Starting phenix.real_space_refine on Sun May 3 08:11:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pwb_71909/05_2026/9pwb_71909.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pwb_71909/05_2026/9pwb_71909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pwb_71909/05_2026/9pwb_71909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pwb_71909/05_2026/9pwb_71909.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pwb_71909/05_2026/9pwb_71909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pwb_71909/05_2026/9pwb_71909.map" } resolution = 2.64 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= 0.023 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 7427 2.51 5 N 1967 2.21 5 O 2168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11620 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4836 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 22, 'TRANS': 590} Chain: "B" Number of atoms: 4413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4413 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 26, 'TRANS': 530} Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 88 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 2, 'TRANS': 8} Chain: "M" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1093 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "S" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1190 Classifications: {'peptide': 141} Link IDs: {'TRANS': 140} Time building chain proxies: 2.90, per 1000 atoms: 0.25 Number of scatterers: 11620 At special positions: 0 Unit cell: (91.98, 102.492, 126.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 2168 8.00 N 1967 7.00 C 7427 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: 0.92 Conformation dependent library (CDL) restraints added in 461.3 milliseconds 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2828 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 4 sheets defined 73.4% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.586A pdb=" N ALA A 14 " --> pdb=" O MET A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 46 removed outlier: 3.523A pdb=" N GLY A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 69 Processing helix chain 'A' and resid 75 through 83 removed outlier: 3.917A pdb=" N VAL A 80 " --> pdb=" O HIS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 105 through 122 removed outlier: 3.548A pdb=" N SER A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 138 Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.554A pdb=" N VAL A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 200 through 215 removed outlier: 3.624A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 225 through 238 removed outlier: 4.045A pdb=" N SER A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 273 through 292 removed outlier: 3.674A pdb=" N GLN A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 321 removed outlier: 4.025A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.752A pdb=" N THR A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 368 Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 382 through 396 Processing helix chain 'A' and resid 401 through 414 removed outlier: 3.667A pdb=" N GLU A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 435 Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.808A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 473 removed outlier: 3.864A pdb=" N ILE A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 512 removed outlier: 3.655A pdb=" N ALA A 512 " --> pdb=" O ASN A 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 512' Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 3.578A pdb=" N LYS A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 Processing helix chain 'A' and resid 555 through 564 Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 590 Processing helix chain 'A' and resid 593 through 599 removed outlier: 3.704A pdb=" N THR A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 620 removed outlier: 3.735A pdb=" N LYS A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 4.091A pdb=" N LYS B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 56 removed outlier: 4.512A pdb=" N VAL B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 62 through 74 Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.942A pdb=" N ASN B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 removed outlier: 3.568A pdb=" N VAL B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 removed outlier: 3.541A pdb=" N THR B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 Processing helix chain 'B' and resid 134 through 150 removed outlier: 3.626A pdb=" N ARG B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 163 through 170 removed outlier: 3.583A pdb=" N ASP B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 189 removed outlier: 3.613A pdb=" N GLU B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 Processing helix chain 'B' and resid 215 through 227 removed outlier: 3.577A pdb=" N SER B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 246 through 249 removed outlier: 3.722A pdb=" N SER B 249 " --> pdb=" O PRO B 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 249' Processing helix chain 'B' and resid 252 through 266 Processing helix chain 'B' and resid 274 through 284 removed outlier: 4.000A pdb=" N ASN B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 291 removed outlier: 3.784A pdb=" N LEU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.836A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.642A pdb=" N PHE B 325 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 350 through 362 Processing helix chain 'B' and resid 366 through 384 removed outlier: 3.624A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.560A pdb=" N VAL B 413 " --> pdb=" O GLU B 409 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 441 through 455 Processing helix chain 'B' and resid 461 through 468 Processing helix chain 'B' and resid 469 through 476 removed outlier: 4.000A pdb=" N GLY B 472 " --> pdb=" O PHE B 469 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE B 473 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS B 474 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 499 through 512 Processing helix chain 'B' and resid 516 through 533 Processing helix chain 'B' and resid 533 through 542 Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.702A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'M' and resid 27 through 37 removed outlier: 3.529A pdb=" N ALA M 31 " --> pdb=" O ASN M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 105 through 115 removed outlier: 3.534A pdb=" N ASP M 113 " --> pdb=" O TYR M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 133 removed outlier: 4.336A pdb=" N PHE M 132 " --> pdb=" O ALA M 128 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 42 removed outlier: 3.789A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 95 removed outlier: 3.629A pdb=" N TYR S 80 " --> pdb=" O ASN S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 127 through 141 Processing sheet with id=AA1, first strand: chain 'M' and resid 16 through 18 Processing sheet with id=AA2, first strand: chain 'M' and resid 116 through 117 Processing sheet with id=AA3, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.336A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE S 5 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N TRP S 19 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ARG S 3 " --> pdb=" O TRP S 19 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 118 through 119 709 hydrogen bonds defined for protein. 2076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3810 1.34 - 1.46: 1747 1.46 - 1.57: 6177 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 11822 Sorted by residual: bond pdb=" C PRO B 286 " pdb=" N PRO B 287 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.36e-02 5.41e+03 4.46e+00 bond pdb=" C THR B 245 " pdb=" N PRO B 246 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.08e-02 8.57e+03 2.82e+00 bond pdb=" C VAL A 535 " pdb=" N PRO A 536 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.35e+00 bond pdb=" CA ASP A 473 " pdb=" CB ASP A 473 " ideal model delta sigma weight residual 1.541 1.557 -0.016 1.20e-02 6.94e+03 1.69e+00 bond pdb=" CA MET B 74 " pdb=" CB MET B 74 " ideal model delta sigma weight residual 1.524 1.540 -0.015 1.30e-02 5.92e+03 1.37e+00 ... (remaining 11817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 15603 1.74 - 3.48: 356 3.48 - 5.22: 45 5.22 - 6.96: 14 6.96 - 8.70: 1 Bond angle restraints: 16019 Sorted by residual: angle pdb=" N ILE A 420 " pdb=" CA ILE A 420 " pdb=" C ILE A 420 " ideal model delta sigma weight residual 113.20 109.29 3.91 9.60e-01 1.09e+00 1.66e+01 angle pdb=" C ARG S 53 " pdb=" CA ARG S 53 " pdb=" CB ARG S 53 " ideal model delta sigma weight residual 115.89 110.68 5.21 1.32e+00 5.74e-01 1.56e+01 angle pdb=" CA ASP A 473 " pdb=" CB ASP A 473 " pdb=" CG ASP A 473 " ideal model delta sigma weight residual 112.60 116.31 -3.71 1.00e+00 1.00e+00 1.37e+01 angle pdb=" N ALA B 251 " pdb=" CA ALA B 251 " pdb=" C ALA B 251 " ideal model delta sigma weight residual 114.75 110.10 4.65 1.26e+00 6.30e-01 1.36e+01 angle pdb=" N ASP A 473 " pdb=" CA ASP A 473 " pdb=" CB ASP A 473 " ideal model delta sigma weight residual 114.17 110.28 3.89 1.14e+00 7.69e-01 1.17e+01 ... (remaining 16014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6152 17.92 - 35.85: 806 35.85 - 53.77: 226 53.77 - 71.70: 59 71.70 - 89.62: 25 Dihedral angle restraints: 7268 sinusoidal: 2933 harmonic: 4335 Sorted by residual: dihedral pdb=" CA HIS B 250 " pdb=" C HIS B 250 " pdb=" N ALA B 251 " pdb=" CA ALA B 251 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA LEU B 199 " pdb=" C LEU B 199 " pdb=" N ASN B 200 " pdb=" CA ASN B 200 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ASN A 448 " pdb=" CB ASN A 448 " pdb=" CG ASN A 448 " pdb=" OD1 ASN A 448 " ideal model delta sinusoidal sigma weight residual 120.00 -166.32 -73.68 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 7265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1117 0.032 - 0.063: 577 0.063 - 0.095: 139 0.095 - 0.127: 44 0.127 - 0.158: 4 Chirality restraints: 1881 Sorted by residual: chirality pdb=" CA TRP A 462 " pdb=" N TRP A 462 " pdb=" C TRP A 462 " pdb=" CB TRP A 462 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ASP A 474 " pdb=" N ASP A 474 " pdb=" C ASP A 474 " pdb=" CB ASP A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CB THR S 40 " pdb=" CA THR S 40 " pdb=" OG1 THR S 40 " pdb=" CG2 THR S 40 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 1878 not shown) Planarity restraints: 2041 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 473 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.25e+00 pdb=" C ASP A 473 " -0.050 2.00e-02 2.50e+03 pdb=" O ASP A 473 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP A 474 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 295 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO B 296 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 200 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO B 201 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 201 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 201 " -0.027 5.00e-02 4.00e+02 ... (remaining 2038 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 139 2.66 - 3.22: 10769 3.22 - 3.78: 17726 3.78 - 4.34: 24373 4.34 - 4.90: 40415 Nonbonded interactions: 93422 Sorted by model distance: nonbonded pdb=" O HIS A 531 " pdb=" OE1 GLU B 556 " model vdw 2.102 3.040 nonbonded pdb=" OH TYR M 20 " pdb=" O LEU M 112 " model vdw 2.130 3.040 nonbonded pdb=" OD1 ASP A 417 " pdb=" OG SER A 419 " model vdw 2.223 3.040 nonbonded pdb=" OG SER A 458 " pdb=" NZ LYS A 615 " model vdw 2.262 3.120 nonbonded pdb=" NH2 ARG B 344 " pdb=" O ASP B 553 " model vdw 2.283 3.120 ... (remaining 93417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.040 Find NCS groups from input model: 0.060 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 0.004 0.035 11822 Z= 0.172 Angle : 0.660 8.704 16019 Z= 0.400 Chirality : 0.040 0.158 1881 Planarity : 0.004 0.051 2041 Dihedral : 18.491 89.619 4440 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.31 % Allowed : 30.84 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.22), residues: 1447 helix: 1.21 (0.17), residues: 977 sheet: -0.76 (0.72), residues: 49 loop : -1.01 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 381 TYR 0.016 0.002 TYR A 347 PHE 0.019 0.002 PHE M 93 TRP 0.013 0.002 TRP A 462 HIS 0.005 0.001 HIS S 36 Details of bonding type rmsd covalent geometry : bond 0.00363 (11822) covalent geometry : angle 0.66038 (16019) hydrogen bonds : bond 0.15299 ( 709) hydrogen bonds : angle 4.96337 ( 2076) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 229 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 383 VAL cc_start: 0.8417 (t) cc_final: 0.8150 (p) REVERT: A 423 GLU cc_start: 0.7592 (tt0) cc_final: 0.7356 (tt0) REVERT: B 83 MET cc_start: 0.1296 (mtt) cc_final: 0.1027 (mtt) REVERT: B 131 LYS cc_start: 0.8546 (mtmm) cc_final: 0.8201 (mttp) REVERT: B 133 GLU cc_start: 0.7715 (tp30) cc_final: 0.7341 (tp30) REVERT: B 171 ASP cc_start: 0.7964 (t0) cc_final: 0.7632 (t0) REVERT: B 386 GLN cc_start: 0.8587 (mp10) cc_final: 0.8351 (mp10) REVERT: B 448 MET cc_start: 0.8609 (tpt) cc_final: 0.8241 (tpt) REVERT: B 484 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8028 (tt) outliers start: 4 outliers final: 2 residues processed: 232 average time/residue: 0.6138 time to fit residues: 152.8938 Evaluate side-chains 222 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 219 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 484 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 81 ASN A 105 ASN A 197 ASN A 307 ASN A 325 ASN A 375 ASN A 448 ASN A 467 GLN A 577 GLN A 578 GLN B 99 ASN B 238 GLN B 408 GLN B 435 ASN B 461 ASN B 516 ASN B 579 ASN M 27 ASN M 62 ASN M 72 ASN S 48 ASN S 77 ASN S 92 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.136175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.117013 restraints weight = 15523.553| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.81 r_work: 0.3442 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11822 Z= 0.132 Angle : 0.518 7.285 16019 Z= 0.275 Chirality : 0.039 0.146 1881 Planarity : 0.004 0.047 2041 Dihedral : 4.318 49.819 1586 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.93 % Allowed : 25.75 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.22), residues: 1447 helix: 1.42 (0.17), residues: 989 sheet: -0.18 (0.74), residues: 43 loop : -0.98 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 61 TYR 0.019 0.001 TYR A 347 PHE 0.018 0.001 PHE M 93 TRP 0.019 0.002 TRP A 462 HIS 0.005 0.001 HIS S 46 Details of bonding type rmsd covalent geometry : bond 0.00300 (11822) covalent geometry : angle 0.51784 (16019) hydrogen bonds : bond 0.04420 ( 709) hydrogen bonds : angle 3.90982 ( 2076) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 229 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 323 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: A 383 VAL cc_start: 0.8387 (t) cc_final: 0.8109 (p) REVERT: A 423 GLU cc_start: 0.7601 (tt0) cc_final: 0.7346 (tt0) REVERT: A 615 LYS cc_start: 0.7687 (tttt) cc_final: 0.7450 (ttmt) REVERT: B 131 LYS cc_start: 0.8603 (mtmm) cc_final: 0.8250 (mtmm) REVERT: B 133 GLU cc_start: 0.7709 (tp30) cc_final: 0.7361 (tp30) REVERT: B 171 ASP cc_start: 0.8045 (t0) cc_final: 0.7719 (t0) REVERT: B 348 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7297 (tp-100) REVERT: B 386 GLN cc_start: 0.8479 (mp10) cc_final: 0.7773 (mp10) REVERT: B 484 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7993 (tt) REVERT: S 33 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7335 (mt-10) outliers start: 51 outliers final: 20 residues processed: 264 average time/residue: 0.6000 time to fit residues: 170.5850 Evaluate side-chains 246 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 137 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 84 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 131 optimal weight: 0.0980 chunk 103 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 560 GLN B 408 GLN B 435 ASN B 512 GLN B 579 ASN M 100 ASN S 97 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.132547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113383 restraints weight = 15519.699| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.79 r_work: 0.3397 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11822 Z= 0.208 Angle : 0.569 8.396 16019 Z= 0.299 Chirality : 0.042 0.166 1881 Planarity : 0.004 0.048 2041 Dihedral : 4.474 49.387 1584 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.01 % Allowed : 23.82 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.88 (0.22), residues: 1447 helix: 1.29 (0.16), residues: 989 sheet: -0.05 (0.72), residues: 43 loop : -1.00 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 138 TYR 0.020 0.002 TYR A 347 PHE 0.027 0.002 PHE M 93 TRP 0.017 0.002 TRP A 462 HIS 0.007 0.001 HIS S 46 Details of bonding type rmsd covalent geometry : bond 0.00507 (11822) covalent geometry : angle 0.56945 (16019) hydrogen bonds : bond 0.05396 ( 709) hydrogen bonds : angle 3.97123 ( 2076) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 227 time to evaluate : 0.444 Fit side-chains REVERT: A 272 GLU cc_start: 0.7893 (mp0) cc_final: 0.7618 (mp0) REVERT: A 323 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: A 359 SER cc_start: 0.8042 (OUTLIER) cc_final: 0.7725 (p) REVERT: A 381 ARG cc_start: 0.7695 (ppt170) cc_final: 0.7452 (ppt170) REVERT: A 382 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: A 423 GLU cc_start: 0.7635 (tt0) cc_final: 0.7368 (tt0) REVERT: B 68 LEU cc_start: 0.8196 (mm) cc_final: 0.7960 (mm) REVERT: B 131 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8272 (mttp) REVERT: B 133 GLU cc_start: 0.7791 (tp30) cc_final: 0.7370 (tp30) REVERT: B 152 ASN cc_start: 0.7831 (t0) cc_final: 0.7579 (t0) REVERT: B 171 ASP cc_start: 0.8089 (t0) cc_final: 0.7720 (t0) REVERT: B 295 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: B 354 VAL cc_start: 0.8154 (m) cc_final: 0.7932 (t) REVERT: B 386 GLN cc_start: 0.8479 (mp10) cc_final: 0.8043 (mp10) REVERT: B 484 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8057 (tt) REVERT: S 33 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7318 (mt-10) outliers start: 65 outliers final: 33 residues processed: 269 average time/residue: 0.6177 time to fit residues: 178.8632 Evaluate side-chains 256 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 137 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN B 205 ASN B 350 ASN B 408 GLN B 435 ASN B 512 GLN B 579 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.115574 restraints weight = 15586.672| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.79 r_work: 0.3426 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11822 Z= 0.123 Angle : 0.489 7.031 16019 Z= 0.259 Chirality : 0.038 0.147 1881 Planarity : 0.004 0.045 2041 Dihedral : 4.273 49.531 1584 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.78 % Allowed : 26.75 % Favored : 69.47 % 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: 1.21 (0.22), residues: 1447 helix: 1.53 (0.17), residues: 991 sheet: 0.39 (0.72), residues: 45 loop : -0.90 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 313 TYR 0.016 0.001 TYR A 347 PHE 0.016 0.001 PHE M 93 TRP 0.023 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00283 (11822) covalent geometry : angle 0.48932 (16019) hydrogen bonds : bond 0.04039 ( 709) hydrogen bonds : angle 3.73196 ( 2076) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 225 time to evaluate : 0.312 Fit side-chains REVERT: A 272 GLU cc_start: 0.7887 (mp0) cc_final: 0.7605 (mp0) REVERT: A 323 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: A 381 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7349 (ptt90) REVERT: A 423 GLU cc_start: 0.7636 (tt0) cc_final: 0.7352 (tt0) REVERT: B 131 LYS cc_start: 0.8609 (mtmm) cc_final: 0.8268 (mtmm) REVERT: B 133 GLU cc_start: 0.7756 (tp30) cc_final: 0.7346 (tp30) REVERT: B 171 ASP cc_start: 0.8044 (t0) cc_final: 0.7684 (t0) REVERT: B 354 VAL cc_start: 0.8105 (m) cc_final: 0.7828 (t) REVERT: B 386 GLN cc_start: 0.8464 (mp10) cc_final: 0.8061 (mp10) REVERT: B 467 GLU cc_start: 0.8236 (tt0) cc_final: 0.7997 (tt0) REVERT: B 484 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8063 (tt) REVERT: S 18 LYS cc_start: 0.8915 (mtpp) cc_final: 0.8696 (tptp) REVERT: S 33 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7343 (mt-10) outliers start: 49 outliers final: 28 residues processed: 260 average time/residue: 0.6343 time to fit residues: 177.1814 Evaluate side-chains 255 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 30 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 136 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 86 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 578 GLN B 435 ASN B 512 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.134945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.115781 restraints weight = 15532.467| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.79 r_work: 0.3433 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11822 Z= 0.115 Angle : 0.478 8.043 16019 Z= 0.252 Chirality : 0.038 0.149 1881 Planarity : 0.004 0.044 2041 Dihedral : 4.031 49.246 1582 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.09 % Allowed : 26.83 % Favored : 69.08 % 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: 1.40 (0.22), residues: 1447 helix: 1.66 (0.17), residues: 993 sheet: 0.45 (0.70), residues: 45 loop : -0.78 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 138 TYR 0.017 0.001 TYR A 347 PHE 0.015 0.001 PHE M 93 TRP 0.022 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00260 (11822) covalent geometry : angle 0.47849 (16019) hydrogen bonds : bond 0.03888 ( 709) hydrogen bonds : angle 3.65385 ( 2076) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 225 time to evaluate : 0.450 Fit side-chains REVERT: A 272 GLU cc_start: 0.7878 (mp0) cc_final: 0.7604 (mp0) REVERT: A 381 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7501 (ptt90) REVERT: A 423 GLU cc_start: 0.7629 (tt0) cc_final: 0.7337 (tt0) REVERT: A 516 ARG cc_start: 0.7529 (tpp-160) cc_final: 0.7308 (tpp-160) REVERT: B 131 LYS cc_start: 0.8616 (mtmm) cc_final: 0.8268 (mtmm) REVERT: B 171 ASP cc_start: 0.8035 (t0) cc_final: 0.7677 (t0) REVERT: B 290 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.8088 (t) REVERT: B 354 VAL cc_start: 0.8095 (m) cc_final: 0.7839 (t) REVERT: B 467 GLU cc_start: 0.8244 (tt0) cc_final: 0.8005 (tt0) REVERT: B 484 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8018 (tt) REVERT: S 18 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8700 (tptp) REVERT: S 33 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7329 (mt-10) outliers start: 53 outliers final: 34 residues processed: 262 average time/residue: 0.6303 time to fit residues: 177.7126 Evaluate side-chains 260 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 77 optimal weight: 0.0870 chunk 70 optimal weight: 4.9990 chunk 81 optimal weight: 0.0980 chunk 61 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 63 optimal weight: 0.1980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 292 GLN B 435 ASN B 512 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.135641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.116522 restraints weight = 15483.310| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.79 r_work: 0.3444 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11822 Z= 0.103 Angle : 0.468 7.489 16019 Z= 0.246 Chirality : 0.038 0.145 1881 Planarity : 0.003 0.043 2041 Dihedral : 3.942 49.327 1582 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.62 % Allowed : 27.68 % Favored : 68.70 % 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: 1.59 (0.22), residues: 1447 helix: 1.79 (0.17), residues: 993 sheet: 0.60 (0.71), residues: 45 loop : -0.69 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 138 TYR 0.017 0.001 TYR A 347 PHE 0.013 0.001 PHE M 93 TRP 0.022 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00227 (11822) covalent geometry : angle 0.46785 (16019) hydrogen bonds : bond 0.03611 ( 709) hydrogen bonds : angle 3.57567 ( 2076) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 227 time to evaluate : 0.461 Fit side-chains REVERT: A 272 GLU cc_start: 0.7895 (mp0) cc_final: 0.7630 (mp0) REVERT: A 381 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7571 (ptt90) REVERT: A 382 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: A 423 GLU cc_start: 0.7620 (tt0) cc_final: 0.7326 (tt0) REVERT: A 516 ARG cc_start: 0.7534 (tpp-160) cc_final: 0.7303 (tpp-160) REVERT: B 131 LYS cc_start: 0.8640 (mtmm) cc_final: 0.8292 (mtmm) REVERT: B 133 GLU cc_start: 0.7716 (tp30) cc_final: 0.7337 (tp30) REVERT: B 171 ASP cc_start: 0.8014 (t0) cc_final: 0.7667 (t0) REVERT: B 290 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.8078 (t) REVERT: B 467 GLU cc_start: 0.8243 (tt0) cc_final: 0.8012 (tt0) REVERT: B 484 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8037 (tt) REVERT: S 18 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8691 (tptp) REVERT: S 33 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7324 (mt-10) outliers start: 47 outliers final: 28 residues processed: 260 average time/residue: 0.6566 time to fit residues: 183.3552 Evaluate side-chains 258 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 137 optimal weight: 0.0670 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN B 195 ASN B 435 ASN B 512 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.135414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116280 restraints weight = 15394.121| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.79 r_work: 0.3434 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11822 Z= 0.121 Angle : 0.486 8.219 16019 Z= 0.253 Chirality : 0.038 0.153 1881 Planarity : 0.003 0.043 2041 Dihedral : 3.952 49.286 1582 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.93 % Allowed : 27.53 % Favored : 68.54 % 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: 1.62 (0.22), residues: 1447 helix: 1.81 (0.17), residues: 993 sheet: 0.58 (0.70), residues: 45 loop : -0.66 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 61 TYR 0.018 0.001 TYR A 418 PHE 0.016 0.001 PHE M 93 TRP 0.020 0.001 TRP A 462 HIS 0.003 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00281 (11822) covalent geometry : angle 0.48628 (16019) hydrogen bonds : bond 0.03895 ( 709) hydrogen bonds : angle 3.58739 ( 2076) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 0.399 Fit side-chains REVERT: A 19 ASP cc_start: 0.7794 (m-30) cc_final: 0.7527 (m-30) REVERT: A 191 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7821 (mtp180) REVERT: A 272 GLU cc_start: 0.7899 (mp0) cc_final: 0.7637 (mp0) REVERT: A 341 ARG cc_start: 0.7203 (mtm-85) cc_final: 0.6960 (mtm-85) REVERT: A 381 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7647 (ptt90) REVERT: A 382 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: A 423 GLU cc_start: 0.7613 (tt0) cc_final: 0.7312 (tt0) REVERT: A 516 ARG cc_start: 0.7484 (tpp-160) cc_final: 0.7259 (tpp-160) REVERT: B 131 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8295 (mtmm) REVERT: B 133 GLU cc_start: 0.7728 (tp30) cc_final: 0.7330 (tp30) REVERT: B 171 ASP cc_start: 0.8029 (t0) cc_final: 0.7670 (t0) REVERT: B 290 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.8105 (t) REVERT: B 354 VAL cc_start: 0.8079 (m) cc_final: 0.7835 (t) REVERT: B 467 GLU cc_start: 0.8230 (tt0) cc_final: 0.7999 (tt0) REVERT: B 484 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8034 (tt) REVERT: S 18 LYS cc_start: 0.8903 (mtpp) cc_final: 0.8685 (tptp) REVERT: S 33 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7325 (mt-10) outliers start: 51 outliers final: 34 residues processed: 262 average time/residue: 0.6434 time to fit residues: 181.4436 Evaluate side-chains 262 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 35 optimal weight: 0.4980 chunk 86 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 98 optimal weight: 0.0050 chunk 39 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN B 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.135999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.116909 restraints weight = 15309.702| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.78 r_work: 0.3439 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11822 Z= 0.107 Angle : 0.476 7.826 16019 Z= 0.249 Chirality : 0.038 0.147 1881 Planarity : 0.003 0.043 2041 Dihedral : 3.899 49.202 1582 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.86 % Allowed : 27.99 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.72 (0.22), residues: 1447 helix: 1.88 (0.17), residues: 993 sheet: 0.80 (0.66), residues: 50 loop : -0.64 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 61 TYR 0.017 0.001 TYR A 418 PHE 0.013 0.001 PHE M 93 TRP 0.022 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00241 (11822) covalent geometry : angle 0.47643 (16019) hydrogen bonds : bond 0.03635 ( 709) hydrogen bonds : angle 3.55085 ( 2076) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 0.346 Fit side-chains REVERT: A 19 ASP cc_start: 0.7803 (m-30) cc_final: 0.7527 (m-30) REVERT: A 272 GLU cc_start: 0.7877 (mp0) cc_final: 0.7623 (mp0) REVERT: A 341 ARG cc_start: 0.7181 (mtm-85) cc_final: 0.6941 (mtm-85) REVERT: A 381 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7650 (ptt90) REVERT: A 382 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: A 400 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8009 (p) REVERT: A 423 GLU cc_start: 0.7608 (tt0) cc_final: 0.7304 (tt0) REVERT: A 516 ARG cc_start: 0.7480 (tpp-160) cc_final: 0.7235 (tpp-160) REVERT: B 131 LYS cc_start: 0.8650 (mtmm) cc_final: 0.8293 (mtmm) REVERT: B 171 ASP cc_start: 0.8025 (t0) cc_final: 0.7673 (t0) REVERT: B 354 VAL cc_start: 0.8103 (m) cc_final: 0.7856 (t) REVERT: B 467 GLU cc_start: 0.8238 (tt0) cc_final: 0.8006 (tt0) REVERT: B 484 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8030 (tt) REVERT: S 18 LYS cc_start: 0.8895 (mtpp) cc_final: 0.8678 (tptp) REVERT: S 33 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7338 (mt-10) outliers start: 50 outliers final: 33 residues processed: 257 average time/residue: 0.6530 time to fit residues: 180.5408 Evaluate side-chains 261 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 131 optimal weight: 0.6980 chunk 85 optimal weight: 0.0470 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 89 optimal weight: 0.0870 chunk 117 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 chunk 39 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN B 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.136478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117435 restraints weight = 15368.596| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.78 r_work: 0.3446 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11822 Z= 0.102 Angle : 0.479 8.733 16019 Z= 0.249 Chirality : 0.038 0.217 1881 Planarity : 0.003 0.042 2041 Dihedral : 3.853 49.164 1582 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.39 % Allowed : 28.22 % Favored : 68.39 % 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: 1.82 (0.22), residues: 1447 helix: 1.95 (0.17), residues: 994 sheet: 0.90 (0.67), residues: 50 loop : -0.60 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 61 TYR 0.018 0.001 TYR A 418 PHE 0.012 0.001 PHE M 93 TRP 0.023 0.001 TRP A 462 HIS 0.002 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00224 (11822) covalent geometry : angle 0.47863 (16019) hydrogen bonds : bond 0.03494 ( 709) hydrogen bonds : angle 3.51841 ( 2076) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.391 Fit side-chains REVERT: A 19 ASP cc_start: 0.7799 (m-30) cc_final: 0.7524 (m-30) REVERT: A 272 GLU cc_start: 0.7910 (mp0) cc_final: 0.7653 (mp0) REVERT: A 341 ARG cc_start: 0.7179 (mtm-85) cc_final: 0.6931 (mtm-85) REVERT: A 381 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7627 (ptt90) REVERT: A 400 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8081 (p) REVERT: A 423 GLU cc_start: 0.7607 (tt0) cc_final: 0.7303 (tt0) REVERT: A 516 ARG cc_start: 0.7477 (tpp-160) cc_final: 0.7237 (tpp-160) REVERT: B 131 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8296 (mtmm) REVERT: B 133 GLU cc_start: 0.7682 (tp30) cc_final: 0.7303 (tp30) REVERT: B 171 ASP cc_start: 0.8029 (t0) cc_final: 0.7695 (t0) REVERT: B 354 VAL cc_start: 0.8098 (m) cc_final: 0.7844 (t) REVERT: B 467 GLU cc_start: 0.8232 (tt0) cc_final: 0.7999 (tt0) REVERT: B 484 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8022 (tt) REVERT: S 18 LYS cc_start: 0.8884 (mtpp) cc_final: 0.8670 (tptp) REVERT: S 33 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7381 (mt-10) outliers start: 44 outliers final: 32 residues processed: 256 average time/residue: 0.6527 time to fit residues: 179.9774 Evaluate side-chains 262 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 578 GLN B 212 ASN B 435 ASN B 512 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116218 restraints weight = 15505.345| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.79 r_work: 0.3428 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11822 Z= 0.125 Angle : 0.506 10.784 16019 Z= 0.261 Chirality : 0.039 0.279 1881 Planarity : 0.003 0.042 2041 Dihedral : 3.924 49.043 1582 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.08 % Allowed : 28.53 % Favored : 68.39 % 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: 1.76 (0.22), residues: 1447 helix: 1.90 (0.16), residues: 994 sheet: 0.82 (0.66), residues: 50 loop : -0.62 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 61 TYR 0.019 0.001 TYR A 418 PHE 0.015 0.001 PHE M 93 TRP 0.018 0.001 TRP A 462 HIS 0.003 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00292 (11822) covalent geometry : angle 0.50634 (16019) hydrogen bonds : bond 0.03914 ( 709) hydrogen bonds : angle 3.57658 ( 2076) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 0.536 Fit side-chains REVERT: A 272 GLU cc_start: 0.7904 (mp0) cc_final: 0.7646 (mp0) REVERT: A 341 ARG cc_start: 0.7200 (mtm-85) cc_final: 0.6954 (mtm-85) REVERT: A 400 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.8129 (p) REVERT: A 423 GLU cc_start: 0.7625 (tt0) cc_final: 0.7325 (tt0) REVERT: A 516 ARG cc_start: 0.7499 (tpp-160) cc_final: 0.7249 (tpp-160) REVERT: B 131 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8311 (mtmm) REVERT: B 133 GLU cc_start: 0.7699 (tp30) cc_final: 0.7321 (tp30) REVERT: B 171 ASP cc_start: 0.8038 (t0) cc_final: 0.7690 (t0) REVERT: B 354 VAL cc_start: 0.8108 (m) cc_final: 0.7879 (t) REVERT: B 467 GLU cc_start: 0.8227 (tt0) cc_final: 0.7993 (tt0) REVERT: B 484 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8036 (tt) REVERT: S 18 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8695 (tptp) REVERT: S 33 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: S 117 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8289 (mtm) outliers start: 40 outliers final: 32 residues processed: 251 average time/residue: 0.6711 time to fit residues: 180.9733 Evaluate side-chains 261 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 117 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 66 optimal weight: 0.0010 chunk 129 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN B 212 ASN B 512 GLN B 575 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.116657 restraints weight = 15430.301| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.79 r_work: 0.3439 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11822 Z= 0.112 Angle : 0.492 10.873 16019 Z= 0.254 Chirality : 0.039 0.282 1881 Planarity : 0.003 0.042 2041 Dihedral : 3.898 49.000 1582 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.24 % Allowed : 28.53 % Favored : 68.23 % 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: 1.84 (0.22), residues: 1447 helix: 1.96 (0.16), residues: 994 sheet: 0.92 (0.67), residues: 50 loop : -0.61 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 61 TYR 0.019 0.001 TYR A 418 PHE 0.013 0.001 PHE M 93 TRP 0.021 0.002 TRP A 462 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00257 (11822) covalent geometry : angle 0.49227 (16019) hydrogen bonds : bond 0.03686 ( 709) hydrogen bonds : angle 3.53970 ( 2076) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4916.72 seconds wall clock time: 84 minutes 24.70 seconds (5064.70 seconds total)