Starting phenix.real_space_refine on Fri Sep 11 14:17:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mid_23847/09_2026/7mid_23847.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mid_23847/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mid_23847/09_2026/7mid_23847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mid_23847/09_2026/7mid_23847.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mid_23847/09_2026/7mid_23847.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mid_23847/09_2026/7mid_23847.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mid_23847/09_2026/7mid_23847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mid_23847/09_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-2.2.1-6174/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: 2.23, per 1000 atoms: 0.23 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: 1.19 Conformation dependent library (CDL) restraints added in 359.9 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: 1.13 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: 1.77 Time building geometry restraints manager: 1.45 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=" O3' DC E 1 " pdb=" P DA E 2 " ideal model delta sigma weight residual 1.607 1.657 -0.050 1.20e-02 6.94e+03 1.71e+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: 1.290 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.710 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.620 ------------------------------------------------------------------------------- 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= 0.532 Angle : 1.388 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 1.03375 / 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 : 0.346 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: 0.8610 (t) REVERT: A 335 CYS cc_start: 0.4387 (m) cc_final: 0.4116 (m) REVERT: A 516 MET cc_start: 0.8354 (mmm) cc_final: 0.8125 (mmm) REVERT: B 479 MET cc_start: 0.7090 (mmp) cc_final: 0.6637 (mmt) REVERT: B 509 ILE cc_start: 0.8087 (mt) cc_final: 0.7722 (mm) outliers start: 52 outliers final: 9 residues processed: 339 average time/residue: 0.1493 time to fit residues: 64.5261 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 : 0.345 ------------------------------------------------------------------------------- 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: 8.9990 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: 2.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 3 HIS D 25 HIS D 32 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.106231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.090923 restraints weight = 38494.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.093362 restraints weight = 21545.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.095014 restraints weight = 14314.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.096133 restraints weight = 10673.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.096829 restraints weight = 8686.018| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10127 Z= 0.199 Angle : 1.080 51.927 13958 Z= 0.435 Chirality : 0.050 0.332 1516 Planarity : 0.007 0.074 1618 Dihedral : 20.209 139.591 1862 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.53 % Favored : 93.38 % Rotamer: Outliers : 3.86 % Allowed : 14.44 % Favored : 81.70 % 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: -1.06 (0.26), residues: 1072 helix: 0.55 (0.23), residues: 489 sheet: -0.54 (0.48), residues: 132 loop : -2.21 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 344 TYR 0.028 0.003 TYR A 527 PHE 0.018 0.002 PHE D 36 TRP 0.030 0.003 TRP D 30 HIS 0.013 0.002 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (10123) covalent geometry : angle 0.79988 / 0.43 (13946) hydrogen bonds : bond 0.07373 / 4.67 ( 463) hydrogen bonds : angle 4.99288 / 3.52 ( 1289) metal coordination : bond 0.01474 / 0.71 ( 4) metal coordination : angle 24.75351 / 13.07 ( 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 226 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.352 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: A 177 MET cc_start: 0.7836 (ttm) cc_final: 0.7575 (ptm) REVERT: A 230 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8011 (pttp) REVERT: A 373 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8436 (mp) REVERT: A 403 MET cc_start: 0.7524 (tpp) cc_final: 0.7254 (mmp) REVERT: A 516 MET cc_start: 0.9125 (mmm) cc_final: 0.8771 (mmm) REVERT: A 536 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8651 (pt0) REVERT: B 225 TYR cc_start: 0.5839 (m-10) cc_final: 0.5615 (m-10) REVERT: B 232 TYR cc_start: 0.5167 (t80) cc_final: 0.4745 (t80) REVERT: B 425 PHE cc_start: 0.6599 (t80) cc_final: 0.6353 (t80) REVERT: B 444 ASP cc_start: 0.8023 (t0) cc_final: 0.7594 (t0) REVERT: B 465 MET cc_start: 0.8496 (ppp) cc_final: 0.8182 (ppp) REVERT: B 479 MET cc_start: 0.6836 (mmp) cc_final: 0.6081 (mmt) REVERT: B 513 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8564 (mm-30) REVERT: B 516 MET cc_start: 0.7575 (tpp) cc_final: 0.6818 (tpp) REVERT: C 22 LYS cc_start: 0.7863 (mtmm) cc_final: 0.7443 (mttt) REVERT: C 90 ARG cc_start: 0.7737 (mtp-110) cc_final: 0.7433 (ptm160) REVERT: D 10 ASP cc_start: 0.7289 (m-30) cc_final: 0.6964 (m-30) REVERT: D 29 CYS cc_start: 0.7428 (t) cc_final: 0.7038 (m) REVERT: D 39 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6852 (ttp80) outliers start: 35 outliers final: 14 residues processed: 211 average time/residue: 0.1227 time to fit residues: 34.6279 Evaluate side-chains 163 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 227 GLN 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 365 ARG Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 27 PHE 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: 0.8980 chunk 4 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 73 optimal weight: 0.0970 chunk 81 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 HIS A 420 ASN D 3 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.097034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.081590 restraints weight = 36844.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.083863 restraints weight = 20576.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.085441 restraints weight = 13781.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.086491 restraints weight = 10348.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.087175 restraints weight = 8476.656| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 10127 Z= 0.234 Angle : 0.948 40.006 13958 Z= 0.435 Chirality : 0.050 0.215 1516 Planarity : 0.007 0.059 1618 Dihedral : 19.933 140.490 1843 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.00 % Favored : 92.91 % Rotamer: Outliers : 3.64 % Allowed : 16.32 % Favored : 80.04 % 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: -0.96 (0.25), residues: 1072 helix: 0.65 (0.24), residues: 474 sheet: -0.16 (0.51), residues: 121 loop : -2.16 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 19 TYR 0.023 0.003 TYR A 527 PHE 0.021 0.002 PHE A 407 TRP 0.021 0.002 TRP D 30 HIS 0.007 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.23 (10123) covalent geometry : angle 0.81205 / 0.43 (13946) hydrogen bonds : bond 0.05874 / 4.10 ( 463) hydrogen bonds : angle 4.88249 / 3.38 ( 1289) metal coordination : bond 0.01697 / 0.83 ( 4) metal coordination : angle 16.67456 / 8.47 ( 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: 33 poor density : 169 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8415 (mm-30) REVERT: A 259 GLN cc_start: 0.7879 (mt0) cc_final: 0.7406 (pt0) REVERT: A 260 VAL cc_start: 0.9319 (t) cc_final: 0.9085 (p) REVERT: A 293 MET cc_start: 0.7970 (mmm) cc_final: 0.7726 (mmm) REVERT: A 394 MET cc_start: 0.7479 (mtp) cc_final: 0.7144 (mtm) REVERT: A 427 TYR cc_start: 0.8374 (m-10) cc_final: 0.8033 (m-80) REVERT: A 429 MET cc_start: 0.9092 (ppp) cc_final: 0.8845 (ppp) REVERT: A 464 MET cc_start: 0.8962 (mmm) cc_final: 0.8691 (tpt) REVERT: A 516 MET cc_start: 0.9053 (mmm) cc_final: 0.8207 (mmm) REVERT: A 536 GLU cc_start: 0.8995 (pt0) cc_final: 0.8739 (pt0) REVERT: B 265 ASN cc_start: 0.9270 (t0) cc_final: 0.8629 (t0) REVERT: B 357 LEU cc_start: 0.7265 (tt) cc_final: 0.7051 (mt) REVERT: B 425 PHE cc_start: 0.7564 (t80) cc_final: 0.7153 (t80) REVERT: B 429 MET cc_start: 0.8296 (ptp) cc_final: 0.8081 (ptp) REVERT: B 431 THR cc_start: 0.9266 (m) cc_final: 0.8930 (p) REVERT: B 479 MET cc_start: 0.7492 (mmp) cc_final: 0.6751 (mmt) REVERT: B 513 GLU cc_start: 0.9270 (mm-30) cc_final: 0.9001 (mm-30) REVERT: B 516 MET cc_start: 0.8124 (tpp) cc_final: 0.7734 (tpp) REVERT: B 543 THR cc_start: 0.8016 (t) cc_final: 0.7566 (p) REVERT: C 22 LYS cc_start: 0.8376 (mtmm) cc_final: 0.8054 (mtmm) REVERT: D 10 ASP cc_start: 0.7768 (m-30) cc_final: 0.7539 (m-30) REVERT: D 29 CYS cc_start: 0.7656 (t) cc_final: 0.7396 (t) REVERT: D 40 LEU cc_start: 0.8269 (mp) cc_final: 0.7688 (mp) REVERT: D 45 ILE cc_start: 0.8134 (pt) cc_final: 0.7929 (pt) outliers start: 33 outliers final: 13 residues processed: 191 average time/residue: 0.1202 time to fit residues: 30.9477 Evaluate side-chains 154 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 357 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 365 ARG 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: 4.9990 chunk 97 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 0.2980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.094684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.079729 restraints weight = 36656.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.081950 restraints weight = 20085.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.083502 restraints weight = 13299.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.084568 restraints weight = 9964.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.085239 restraints weight = 8104.444| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10127 Z= 0.161 Angle : 0.782 28.956 13958 Z= 0.374 Chirality : 0.046 0.212 1516 Planarity : 0.005 0.047 1618 Dihedral : 19.757 138.271 1842 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.97 % Allowed : 17.97 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.54 (0.26), residues: 1072 helix: 1.05 (0.24), residues: 479 sheet: -0.10 (0.51), residues: 123 loop : -1.99 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 15 TYR 0.019 0.002 TYR A 527 PHE 0.023 0.002 PHE A 407 TRP 0.018 0.001 TRP D 30 HIS 0.003 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (10123) covalent geometry : angle 0.69767 / 0.37 (13946) hydrogen bonds : bond 0.05069 / 3.43 ( 463) hydrogen bonds : angle 4.55781 / 3.19 ( 1289) metal coordination : bond 0.01345 / 0.66 ( 4) metal coordination : angle 12.06759 / 6.02 ( 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 184 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8448 (mm-30) REVERT: A 259 GLN cc_start: 0.7898 (mt0) cc_final: 0.7426 (pt0) REVERT: A 321 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7615 (mm) REVERT: A 403 MET cc_start: 0.7625 (mmm) cc_final: 0.7304 (tpt) REVERT: A 427 TYR cc_start: 0.8545 (m-10) cc_final: 0.7950 (m-80) REVERT: A 464 MET cc_start: 0.9126 (mmm) cc_final: 0.8869 (tpt) REVERT: A 465 MET cc_start: 0.7801 (ppp) cc_final: 0.7500 (ppp) REVERT: A 516 MET cc_start: 0.9003 (mmm) cc_final: 0.8713 (mmm) REVERT: A 536 GLU cc_start: 0.8954 (pt0) cc_final: 0.8721 (pt0) REVERT: B 259 GLN cc_start: 0.8933 (pt0) cc_final: 0.8663 (pt0) REVERT: B 265 ASN cc_start: 0.9190 (t0) cc_final: 0.8946 (t0) REVERT: B 364 MET cc_start: 0.4782 (mmm) cc_final: 0.4104 (mtp) REVERT: B 425 PHE cc_start: 0.7725 (t80) cc_final: 0.7453 (t80) REVERT: B 431 THR cc_start: 0.9244 (m) cc_final: 0.8930 (p) REVERT: B 479 MET cc_start: 0.7518 (mmp) cc_final: 0.7024 (mmt) REVERT: B 513 GLU cc_start: 0.9220 (mm-30) cc_final: 0.9017 (mm-30) REVERT: B 516 MET cc_start: 0.8392 (tpp) cc_final: 0.7873 (tpp) REVERT: B 533 ARG cc_start: 0.6468 (OUTLIER) cc_final: 0.5650 (ptm-80) REVERT: C 23 THR cc_start: 0.8998 (m) cc_final: 0.8770 (p) REVERT: C 44 ARG cc_start: 0.8704 (mmm-85) cc_final: 0.8268 (mmm-85) REVERT: D 29 CYS cc_start: 0.7679 (t) cc_final: 0.7425 (t) REVERT: D 40 LEU cc_start: 0.8118 (mp) cc_final: 0.7317 (mp) REVERT: D 64 LEU cc_start: 0.9055 (mt) cc_final: 0.8812 (mt) REVERT: D 67 ASP cc_start: 0.8079 (t0) cc_final: 0.7795 (m-30) REVERT: D 86 ASP cc_start: 0.8412 (t0) cc_final: 0.8161 (m-30) outliers start: 36 outliers final: 16 residues processed: 177 average time/residue: 0.1093 time to fit residues: 26.2932 Evaluate side-chains 143 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 235 LYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 SER 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 365 ARG 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: 9.9990 chunk 86 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS ** C 91 GLN ** 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 = 0.3691 r_free = 0.3691 target = 0.087401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.072503 restraints weight = 36702.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.074619 restraints weight = 20237.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.076042 restraints weight = 13561.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.076982 restraints weight = 10318.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.077688 restraints weight = 8557.930| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 10127 Z= 0.224 Angle : 0.808 25.555 13958 Z= 0.396 Chirality : 0.046 0.158 1516 Planarity : 0.005 0.054 1618 Dihedral : 19.800 139.098 1842 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.82 % Rotamer: Outliers : 3.09 % Allowed : 20.29 % Favored : 76.63 % 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: -0.39 (0.26), residues: 1072 helix: 1.21 (0.24), residues: 473 sheet: -0.06 (0.51), residues: 124 loop : -1.90 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 279 TYR 0.020 0.002 TYR A 387 PHE 0.025 0.002 PHE A 407 TRP 0.014 0.002 TRP D 30 HIS 0.009 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.22 (10123) covalent geometry : angle 0.74514 / 0.39 (13946) hydrogen bonds : bond 0.05307 / 3.68 ( 463) hydrogen bonds : angle 4.59050 / 3.20 ( 1289) metal coordination : bond 0.01425 / 0.70 ( 4) metal coordination : angle 10.67934 / 5.25 ( 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 159 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8470 (mm-30) REVERT: A 105 LYS cc_start: 0.8810 (mmmm) cc_final: 0.8583 (ttmm) REVERT: A 230 LYS cc_start: 0.8874 (pttm) cc_final: 0.8470 (pttm) REVERT: A 259 GLN cc_start: 0.7727 (mt0) cc_final: 0.7230 (pt0) REVERT: A 357 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7057 (tt) REVERT: A 380 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8383 (mm-30) REVERT: A 403 MET cc_start: 0.7817 (mmm) cc_final: 0.7599 (tpp) REVERT: A 427 TYR cc_start: 0.8488 (m-10) cc_final: 0.8144 (m-80) REVERT: A 429 MET cc_start: 0.9164 (ppp) cc_final: 0.8876 (ppp) REVERT: A 465 MET cc_start: 0.7920 (ppp) cc_final: 0.7494 (ppp) REVERT: A 536 GLU cc_start: 0.8875 (pt0) cc_final: 0.8577 (pt0) REVERT: B 259 GLN cc_start: 0.9123 (pt0) cc_final: 0.8803 (pt0) REVERT: B 265 ASN cc_start: 0.9107 (t0) cc_final: 0.8844 (t0) REVERT: B 364 MET cc_start: 0.4987 (OUTLIER) cc_final: 0.4428 (mtp) REVERT: B 403 MET cc_start: 0.5850 (mpp) cc_final: 0.5588 (mpp) REVERT: B 425 PHE cc_start: 0.7846 (t80) cc_final: 0.7599 (t80) REVERT: B 479 MET cc_start: 0.7635 (mmp) cc_final: 0.7223 (mmt) REVERT: B 516 MET cc_start: 0.8592 (tpp) cc_final: 0.8240 (tpp) REVERT: B 533 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6558 (ptm-80) REVERT: C 23 THR cc_start: 0.9103 (m) cc_final: 0.8780 (p) REVERT: C 44 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.8346 (mmm-85) REVERT: D 29 CYS cc_start: 0.7729 (t) cc_final: 0.7514 (t) REVERT: D 40 LEU cc_start: 0.8334 (mp) cc_final: 0.8129 (mp) REVERT: D 48 MET cc_start: 0.8863 (tpp) cc_final: 0.8569 (mtt) REVERT: D 49 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7692 (tm-30) REVERT: D 64 LEU cc_start: 0.8843 (mt) cc_final: 0.8598 (mt) outliers start: 28 outliers final: 16 residues processed: 152 average time/residue: 0.1204 time to fit residues: 24.4577 Evaluate side-chains 134 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 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 177 MET Chi-restraints excluded: chain A residue 357 LEU 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 339 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 ARG 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 Chi-restraints excluded: chain C residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** 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 = 0.3708 r_free = 0.3708 target = 0.088237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.073384 restraints weight = 36751.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075513 restraints weight = 20092.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.077006 restraints weight = 13333.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.078010 restraints weight = 10031.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.078632 restraints weight = 8231.266| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10127 Z= 0.138 Angle : 0.712 16.921 13958 Z= 0.354 Chirality : 0.044 0.180 1516 Planarity : 0.004 0.039 1618 Dihedral : 19.664 137.710 1840 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.20 % Allowed : 20.84 % Favored : 75.96 % 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: -0.17 (0.26), residues: 1072 helix: 1.43 (0.24), residues: 471 sheet: 0.13 (0.51), residues: 122 loop : -1.85 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 42 TYR 0.017 0.001 TYR A 527 PHE 0.022 0.001 PHE A 407 TRP 0.018 0.001 TRP D 30 HIS 0.003 0.001 HIS D 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (10123) covalent geometry : angle 0.66846 / 0.35 (13946) hydrogen bonds : bond 0.04623 / 3.17 ( 463) hydrogen bonds : angle 4.35325 / 3.07 ( 1289) metal coordination : bond 0.00839 / 0.41 ( 4) metal coordination : angle 8.36959 / 4.03 ( 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 161 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9014 (mpp) cc_final: 0.8651 (mmm) REVERT: A 105 LYS cc_start: 0.8800 (mmmm) cc_final: 0.8569 (ttmm) REVERT: A 230 LYS cc_start: 0.8838 (pttm) cc_final: 0.8469 (pttm) REVERT: A 259 GLN cc_start: 0.7692 (mt0) cc_final: 0.7248 (pt0) REVERT: A 293 MET cc_start: 0.8128 (mmm) cc_final: 0.7706 (mmm) REVERT: A 357 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6951 (tt) REVERT: A 380 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8263 (tp30) REVERT: A 427 TYR cc_start: 0.8553 (m-10) cc_final: 0.8182 (m-80) REVERT: A 429 MET cc_start: 0.9172 (ppp) cc_final: 0.8835 (ppp) REVERT: A 465 MET cc_start: 0.7714 (ppp) cc_final: 0.7371 (ppp) REVERT: A 516 MET cc_start: 0.9164 (mmm) cc_final: 0.8925 (tpt) REVERT: B 265 ASN cc_start: 0.9051 (t0) cc_final: 0.8803 (t0) REVERT: B 403 MET cc_start: 0.5831 (mpp) cc_final: 0.5627 (mpp) REVERT: B 479 MET cc_start: 0.7658 (mmp) cc_final: 0.7263 (mmt) REVERT: B 516 MET cc_start: 0.8517 (tpp) cc_final: 0.8183 (tpp) REVERT: B 533 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6707 (ptm160) REVERT: C 23 THR cc_start: 0.9099 (m) cc_final: 0.8771 (p) REVERT: C 48 MET cc_start: 0.8747 (mmm) cc_final: 0.8509 (mmm) REVERT: D 29 CYS cc_start: 0.7528 (t) cc_final: 0.7280 (t) REVERT: D 64 LEU cc_start: 0.8871 (mt) cc_final: 0.8656 (mt) REVERT: D 67 ASP cc_start: 0.8115 (t0) cc_final: 0.7838 (m-30) outliers start: 29 outliers final: 21 residues processed: 153 average time/residue: 0.1282 time to fit residues: 26.1322 Evaluate side-chains 141 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 357 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 262 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 365 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.085494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.070889 restraints weight = 36766.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.073023 restraints weight = 20084.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.074453 restraints weight = 13374.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.075375 restraints weight = 10104.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.076085 restraints weight = 8360.997| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10127 Z= 0.169 Angle : 0.731 15.663 13958 Z= 0.364 Chirality : 0.044 0.169 1516 Planarity : 0.005 0.040 1618 Dihedral : 19.700 137.655 1840 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.65 % Allowed : 22.27 % Favored : 75.08 % 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: -0.14 (0.26), residues: 1072 helix: 1.45 (0.24), residues: 472 sheet: 0.10 (0.51), residues: 122 loop : -1.80 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 412 TYR 0.015 0.001 TYR A 527 PHE 0.019 0.001 PHE A 407 TRP 0.016 0.002 TRP D 30 HIS 0.005 0.001 HIS D 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (10123) covalent geometry : angle 0.68795 / 0.36 (13946) hydrogen bonds : bond 0.04629 / 3.16 ( 463) hydrogen bonds : angle 4.35927 / 3.05 ( 1289) metal coordination : bond 0.00986 / 0.49 ( 4) metal coordination : angle 8.41037 / 4.11 ( 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 155 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9013 (mpp) cc_final: 0.8791 (mmt) REVERT: A 105 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8642 (ttmm) REVERT: A 230 LYS cc_start: 0.8776 (pttm) cc_final: 0.8388 (pttm) REVERT: A 259 GLN cc_start: 0.7791 (mt0) cc_final: 0.7333 (pt0) REVERT: A 293 MET cc_start: 0.8123 (mmm) cc_final: 0.7881 (mmm) REVERT: A 380 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8333 (tp30) REVERT: A 427 TYR cc_start: 0.8495 (m-10) cc_final: 0.8126 (m-80) REVERT: A 429 MET cc_start: 0.9119 (ppp) cc_final: 0.8867 (ppp) REVERT: A 465 MET cc_start: 0.7931 (ppp) cc_final: 0.7619 (ppp) REVERT: B 479 MET cc_start: 0.7801 (mmp) cc_final: 0.7170 (mmt) REVERT: B 516 MET cc_start: 0.8632 (tpp) cc_final: 0.8326 (tpp) REVERT: B 533 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6933 (ptm160) REVERT: C 23 THR cc_start: 0.9145 (m) cc_final: 0.8914 (t) REVERT: D 29 CYS cc_start: 0.7644 (t) cc_final: 0.7373 (t) REVERT: D 64 LEU cc_start: 0.8926 (mt) cc_final: 0.8678 (mt) outliers start: 24 outliers final: 18 residues processed: 149 average time/residue: 0.1111 time to fit residues: 22.6132 Evaluate side-chains 138 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 214 ILE Chi-restraints excluded: chain A residue 320 CYS 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 293 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 509 ILE 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 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: 1.9990 chunk 75 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 78 optimal weight: 0.0970 chunk 67 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN B 522 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.086562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.071802 restraints weight = 36286.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.073966 restraints weight = 19786.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.075421 restraints weight = 13157.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.076366 restraints weight = 9931.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.077102 restraints weight = 8195.875| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10127 Z= 0.134 Angle : 0.698 15.672 13958 Z= 0.350 Chirality : 0.043 0.170 1516 Planarity : 0.004 0.041 1618 Dihedral : 19.625 136.872 1840 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.50 % Favored : 94.40 % Rotamer: Outliers : 2.32 % Allowed : 23.04 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.26), residues: 1072 helix: 1.55 (0.24), residues: 469 sheet: 0.27 (0.54), residues: 111 loop : -1.84 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 393 TYR 0.016 0.001 TYR A 527 PHE 0.032 0.001 PHE A 407 TRP 0.023 0.002 TRP A 327 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10123) covalent geometry : angle 0.66462 / 0.35 (13946) hydrogen bonds : bond 0.04299 / 2.94 ( 463) hydrogen bonds : angle 4.22267 / 2.97 ( 1289) metal coordination : bond 0.00655 / 0.33 ( 4) metal coordination : angle 7.34423 / 3.55 ( 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 148 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9026 (mpp) cc_final: 0.8708 (mmm) REVERT: A 49 ARG cc_start: 0.9101 (ttp80) cc_final: 0.8866 (mtm110) REVERT: A 105 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8525 (ttmm) REVERT: A 259 GLN cc_start: 0.7951 (mt0) cc_final: 0.7485 (pt0) REVERT: A 293 MET cc_start: 0.8122 (mmm) cc_final: 0.7852 (mmm) REVERT: A 380 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8394 (tp30) REVERT: A 394 MET cc_start: 0.7479 (mtp) cc_final: 0.7233 (mtm) REVERT: A 427 TYR cc_start: 0.8519 (m-10) cc_final: 0.8119 (m-80) REVERT: A 429 MET cc_start: 0.9141 (ppp) cc_final: 0.8702 (ppp) REVERT: B 342 ASN cc_start: 0.8027 (m-40) cc_final: 0.7798 (m110) REVERT: B 403 MET cc_start: 0.5372 (mpp) cc_final: 0.5089 (mpp) REVERT: B 483 ASN cc_start: 0.6988 (p0) cc_final: 0.6437 (m-40) REVERT: B 492 VAL cc_start: 0.8698 (t) cc_final: 0.8435 (m) REVERT: B 516 MET cc_start: 0.8678 (tpp) cc_final: 0.8371 (tpp) REVERT: B 533 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6907 (ptm160) REVERT: C 23 THR cc_start: 0.9176 (m) cc_final: 0.8974 (t) REVERT: D 29 CYS cc_start: 0.7546 (t) cc_final: 0.7269 (t) REVERT: D 64 LEU cc_start: 0.8913 (mt) cc_final: 0.8660 (mt) REVERT: D 67 ASP cc_start: 0.7992 (t0) cc_final: 0.7726 (m-30) outliers start: 21 outliers final: 14 residues processed: 143 average time/residue: 0.1169 time to fit residues: 23.0513 Evaluate side-chains 137 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 227 GLN Chi-restraints excluded: chain A residue 320 CYS 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 293 MET 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 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: 0.1980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.0670 chunk 19 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 342 ASN C 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.086544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.071792 restraints weight = 35744.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073943 restraints weight = 19654.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.075401 restraints weight = 13124.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.076391 restraints weight = 9917.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.077093 restraints weight = 8129.237| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.7345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10127 Z= 0.131 Angle : 0.686 15.678 13958 Z= 0.346 Chirality : 0.043 0.177 1516 Planarity : 0.004 0.046 1618 Dihedral : 19.610 136.910 1840 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.54 % Allowed : 24.04 % Favored : 74.42 % 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: -0.02 (0.26), residues: 1072 helix: 1.63 (0.24), residues: 468 sheet: 0.36 (0.53), residues: 111 loop : -1.84 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 505 TYR 0.019 0.001 TYR A 288 PHE 0.030 0.001 PHE A 407 TRP 0.019 0.001 TRP D 30 HIS 0.002 0.000 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (10123) covalent geometry : angle 0.65496 / 0.35 (13946) hydrogen bonds : bond 0.04219 / 2.90 ( 463) hydrogen bonds : angle 4.19922 / 2.95 ( 1289) metal coordination : bond 0.00564 / 0.28 ( 4) metal coordination : angle 6.97796 / 3.32 ( 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 139 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9003 (mpp) cc_final: 0.8688 (mmm) REVERT: A 49 ARG cc_start: 0.9086 (ttp80) cc_final: 0.8857 (mtm110) REVERT: A 105 LYS cc_start: 0.8873 (mmmm) cc_final: 0.8629 (ttmm) REVERT: A 259 GLN cc_start: 0.7959 (mt0) cc_final: 0.7511 (pt0) REVERT: A 293 MET cc_start: 0.8062 (mmm) cc_final: 0.7774 (mmm) REVERT: A 380 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8415 (tp30) REVERT: A 403 MET cc_start: 0.7811 (mmm) cc_final: 0.7491 (tpt) REVERT: A 427 TYR cc_start: 0.8565 (m-10) cc_final: 0.8126 (m-80) REVERT: A 429 MET cc_start: 0.9156 (ppp) cc_final: 0.8699 (ppp) REVERT: A 516 MET cc_start: 0.9036 (tpt) cc_final: 0.8790 (tpt) REVERT: B 479 MET cc_start: 0.7074 (mmt) cc_final: 0.6225 (mpp) REVERT: B 483 ASN cc_start: 0.7029 (p0) cc_final: 0.6424 (m-40) REVERT: B 516 MET cc_start: 0.8696 (tpp) cc_final: 0.8376 (tpp) REVERT: D 29 CYS cc_start: 0.7513 (t) cc_final: 0.7227 (t) REVERT: D 64 LEU cc_start: 0.8923 (mt) cc_final: 0.8665 (mt) outliers start: 14 outliers final: 12 residues processed: 137 average time/residue: 0.1094 time to fit residues: 20.4564 Evaluate side-chains 136 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 293 MET 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 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: 9.9990 chunk 103 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 80 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.087071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.072301 restraints weight = 35766.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.074421 restraints weight = 19651.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075881 restraints weight = 13107.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.076894 restraints weight = 9904.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.077585 restraints weight = 8102.535| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.7466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10127 Z= 0.134 Angle : 0.698 15.575 13958 Z= 0.351 Chirality : 0.043 0.159 1516 Planarity : 0.004 0.046 1618 Dihedral : 19.596 136.851 1840 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.87 % Allowed : 24.70 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1072 helix: 1.64 (0.24), residues: 469 sheet: 0.38 (0.52), residues: 111 loop : -1.85 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 16 TYR 0.016 0.001 TYR A 527 PHE 0.032 0.001 PHE A 407 TRP 0.019 0.001 TRP D 30 HIS 0.002 0.000 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10123) covalent geometry : angle 0.66833 / 0.35 (13946) hydrogen bonds : bond 0.04141 / 2.85 ( 463) hydrogen bonds : angle 4.17461 / 2.93 ( 1289) metal coordination : bond 0.00616 / 0.31 ( 4) metal coordination : angle 6.84297 / 3.24 ( 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 142 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.8990 (mpp) cc_final: 0.8673 (mmm) REVERT: A 49 ARG cc_start: 0.9139 (ttp80) cc_final: 0.8894 (mtm110) REVERT: A 105 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8636 (ttmm) REVERT: A 259 GLN cc_start: 0.8005 (mt0) cc_final: 0.7526 (pt0) REVERT: A 293 MET cc_start: 0.8052 (mmm) cc_final: 0.7745 (mmm) REVERT: A 380 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8468 (tp30) REVERT: A 403 MET cc_start: 0.7793 (mmm) cc_final: 0.7469 (tpt) REVERT: A 427 TYR cc_start: 0.8587 (m-10) cc_final: 0.8132 (m-80) REVERT: A 429 MET cc_start: 0.9168 (ppp) cc_final: 0.8702 (ppp) REVERT: A 435 THR cc_start: 0.8426 (m) cc_final: 0.8211 (m) REVERT: A 516 MET cc_start: 0.9055 (tpt) cc_final: 0.8802 (tpt) REVERT: B 479 MET cc_start: 0.7078 (mmt) cc_final: 0.6256 (mpp) REVERT: B 483 ASN cc_start: 0.6957 (p0) cc_final: 0.6426 (m-40) REVERT: B 516 MET cc_start: 0.8736 (tpp) cc_final: 0.8402 (tpp) REVERT: D 29 CYS cc_start: 0.7231 (t) cc_final: 0.6898 (t) REVERT: D 64 LEU cc_start: 0.8922 (mt) cc_final: 0.8651 (mt) outliers start: 17 outliers final: 15 residues processed: 140 average time/residue: 0.1107 time to fit residues: 21.0532 Evaluate side-chains 135 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 377 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 396 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 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: 5.9990 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN C 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.086669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.072147 restraints weight = 36564.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.074243 restraints weight = 19902.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075684 restraints weight = 13235.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.076627 restraints weight = 9949.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.077330 restraints weight = 8208.255| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.7771 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= 0.129 Angle : 0.695 15.286 13958 Z= 0.348 Chirality : 0.043 0.150 1516 Planarity : 0.005 0.077 1618 Dihedral : 19.558 137.163 1840 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.87 % Allowed : 24.37 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1072 helix: 1.57 (0.24), residues: 480 sheet: 0.48 (0.53), residues: 111 loop : -1.87 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 412 TYR 0.024 0.001 TYR A 288 PHE 0.028 0.001 PHE A 407 TRP 0.025 0.002 TRP A 327 HIS 0.005 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (10123) covalent geometry : angle 0.67009 / 0.35 (13946) hydrogen bonds : bond 0.03948 / 2.70 ( 463) hydrogen bonds : angle 4.11597 / 2.89 ( 1289) metal coordination : bond 0.00579 / 0.29 ( 4) metal coordination : angle 6.38564 / 2.96 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1753.47 seconds wall clock time: 30 minutes 55.28 seconds (1855.28 seconds total)