3.816A pdb=" N GLY A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.681A pdb=" N ARG A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 315 Processing helix chain 'A' and resid 316 through 342 Processing helix chain 'A' and resid 353 through 369 Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.970A pdb=" N LEU A 395 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.021A pdb=" N ARG A 410 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 440 removed outlier: 4.066A pdb=" N ARG A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU A 433 " --> pdb=" O MET A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 467 through 483 removed outlier: 4.546A pdb=" N LEU A 471 " --> pdb=" O PRO A 467 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 501 through 517 removed outlier: 3.512A pdb=" N ARG A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 removed outlier: 3.551A pdb=" N GLU A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 300 through 315 removed outlier: 4.630A pdb=" N VAL B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 305 " --> pdb=" O HIS B 301 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 306 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE B 315 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 343 Processing helix chain 'B' and resid 353 through 369 Processing helix chain 'B' and resid 372 through 390 removed outlier: 3.921A pdb=" N HIS B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 395 Processing helix chain 'B' and resid 417 through 441 removed outlier: 3.536A pdb=" N VAL B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 473 removed outlier: 4.182A pdb=" N GLU B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Proline residue: B 467 - end of helix Proline residue: B 470 - end of helix Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 487 through 489 No H-bonds generated for 'chain 'B' and resid 487 through 489' Processing helix chain 'B' and resid 501 through 517 Processing helix chain 'B' and resid 531 through 546 removed outlier: 4.196A pdb=" N GLU B 536 " --> pdb=" O ARG B 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 28 Processing helix chain 'C' and resid 41 through 52 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'D' and resid 13 through 28 Processing helix chain 'D' and resid 41 through 52 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.191A pdb=" N ILE A 11 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N LYS A 85 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR A 83 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER A 76 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS A 85 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N SER A 74 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP A 87 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.191A pdb=" N ILE A 11 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N LYS A 85 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N ILE A 86 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TYR A 101 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N TYR A 141 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP A 100 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 226 removed outlier: 7.191A pdb=" N LEU A 222 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ALA A 261 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A 224 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE A 263 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 226 " --> pdb=" O PHE A 263 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N THR A 284 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 260 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 286 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A 262 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 294 " --> pdb=" O TRP B 285 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR B 284 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL B 260 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B 286 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU B 262 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU B 222 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ALA B 261 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 224 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 251 removed outlier: 5.558A pdb=" N ARG A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLU A 244 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS A 239 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 236 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 491 through 493 Processing sheet with id=AA6, first strand: chain 'A' and resid 519 through 521 Processing sheet with id=AA7, first strand: chain 'B' and resid 248 through 251 removed outlier: 6.854A pdb=" N ILE B 242 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU B 251 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 240 " --> pdb=" O GLU B 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 491 through 493 Processing sheet with id=AA9, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.502A pdb=" N VAL C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU C 4 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 78 through 80 removed outlier: 6.764A pdb=" N LEU D 4 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 4387 1.42 - 1.64: 5639 1.64 - 1.85: 85 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 10123 Sorted by residual: bond pdb=" C1' DG F 23 " pdb=" N9 DG F 23 " ideal model delta sigma weight residual 1.468 1.357 0.111 1.40e-02 5.10e+03 6.29e+01 bond pdb=" C1' DA F 21 " pdb=" N9 DA F 21 " ideal model delta sigma weight residual 1.468 1.377 0.091 1.40e-02 5.10e+03 4.26e+01 bond pdb=" C1' DT F 22 " pdb=" N1 DT F 22 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.07e+01 bond pdb=" C1' DC E 1 " pdb=" N1 DC E 1 " ideal model delta sigma weight residual 1.468 1.531 -0.063 1.40e-02 5.10e+03 2.04e+01 bond pdb=" N1 DC F 14 " pdb=" C6 DC F 14 " ideal model delta sigma weight residual 1.367 1.346 0.021 6.00e-03 2.78e+04 1.26e+01 ... (remaining 10118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 13821 3.78 - 7.55: 97 7.55 - 11.33: 18 11.33 - 15.11: 6 15.11 - 18.89: 4 Bond angle restraints: 13946 Sorted by residual: angle pdb=" C4' DA E 22 " pdb=" O4' DA E 22 " pdb=" C1' DA E 22 " ideal model delta sigma weight residual 110.10 97.14 12.96 1.00e+00 1.00e+00 1.68e+02 angle pdb=" O4' DA E 22 " pdb=" C4' DA E 22 " pdb=" C3' DA E 22 " ideal model delta sigma weight residual 106.00 99.62 6.38 6.00e-01 2.78e+00 1.13e+02 angle pdb=" CD ARG A 146 " pdb=" NE ARG A 146 " pdb=" CZ ARG A 146 " ideal model delta sigma weight residual 124.40 138.27 -13.87 1.40e+00 5.10e-01 9.81e+01 angle pdb=" CG ARG B 386 " pdb=" CD ARG B 386 " pdb=" NE ARG B 386 " ideal model delta sigma weight residual 112.00 130.89 -18.89 2.20e+00 2.07e-01 7.37e+01 angle pdb=" CA LYS C 22 " pdb=" CB LYS C 22 " pdb=" CG LYS C 22 " ideal model delta sigma weight residual 114.10 129.60 -15.50 2.00e+00 2.50e-01 6.01e+01 ... (remaining 13941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.46: 5346 28.46 - 56.92: 504 56.92 - 85.38: 67 85.38 - 113.84: 3 113.84 - 142.30: 2 Dihedral angle restraints: 5922 sinusoidal: 2822 harmonic: 3100 Sorted by residual: dihedral pdb=" CD ARG A 146 " pdb=" NE ARG A 146 " pdb=" CZ ARG A 146 " pdb=" NH1 ARG A 146 " ideal model delta sinusoidal sigma weight residual 0.00 -57.87 57.87 1 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" CA ARG A 412 " pdb=" C ARG A 412 " pdb=" N ARG A 413 " pdb=" CA ARG A 413 " ideal model delta harmonic sigma weight residual -180.00 -147.79 -32.21 0 5.00e+00 4.00e-02 4.15e+01 dihedral pdb=" CA ARG A 393 " pdb=" C ARG A 393 " pdb=" N MET A 394 " pdb=" CA MET A 394 " ideal model delta harmonic sigma weight residual -180.00 -150.33 -29.67 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 5919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1393 0.102 - 0.205: 117 0.205 - 0.307: 4 0.307 - 0.409: 0 0.409 - 0.511: 2 Chirality restraints: 1516 Sorted by residual: chirality pdb=" C3' DA E 22 " pdb=" C4' DA E 22 " pdb=" O3' DA E 22 " pdb=" C2' DA E 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.22 -0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" C4' DA E 22 " pdb=" C5' DA E 22 " pdb=" O4' DA E 22 " pdb=" C3' DA E 22 " both_signs ideal model delta sigma weight residual False -2.53 -2.11 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA ARG A 146 " pdb=" N ARG A 146 " pdb=" C ARG A 146 " pdb=" CB ARG A 146 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 1513 not shown) Planarity restraints: 1618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 146 " -0.412 9.50e-02 1.11e+02 1.97e-01 7.98e+01 pdb=" NE ARG A 146 " 0.072 2.00e-02 2.50e+03 pdb=" CZ ARG A 146 " -0.128 2.00e-02 2.50e+03 pdb=" NH1 ARG A 146 " 0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG A 146 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA E 22 " 0.031 2.00e-02 2.50e+03 1.64e-02 7.43e+00 pdb=" N9 DA E 22 " -0.044 2.00e-02 2.50e+03 pdb=" C8 DA E 22 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA E 22 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA E 22 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DA E 22 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA E 22 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DA E 22 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA E 22 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA E 22 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA E 22 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 316 " 0.043 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO B 317 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 317 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 317 " 0.036 5.00e-02 4.00e+02 ... (remaining 1615 not shown) Histogram of nonbonded interaction distances: 0.92 - 1.71: 8 1.71 - 2.51: 117 2.51 - 3.31: 11314 3.31 - 4.10: 24455 4.10 - 4.90: 45303 Warning: very small nonbonded interaction distances. Nonbonded interactions: 81197 Sorted by model distance: nonbonded pdb=" N3 DC E 23 " pdb=" O6 DG F 4 " model vdw 0.918 2.496 nonbonded pdb=" N1 DG E 24 " pdb=" N4 DC F 3 " model vdw 0.939 2.560 nonbonded pdb=" N2 DG E 24 " pdb=" N3 DC F 3 " model vdw 1.029 2.560 nonbonded pdb=" CD2 TYR B 232 " pdb=" N1 DA E 2 " model vdw 1.049 3.420 nonbonded pdb=" CG TYR B 232 " pdb=" C2 DA E 2 " model vdw 1.295 3.560 ... (remaining 81192 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 91 or resid 101)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.380 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 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 : 0.010 0.169 10127 Z= 0.530 Angle : 1.387 62.387 13958 Z= 0.644 Chirality : 0.059 0.511 1516 Planarity : 0.008 0.197 1618 Dihedral : 20.373 142.304 3934 Min Nonbonded Distance : 0.918 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.58 % Favored : 91.32 % Rotamer: Outliers : 5.73 % Allowed : 1.98 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.26), residues: 1072 helix: 0.17 (0.23), residues: 493 sheet: -0.70 (0.47), residues: 138 loop : -2.10 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.133 0.002 ARG A 146 TYR 0.019 0.002 TYR B 545 PHE 0.022 0.002 PHE B 425 TRP 0.014 0.002 TRP D 30 HIS 0.011 0.002 HIS B 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00960 / 0.53 (10123) covalent geometry : angle 1.03350 / 0.64 (13946) hydrogen bonds : bond 0.16006 / 11.30 ( 463) hydrogen bonds : angle 8.15015 / 5.35 ( 1289) metal coordination : bond 0.09359 / 4.53 ( 4) metal coordination : angle 31.58409 / 16.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 312 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 VAL cc_start: 0.8895 (t) cc_final: 0.8609 (t) REVERT: A 335 CYS cc_start: 0.4387 (m) cc_final: 0.4113 (m) REVERT: A 516 MET cc_start: 0.8354 (mmm) cc_final: 0.8126 (mmm) REVERT: B 432 ARG cc_start: 0.7663 (ttt90) cc_final: 0.7451 (mtt180) REVERT: B 479 MET cc_start: 0.7090 (mmp) cc_final: 0.6646 (mmt) REVERT: B 509 ILE cc_start: 0.8087 (mt) cc_final: 0.7717 (mm) outliers start: 52 outliers final: 9 residues processed: 339 average time/residue: 0.1222 time to fit residues: 52.9163 Evaluate side-chains 173 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain D residue 22 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 HIS A 227 GLN A 334 ASN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 GLN B 274 HIS ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 25 HIS D 32 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.106510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.091236 restraints weight = 38428.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.093654 restraints weight = 21447.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.095346 restraints weight = 14239.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.096419 restraints weight = 10560.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.097224 restraints weight = 8623.949| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10127 Z= 0.198 Angle : 1.082 49.662 13958 Z= 0.449 Chirality : 0.052 0.306 1516 Planarity : 0.007 0.071 1618 Dihedral : 20.227 139.660 1862 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.34 % Favored : 93.56 % Rotamer: Outliers : 3.97 % Allowed : 13.89 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.25), residues: 1072 helix: 0.52 (0.23), residues: 486 sheet: -0.47 (0.48), residues: 132 loop : -2.22 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 344 TYR 0.031 0.003 TYR A 527 PHE 0.020 0.002 PHE D 36 TRP 0.031 0.003 TRP D 30 HIS 0.013 0.002 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 (10123) covalent geometry : angle 0.83491 / 0.44 (13946) hydrogen bonds : bond 0.06548 / 4.06 ( 463) hydrogen bonds : angle 4.93080 / 3.48 ( 1289) metal coordination : bond 0.01057 / 0.52 ( 4) metal coordination : angle 23.50005 / 12.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7838 (ttm) cc_final: 0.7563 (ptm) REVERT: A 230 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7948 (pttp) REVERT: A 373 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 516 MET cc_start: 0.9122 (mmm) cc_final: 0.8732 (mmm) REVERT: A 536 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8626 (pt0) REVERT: B 225 TYR cc_start: 0.5834 (m-10) cc_final: 0.5613 (m-10) REVERT: B 425 PHE cc_start: 0.6597 (t80) cc_final: 0.6290 (t80) REVERT: B 429 MET cc_start: 0.8089 (ptp) cc_final: 0.7722 (ptp) REVERT: B 432 ARG cc_start: 0.8632 (ttt90) cc_final: 0.7581 (mtt180) REVERT: B 444 ASP cc_start: 0.8050 (t0) cc_final: 0.7672 (t0) REVERT: B 465 MET cc_start: 0.8508 (ppp) cc_final: 0.8209 (ppp) REVERT: B 479 MET cc_start: 0.6861 (mmp) cc_final: 0.6095 (mmt) REVERT: B 512 PHE cc_start: 0.7585 (t80) cc_final: 0.7385 (t80) REVERT: B 516 MET cc_start: 0.7416 (tpp) cc_final: 0.6840 (tpp) REVERT: B 543 THR cc_start: 0.7594 (t) cc_final: 0.7040 (p) REVERT: C 22 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7757 (mttt) REVERT: C 90 ARG cc_start: 0.7659 (mtp-110) cc_final: 0.7353 (ptm160) REVERT: D 10 ASP cc_start: 0.7451 (m-30) cc_final: 0.7235 (m-30) REVERT: D 29 CYS cc_start: 0.7369 (t) cc_final: 0.6966 (m) REVERT: D 39 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.6796 (ttp80) outliers start: 36 outliers final: 11 residues processed: 213 average time/residue: 0.0973 time to fit residues: 27.5944 Evaluate side-chains 161 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 66 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 93 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 105 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 HIS A 420 ASN C 3 HIS ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.095264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.079707 restraints weight = 36646.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.081924 restraints weight = 20448.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.083449 restraints weight = 13764.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.084421 restraints weight = 10417.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.085184 restraints weight = 8633.539| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 10127 Z= 0.252 Angle : 0.945 40.506 13958 Z= 0.435 Chirality : 0.049 0.173 1516 Planarity : 0.007 0.088 1618 Dihedral : 19.989 141.101 1843 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.54 % Rotamer: Outliers : 3.97 % Allowed : 15.77 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.25), residues: 1072 helix: 0.59 (0.24), residues: 480 sheet: -0.08 (0.51), residues: 121 loop : -2.19 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 15 TYR 0.020 0.002 TYR A 527 PHE 0.030 0.002 PHE B 407 TRP 0.033 0.003 TRP D 30 HIS 0.011 0.002 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.25 (10123) covalent geometry : angle 0.80685 / 0.43 (13946) hydrogen bonds : bond 0.06137 / 4.33 ( 463) hydrogen bonds : angle 4.94937 / 3.43 ( 1289) metal coordination : bond 0.01639 / 0.80 ( 4) metal coordination : angle 16.77061 / 8.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.7912 (mt0) cc_final: 0.7301 (pt0) REVERT: A 293 MET cc_start: 0.7912 (mmm) cc_final: 0.7447 (mmm) REVERT: A 336 ARG cc_start: 0.7551 (ttp80) cc_final: 0.7079 (ttp-110) REVERT: A 394 MET cc_start: 0.7513 (mtp) cc_final: 0.6764 (mtp) REVERT: A 427 TYR cc_start: 0.8491 (m-10) cc_final: 0.8130 (m-80) REVERT: A 429 MET cc_start: 0.9113 (ppp) cc_final: 0.8855 (ppp) REVERT: A 464 MET cc_start: 0.9009 (mmm) cc_final: 0.8808 (tpt) REVERT: A 516 MET cc_start: 0.8951 (mmm) cc_final: 0.8188 (mmm) REVERT: A 536 GLU cc_start: 0.8992 (pt0) cc_final: 0.8736 (pt0) REVERT: B 425 PHE cc_start: 0.7471 (t80) cc_final: 0.7053 (t80) REVERT: B 479 MET cc_start: 0.7571 (mmp) cc_final: 0.6822 (mmt) REVERT: B 513 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8973 (mm-30) REVERT: B 516 MET cc_start: 0.8245 (tpp) cc_final: 0.7850 (tpp) REVERT: C 22 LYS cc_start: 0.8323 (mtmm) cc_final: 0.7953 (mttt) REVERT: C 23 THR cc_start: 0.9007 (m) cc_final: 0.8791 (p) REVERT: D 29 CYS cc_start: 0.7644 (t) cc_final: 0.7217 (m) REVERT: D 40 LEU cc_start: 0.8218 (mp) cc_final: 0.7081 (mp) outliers start: 36 outliers final: 16 residues processed: 192 average time/residue: 0.0943 time to fit residues: 24.3571 Evaluate side-chains 145 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 66 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS D 25 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.091705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.076593 restraints weight = 37191.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.078772 restraints weight = 20532.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.080278 restraints weight = 13753.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.081266 restraints weight = 10379.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.081963 restraints weight = 8589.627| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10127 Z= 0.180 Angle : 0.786 28.907 13958 Z= 0.378 Chirality : 0.046 0.192 1516 Planarity : 0.005 0.045 1618 Dihedral : 19.792 138.873 1842 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.09 % Allowed : 18.96 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.26), residues: 1072 helix: 1.06 (0.24), residues: 478 sheet: -0.10 (0.50), residues: 124 loop : -2.05 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 393 TYR 0.020 0.002 TYR A 527 PHE 0.023 0.002 PHE A 407 TRP 0.034 0.002 TRP A 343 HIS 0.004 0.001 HIS C 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (10123) covalent geometry : angle 0.70375 / 0.38 (13946) hydrogen bonds : bond 0.05125 / 3.46 ( 463) hydrogen bonds : angle 4.56506 / 3.18 ( 1289) metal coordination : bond 0.01252 / 0.61 ( 4) metal coordination : angle 11.92831 / 5.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.7953 (mt0) cc_final: 0.7411 (pt0) REVERT: A 321 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7591 (mm) REVERT: A 336 ARG cc_start: 0.7558 (ttp80) cc_final: 0.7011 (ttp-110) REVERT: A 427 TYR cc_start: 0.8570 (m-10) cc_final: 0.8115 (m-80) REVERT: A 464 MET cc_start: 0.9167 (mmm) cc_final: 0.8950 (tpt) REVERT: A 516 MET cc_start: 0.8867 (mmm) cc_final: 0.8340 (mmm) REVERT: A 536 GLU cc_start: 0.8945 (pt0) cc_final: 0.8717 (pt0) REVERT: A 542 LEU cc_start: 0.9410 (tp) cc_final: 0.9187 (tt) REVERT: B 259 GLN cc_start: 0.8992 (pt0) cc_final: 0.8739 (pt0) REVERT: B 364 MET cc_start: 0.4652 (mmm) cc_final: 0.4370 (mtp) REVERT: B 429 MET cc_start: 0.8202 (ptp) cc_final: 0.7988 (ptp) REVERT: B 479 MET cc_start: 0.7611 (mmp) cc_final: 0.7316 (mmt) REVERT: B 513 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8958 (mm-30) REVERT: B 516 MET cc_start: 0.8462 (tpp) cc_final: 0.8081 (tpp) REVERT: B 533 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6305 (ptm160) REVERT: C 9 TYR cc_start: 0.8603 (p90) cc_final: 0.8386 (p90) REVERT: C 23 THR cc_start: 0.9008 (m) cc_final: 0.8739 (p) REVERT: D 29 CYS cc_start: 0.7764 (t) cc_final: 0.7533 (t) REVERT: D 64 LEU cc_start: 0.8943 (mt) cc_final: 0.8702 (mt) REVERT: D 67 ASP cc_start: 0.8033 (t0) cc_final: 0.7621 (m-30) REVERT: D 86 ASP cc_start: 0.8458 (t0) cc_final: 0.8198 (m-30) outliers start: 28 outliers final: 14 residues processed: 158 average time/residue: 0.0925 time to fit residues: 20.1025 Evaluate side-chains 137 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 66 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.089524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.074712 restraints weight = 36530.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.076846 restraints weight = 20105.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.078291 restraints weight = 13448.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.079301 restraints weight = 10184.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.079957 restraints weight = 8367.160| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10127 Z= 0.163 Angle : 0.727 20.637 13958 Z= 0.362 Chirality : 0.044 0.160 1516 Planarity : 0.005 0.048 1618 Dihedral : 19.699 138.906 1840 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.09 % Allowed : 20.18 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.26), residues: 1072 helix: 1.29 (0.24), residues: 473 sheet: 0.08 (0.51), residues: 124 loop : -1.90 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 15 TYR 0.024 0.002 TYR A 387 PHE 0.017 0.001 PHE A 407 TRP 0.020 0.002 TRP D 30 HIS 0.006 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (10123) covalent geometry : angle 0.67596 / 0.36 (13946) hydrogen bonds : bond 0.04713 / 3.27 ( 463) hydrogen bonds : angle 4.39647 / 3.07 ( 1289) metal coordination : bond 0.01082 / 0.53 ( 4) metal coordination : angle 9.12136 / 4.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8659 (ttmm) REVERT: A 230 LYS cc_start: 0.8710 (pttm) cc_final: 0.8429 (pttm) REVERT: A 259 GLN cc_start: 0.7869 (mt0) cc_final: 0.7367 (pt0) REVERT: A 293 MET cc_start: 0.7871 (mmm) cc_final: 0.7614 (mmm) REVERT: A 394 MET cc_start: 0.8068 (mtm) cc_final: 0.7725 (mtm) REVERT: A 427 TYR cc_start: 0.8560 (m-10) cc_final: 0.8099 (m-80) REVERT: A 429 MET cc_start: 0.9142 (ppp) cc_final: 0.8867 (ppp) REVERT: A 464 MET cc_start: 0.9191 (mmm) cc_final: 0.8950 (tpt) REVERT: A 516 MET cc_start: 0.8875 (mmm) cc_final: 0.8451 (mmm) REVERT: A 536 GLU cc_start: 0.8877 (pt0) cc_final: 0.8587 (pt0) REVERT: B 259 GLN cc_start: 0.9090 (pt0) cc_final: 0.8799 (pt0) REVERT: B 479 MET cc_start: 0.7813 (mmp) cc_final: 0.7377 (mmt) REVERT: B 516 MET cc_start: 0.8526 (tpp) cc_final: 0.8183 (tpp) REVERT: B 533 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6564 (ptm160) REVERT: C 8 SER cc_start: 0.8985 (p) cc_final: 0.8766 (p) REVERT: C 20 LEU cc_start: 0.9255 (tp) cc_final: 0.9027 (tp) REVERT: C 23 THR cc_start: 0.9070 (m) cc_final: 0.8738 (p) REVERT: D 29 CYS cc_start: 0.7643 (t) cc_final: 0.7426 (t) REVERT: D 64 LEU cc_start: 0.8823 (mt) cc_final: 0.8580 (mt) outliers start: 28 outliers final: 15 residues processed: 152 average time/residue: 0.0974 time to fit residues: 19.8719 Evaluate side-chains 135 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 68 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 54 optimal weight: 0.0870 chunk 50 optimal weight: 1.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.088290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.073549 restraints weight = 36867.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.075711 restraints weight = 20065.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.077179 restraints weight = 13347.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.078164 restraints weight = 10018.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.078798 restraints weight = 8224.336| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10127 Z= 0.145 Angle : 0.707 15.382 13958 Z= 0.353 Chirality : 0.043 0.162 1516 Planarity : 0.005 0.046 1618 Dihedral : 19.647 137.602 1840 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.31 % Allowed : 20.84 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.26), residues: 1072 helix: 1.42 (0.24), residues: 470 sheet: 0.46 (0.53), residues: 117 loop : -1.92 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 90 TYR 0.016 0.001 TYR A 527 PHE 0.031 0.001 PHE A 407 TRP 0.019 0.001 TRP D 30 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (10123) covalent geometry : angle 0.66723 / 0.35 (13946) hydrogen bonds : bond 0.04441 / 3.03 ( 463) hydrogen bonds : angle 4.30212 / 3.00 ( 1289) metal coordination : bond 0.00832 / 0.41 ( 4) metal coordination : angle 8.01399 / 3.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8653 (ttmm) REVERT: A 259 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7368 (pt0) REVERT: A 293 MET cc_start: 0.7866 (mmm) cc_final: 0.7454 (mmm) REVERT: A 394 MET cc_start: 0.7941 (mtm) cc_final: 0.7560 (mtm) REVERT: A 427 TYR cc_start: 0.8583 (m-10) cc_final: 0.8085 (m-80) REVERT: A 429 MET cc_start: 0.9188 (ppp) cc_final: 0.8844 (ppp) REVERT: A 516 MET cc_start: 0.8823 (mmm) cc_final: 0.8512 (mmm) REVERT: B 259 GLN cc_start: 0.9158 (pt0) cc_final: 0.8932 (pt0) REVERT: B 403 MET cc_start: 0.5578 (mpp) cc_final: 0.5116 (mpp) REVERT: B 479 MET cc_start: 0.7713 (mmp) cc_final: 0.7322 (mmt) REVERT: B 516 MET cc_start: 0.8606 (tpp) cc_final: 0.8287 (tpp) REVERT: C 20 LEU cc_start: 0.9250 (tp) cc_final: 0.9021 (tp) REVERT: D 10 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.8048 (m-30) REVERT: D 29 CYS cc_start: 0.7401 (t) cc_final: 0.7151 (t) REVERT: D 40 LEU cc_start: 0.7994 (mp) cc_final: 0.6786 (mp) REVERT: D 44 ARG cc_start: 0.7422 (mmm-85) cc_final: 0.6613 (tpt170) REVERT: D 64 LEU cc_start: 0.8839 (mt) cc_final: 0.8579 (mt) REVERT: D 67 ASP cc_start: 0.8040 (t0) cc_final: 0.7755 (m-30) outliers start: 30 outliers final: 24 residues processed: 153 average time/residue: 0.0940 time to fit residues: 19.7583 Evaluate side-chains 141 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 66 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.085001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.070328 restraints weight = 36883.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.072442 restraints weight = 20310.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.073875 restraints weight = 13586.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.074868 restraints weight = 10256.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075477 restraints weight = 8422.499| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.7112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10127 Z= 0.186 Angle : 0.737 16.423 13958 Z= 0.371 Chirality : 0.045 0.218 1516 Planarity : 0.006 0.115 1618 Dihedral : 19.661 137.644 1840 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.25 % Favored : 93.66 % Rotamer: Outliers : 2.76 % Allowed : 22.38 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.26), residues: 1072 helix: 1.36 (0.24), residues: 471 sheet: 0.34 (0.52), residues: 117 loop : -1.85 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 44 TYR 0.015 0.002 TYR A 527 PHE 0.030 0.002 PHE A 407 TRP 0.015 0.002 TRP D 30 HIS 0.005 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (10123) covalent geometry : angle 0.69324 / 0.37 (13946) hydrogen bonds : bond 0.04865 / 3.39 ( 463) hydrogen bonds : angle 4.39559 / 3.06 ( 1289) metal coordination : bond 0.00939 / 0.47 ( 4) metal coordination : angle 8.52196 / 4.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8547 (ttmm) REVERT: A 259 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7420 (pt0) REVERT: A 394 MET cc_start: 0.7869 (mtm) cc_final: 0.7378 (mtm) REVERT: A 429 MET cc_start: 0.9156 (ppp) cc_final: 0.8904 (ppp) REVERT: B 277 LEU cc_start: 0.8885 (tp) cc_final: 0.8674 (tp) REVERT: B 342 ASN cc_start: 0.8047 (m-40) cc_final: 0.7587 (m110) REVERT: B 358 MET cc_start: 0.8302 (mmp) cc_final: 0.7993 (mmm) REVERT: B 394 MET cc_start: 0.8160 (mmp) cc_final: 0.7842 (mmp) REVERT: B 479 MET cc_start: 0.7826 (mmp) cc_final: 0.7207 (mmt) REVERT: B 516 MET cc_start: 0.8757 (tpp) cc_final: 0.8501 (tpp) REVERT: B 536 GLU cc_start: 0.8507 (tt0) cc_final: 0.7789 (mm-30) REVERT: D 29 CYS cc_start: 0.7811 (t) cc_final: 0.7586 (t) REVERT: D 40 LEU cc_start: 0.8174 (mp) cc_final: 0.6396 (mp) REVERT: D 44 ARG cc_start: 0.7574 (mmm-85) cc_final: 0.6894 (tpt170) REVERT: D 64 LEU cc_start: 0.8917 (mt) cc_final: 0.8618 (mt) outliers start: 25 outliers final: 21 residues processed: 141 average time/residue: 0.0914 time to fit residues: 17.7205 Evaluate side-chains 136 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 66 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 0.0270 chunk 3 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 522 HIS ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.086239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.071579 restraints weight = 36520.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.073726 restraints weight = 19957.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075160 restraints weight = 13325.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.076157 restraints weight = 10088.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.076825 restraints weight = 8252.221| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.7343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10127 Z= 0.132 Angle : 0.695 15.975 13958 Z= 0.347 Chirality : 0.043 0.156 1516 Planarity : 0.005 0.059 1618 Dihedral : 19.574 136.857 1840 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.21 % Allowed : 23.26 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.26), residues: 1072 helix: 1.62 (0.25), residues: 471 sheet: 0.35 (0.52), residues: 117 loop : -1.81 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 410 TYR 0.017 0.001 TYR A 527 PHE 0.026 0.001 PHE A 407 TRP 0.020 0.002 TRP A 327 HIS 0.002 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (10123) covalent geometry : angle 0.66202 / 0.35 (13946) hydrogen bonds : bond 0.04270 / 2.96 ( 463) hydrogen bonds : angle 4.18210 / 2.93 ( 1289) metal coordination : bond 0.00500 / 0.25 ( 4) metal coordination : angle 7.24887 / 3.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.9091 (ttp80) cc_final: 0.8866 (mtm110) REVERT: A 105 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8545 (ttmm) REVERT: A 230 LYS cc_start: 0.8642 (pttm) cc_final: 0.8430 (pttm) REVERT: A 259 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7481 (pt0) REVERT: A 362 ASP cc_start: 0.8488 (t0) cc_final: 0.8086 (t0) REVERT: A 365 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7409 (tmm-80) REVERT: A 394 MET cc_start: 0.7930 (mtm) cc_final: 0.7409 (mtm) REVERT: A 429 MET cc_start: 0.9194 (ppp) cc_final: 0.8777 (ppp) REVERT: A 435 THR cc_start: 0.8439 (m) cc_final: 0.8218 (m) REVERT: B 247 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8255 (p) REVERT: B 259 GLN cc_start: 0.9006 (pt0) cc_final: 0.8707 (pt0) REVERT: B 277 LEU cc_start: 0.8825 (tp) cc_final: 0.8616 (tp) REVERT: B 342 ASN cc_start: 0.7976 (m-40) cc_final: 0.7493 (m110) REVERT: B 358 MET cc_start: 0.8284 (mmp) cc_final: 0.7976 (mmm) REVERT: B 394 MET cc_start: 0.8063 (mmp) cc_final: 0.7707 (mmp) REVERT: B 479 MET cc_start: 0.7603 (mmp) cc_final: 0.7323 (mmt) REVERT: B 483 ASN cc_start: 0.6997 (p0) cc_final: 0.6371 (m-40) REVERT: B 516 MET cc_start: 0.8760 (tpp) cc_final: 0.8486 (tpp) REVERT: D 29 CYS cc_start: 0.7545 (t) cc_final: 0.7204 (t) REVERT: D 44 ARG cc_start: 0.7533 (mmm-85) cc_final: 0.7089 (tpt-90) REVERT: D 64 LEU cc_start: 0.8928 (mt) cc_final: 0.8644 (mt) outliers start: 20 outliers final: 15 residues processed: 140 average time/residue: 0.0859 time to fit residues: 16.4930 Evaluate side-chains 140 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.0570 chunk 62 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.083607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.069142 restraints weight = 36229.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.071166 restraints weight = 20370.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.072546 restraints weight = 13814.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.073481 restraints weight = 10537.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.074093 restraints weight = 8729.282| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.7806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10127 Z= 0.173 Angle : 0.723 17.468 13958 Z= 0.362 Chirality : 0.044 0.190 1516 Planarity : 0.005 0.050 1618 Dihedral : 19.620 138.440 1840 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.87 % Allowed : 23.26 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1072 helix: 1.55 (0.24), residues: 478 sheet: 0.29 (0.53), residues: 111 loop : -1.77 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 246 TYR 0.017 0.002 TYR D 5 PHE 0.030 0.001 PHE A 407 TRP 0.022 0.002 TRP A 327 HIS 0.005 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (10123) covalent geometry : angle 0.68162 / 0.36 (13946) hydrogen bonds : bond 0.04678 / 3.22 ( 463) hydrogen bonds : angle 4.29544 / 2.99 ( 1289) metal coordination : bond 0.00896 / 0.45 ( 4) metal coordination : angle 8.20273 / 4.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.9122 (ttp80) cc_final: 0.8888 (mtm110) REVERT: A 105 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8545 (ttmm) REVERT: A 230 LYS cc_start: 0.8659 (pttm) cc_final: 0.8380 (pttm) REVERT: A 259 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7342 (pt0) REVERT: A 325 ARG cc_start: 0.6962 (ptp-110) cc_final: 0.6616 (ptp90) REVERT: A 362 ASP cc_start: 0.8619 (t0) cc_final: 0.8229 (t0) REVERT: A 365 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7531 (tmm-80) REVERT: A 394 MET cc_start: 0.8059 (mtm) cc_final: 0.7555 (mtm) REVERT: A 403 MET cc_start: 0.7741 (mmm) cc_final: 0.7461 (tpt) REVERT: A 429 MET cc_start: 0.9184 (ppp) cc_final: 0.8925 (ppp) REVERT: B 342 ASN cc_start: 0.8261 (m-40) cc_final: 0.7734 (m-40) REVERT: B 358 MET cc_start: 0.8357 (mmp) cc_final: 0.8065 (mmm) REVERT: B 394 MET cc_start: 0.8200 (mmp) cc_final: 0.7922 (mmp) REVERT: B 479 MET cc_start: 0.7621 (mmp) cc_final: 0.7205 (mmm) REVERT: B 516 MET cc_start: 0.8731 (tpp) cc_final: 0.8497 (tpp) REVERT: B 536 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7636 (mm-30) REVERT: C 13 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.7629 (t0) REVERT: D 29 CYS cc_start: 0.7551 (t) cc_final: 0.7322 (t) REVERT: D 44 ARG cc_start: 0.7680 (mmm-85) cc_final: 0.7288 (mmm-85) REVERT: D 64 LEU cc_start: 0.8940 (mt) cc_final: 0.8663 (mt) outliers start: 26 outliers final: 17 residues processed: 141 average time/residue: 0.0875 time to fit residues: 16.7361 Evaluate side-chains 142 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 80 optimal weight: 0.0980 chunk 95 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.084248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.069792 restraints weight = 36110.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.071856 restraints weight = 19958.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.073288 restraints weight = 13402.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.074243 restraints weight = 10120.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.074885 restraints weight = 8335.256| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.7958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10127 Z= 0.136 Angle : 0.706 16.369 13958 Z= 0.353 Chirality : 0.043 0.147 1516 Planarity : 0.005 0.050 1618 Dihedral : 19.582 136.797 1840 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.98 % Allowed : 24.04 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.26), residues: 1072 helix: 1.65 (0.25), residues: 476 sheet: 0.51 (0.52), residues: 116 loop : -1.80 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 42 TYR 0.020 0.001 TYR D 5 PHE 0.027 0.001 PHE A 407 TRP 0.023 0.002 TRP A 327 HIS 0.006 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (10123) covalent geometry : angle 0.67329 / 0.35 (13946) hydrogen bonds : bond 0.04269 / 2.95 ( 463) hydrogen bonds : angle 4.23024 / 2.96 ( 1289) metal coordination : bond 0.00633 / 0.32 ( 4) metal coordination : angle 7.27243 / 3.62 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.9121 (ttp80) cc_final: 0.8897 (mtm110) REVERT: A 105 LYS cc_start: 0.8773 (mmmm) cc_final: 0.8549 (ttmm) REVERT: A 230 LYS cc_start: 0.8677 (pttm) cc_final: 0.8386 (pttm) REVERT: A 259 GLN cc_start: 0.7936 (mt0) cc_final: 0.7491 (pt0) REVERT: A 293 MET cc_start: 0.7968 (mmm) cc_final: 0.7752 (mmm) REVERT: A 394 MET cc_start: 0.8043 (mtm) cc_final: 0.7450 (mtm) REVERT: A 403 MET cc_start: 0.7824 (mmm) cc_final: 0.7534 (tpt) REVERT: A 429 MET cc_start: 0.9194 (ppp) cc_final: 0.8791 (ppp) REVERT: A 435 THR cc_start: 0.8426 (m) cc_final: 0.8223 (m) REVERT: A 516 MET cc_start: 0.9010 (mmm) cc_final: 0.8703 (tpt) REVERT: B 259 GLN cc_start: 0.8941 (pt0) cc_final: 0.8736 (pm20) REVERT: B 342 ASN cc_start: 0.8250 (m-40) cc_final: 0.7733 (m-40) REVERT: B 394 MET cc_start: 0.8203 (mmp) cc_final: 0.7786 (mmp) REVERT: B 516 MET cc_start: 0.8776 (tpp) cc_final: 0.8549 (tpp) REVERT: B 536 GLU cc_start: 0.8540 (tt0) cc_final: 0.7499 (mm-30) REVERT: D 29 CYS cc_start: 0.7142 (t) cc_final: 0.6876 (t) REVERT: D 64 LEU cc_start: 0.8940 (mt) cc_final: 0.8688 (mt) outliers start: 18 outliers final: 16 residues processed: 145 average time/residue: 0.0902 time to fit residues: 17.6988 Evaluate side-chains 140 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.084149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.069708 restraints weight = 36693.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.071721 restraints weight = 20550.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.073089 restraints weight = 13932.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.073996 restraints weight = 10654.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074685 restraints weight = 8862.293| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.8125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10127 Z= 0.138 Angle : 0.715 16.116 13958 Z= 0.354 Chirality : 0.043 0.160 1516 Planarity : 0.005 0.053 1618 Dihedral : 19.579 137.829 1840 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.98 % Allowed : 24.70 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.26), residues: 1072 helix: 1.77 (0.25), residues: 471 sheet: 0.47 (0.54), residues: 111 loop : -1.72 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 42 TYR 0.019 0.001 TYR D 5 PHE 0.027 0.001 PHE A 407 TRP 0.021 0.001 TRP A 327 HIS 0.014 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (10123) covalent geometry : angle 0.68439 / 0.35 (13946) hydrogen bonds : bond 0.04236 / 2.91 ( 463) hydrogen bonds : angle 4.18223 / 2.92 ( 1289) metal coordination : bond 0.00654 / 0.33 ( 4) metal coordination : angle 7.04287 / 3.45 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1423.00 seconds wall clock time: 25 minutes 13.81 seconds (1513.81 seconds total)