Starting phenix.real_space_refine on Thu Jul 2 23:49:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t0v_40947/07_2026/8t0v_40947_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t0v_40947/07_2026/8t0v_40947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t0v_40947/07_2026/8t0v_40947_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t0v_40947/07_2026/8t0v_40947_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t0v_40947/07_2026/8t0v_40947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t0v_40947/07_2026/8t0v_40947.map" } resolution = 3.0 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= -0.000 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Co 1 6.85 5 P 2 5.49 5 S 58 5.16 5 C 6944 2.51 5 N 1838 2.21 5 O 2049 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10892 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1971 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 9, 'TRANS': 245} Chain: "C" Number of atoms: 4066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4066 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 18, 'TRANS': 498} Chain: "D" Number of atoms: 4066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4066 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 18, 'TRANS': 498} Chain: "A" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 655 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 91 Unusual residues: {'B12': 1} Classifications: {'undetermined': 1} Unsupported chir.volume_sign: {'cros': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'5AD': 1, 'X6I': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.76, per 1000 atoms: 0.25 Number of scatterers: 10892 At special positions: 0 Unit cell: (87.318, 89.474, 156.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Co 1 26.99 S 58 16.00 P 2 15.00 O 2049 8.00 N 1838 7.00 C 6944 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 420.7 milliseconds 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 7 sheets defined 56.2% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 45 through 60 Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.672A pdb=" N SER B 93 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE B 94 " --> pdb=" O TYR B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 94' Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 191 through 193 No H-bonds generated for 'chain 'B' and resid 191 through 193' Processing helix chain 'B' and resid 194 through 211 removed outlier: 3.598A pdb=" N LYS B 198 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 234 Processing helix chain 'B' and resid 244 through 259 Processing helix chain 'B' and resid 263 through 267 removed outlier: 4.061A pdb=" N GLY B 266 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 33 removed outlier: 3.834A pdb=" N LYS C 15 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 31 " --> pdb=" O THR C 27 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 47 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.741A pdb=" N TYR C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 113 through 147 removed outlier: 3.820A pdb=" N ASP C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS C 127 " --> pdb=" O ASP C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 177 removed outlier: 4.359A pdb=" N VAL C 168 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 229 Processing helix chain 'C' and resid 242 through 253 Processing helix chain 'C' and resid 261 through 269 removed outlier: 4.335A pdb=" N GLY C 265 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 291 removed outlier: 3.593A pdb=" N PHE C 281 " --> pdb=" O MET C 277 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.574A pdb=" N TYR C 301 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 328 removed outlier: 3.747A pdb=" N VAL C 314 " --> pdb=" O LYS C 310 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 328 " --> pdb=" O PHE C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 349 through 365 removed outlier: 3.570A pdb=" N MET C 360 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.547A pdb=" N VAL C 396 " --> pdb=" O MET C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 436 removed outlier: 3.571A pdb=" N TYR C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 442 removed outlier: 3.619A pdb=" N GLU C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 442' Processing helix chain 'C' and resid 449 through 473 removed outlier: 3.710A pdb=" N LYS C 460 " --> pdb=" O ASN C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 480 Processing helix chain 'C' and resid 495 through 497 No H-bonds generated for 'chain 'C' and resid 495 through 497' Processing helix chain 'C' and resid 508 through 516 removed outlier: 4.156A pdb=" N ASP C 512 " --> pdb=" O ASN C 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 33 removed outlier: 3.854A pdb=" N VAL D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 47 removed outlier: 3.721A pdb=" N GLU D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 72 through 75 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.931A pdb=" N TYR D 80 " --> pdb=" O GLY D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 113 through 147 removed outlier: 4.256A pdb=" N ASP D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 177 removed outlier: 3.548A pdb=" N VAL D 168 " --> pdb=" O TYR D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 229 Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 261 through 269 removed outlier: 4.311A pdb=" N GLY D 265 " --> pdb=" O ASP D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 291 removed outlier: 3.991A pdb=" N PHE D 281 " --> pdb=" O MET D 277 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 311 through 328 removed outlier: 3.903A pdb=" N LEU D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 328 " --> pdb=" O PHE D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 349 through 365 removed outlier: 3.557A pdb=" N ALA D 356 " --> pdb=" O LEU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 401 Processing helix chain 'D' and resid 418 through 436 Processing helix chain 'D' and resid 449 through 473 removed outlier: 3.515A pdb=" N GLU D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 480 Processing helix chain 'D' and resid 495 through 499 removed outlier: 3.691A pdb=" N VAL D 499 " --> pdb=" O LEU D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 517 removed outlier: 4.525A pdb=" N ASP D 512 " --> pdb=" O ASN D 508 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU D 513 " --> pdb=" O PRO D 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 60 removed outlier: 3.603A pdb=" N VAL A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 65 through 71 removed outlier: 5.507A pdb=" N VAL B 66 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR B 82 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS B 33 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N THR A 39 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N THR B 39 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS A 33 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 83 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N TYR A 82 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL A 66 " --> pdb=" O TYR A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 158 through 162 removed outlier: 6.768A pdb=" N VAL B 121 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N TYR B 161 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL B 123 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL B 122 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU B 185 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 124 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'C' and resid 153 through 158 removed outlier: 6.466A pdb=" N ILE C 181 " --> pdb=" O CYS C 235 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N TYR C 237 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N VAL C 183 " --> pdb=" O TYR C 237 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU C 234 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU C 259 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASN C 236 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N MET C 258 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C 294 " --> pdb=" O GLY C 336 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY C 338 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR C 296 " --> pdb=" O GLY C 338 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ALA C 340 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LYS C 371 " --> pdb=" O MET C 335 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU C 337 " --> pdb=" O LYS C 371 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N MET C 373 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N HIS C 339 " --> pdb=" O MET C 373 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR C 372 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU C 153 " --> pdb=" O HIS C 405 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 443 through 445 removed outlier: 3.555A pdb=" N TYR C 444 " --> pdb=" O TYR D 444 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=AA7, first strand: chain 'D' and resid 335 through 336 removed outlier: 6.750A pdb=" N ILE D 294 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET D 258 " --> pdb=" O ASN D 295 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU D 234 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N LEU D 259 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASN D 236 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE D 181 " --> pdb=" O CYS D 235 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N TYR D 237 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N HIS D 339 " --> pdb=" O MET D 373 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1617 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: 1.97 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.29: 1872 1.29 - 1.44: 2697 1.44 - 1.59: 6405 1.59 - 1.75: 3 1.75 - 1.90: 113 Bond restraints: 11090 Sorted by residual: bond pdb=" C7 X6I D 602 " pdb=" N2 X6I D 602 " ideal model delta sigma weight residual 1.263 1.450 -0.187 2.00e-02 2.50e+03 8.73e+01 bond pdb=" C2 X6I D 602 " pdb=" N1 X6I D 602 " ideal model delta sigma weight residual 1.322 1.483 -0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" C4 B12 B 301 " pdb=" N21 B12 B 301 " ideal model delta sigma weight residual 1.416 1.260 0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" C3 X6I D 602 " pdb=" C4 X6I D 602 " ideal model delta sigma weight residual 1.383 1.524 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C14 B12 B 301 " pdb=" N23 B12 B 301 " ideal model delta sigma weight residual 1.416 1.294 0.122 2.00e-02 2.50e+03 3.73e+01 ... (remaining 11085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.58: 14914 4.58 - 9.17: 71 9.17 - 13.75: 19 13.75 - 18.33: 5 18.33 - 22.92: 1 Bond angle restraints: 15010 Sorted by residual: angle pdb=" C4 B12 B 301 " pdb=" N21 B12 B 301 " pdb="CO B12 B 301 " ideal model delta sigma weight residual 109.50 132.42 -22.92 3.00e+00 1.11e-01 5.84e+01 angle pdb=" CA PRO C 92 " pdb=" N PRO C 92 " pdb=" CD PRO C 92 " ideal model delta sigma weight residual 112.00 102.09 9.91 1.40e+00 5.10e-01 5.01e+01 angle pdb=" C30 B12 B 301 " pdb=" C3 B12 B 301 " pdb=" C4 B12 B 301 " ideal model delta sigma weight residual 109.47 127.11 -17.64 3.00e+00 1.11e-01 3.46e+01 angle pdb=" C18 B12 B 301 " pdb=" C19 B12 B 301 " pdb=" N24 B12 B 301 " ideal model delta sigma weight residual 120.00 102.37 17.63 3.00e+00 1.11e-01 3.45e+01 angle pdb=" C14 B12 B 301 " pdb=" N23 B12 B 301 " pdb="CO B12 B 301 " ideal model delta sigma weight residual 109.50 126.93 -17.43 3.00e+00 1.11e-01 3.37e+01 ... (remaining 15005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 6385 35.02 - 70.04: 328 70.04 - 105.06: 22 105.06 - 140.08: 1 140.08 - 175.10: 2 Dihedral angle restraints: 6738 sinusoidal: 2780 harmonic: 3958 Sorted by residual: dihedral pdb=" C2R B12 B 301 " pdb=" C3R B12 B 301 " pdb=" O2 B12 B 301 " pdb=" P B12 B 301 " ideal model delta sinusoidal sigma weight residual 121.90 -63.00 -175.10 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C2P B12 B 301 " pdb=" O3 B12 B 301 " pdb=" P B12 B 301 " pdb=" O4 B12 B 301 " ideal model delta sinusoidal sigma weight residual -64.57 85.12 -149.70 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" C38 B12 B 301 " pdb=" C37 B12 B 301 " pdb=" C7 B12 B 301 " pdb=" C8 B12 B 301 " ideal model delta sinusoidal sigma weight residual -59.07 66.47 -125.54 1 2.00e+01 2.50e-03 3.80e+01 ... (remaining 6735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.028: 1694 1.028 - 2.056: 0 2.056 - 3.083: 2 3.083 - 4.111: 0 4.111 - 5.139: 2 Chirality restraints: 1698 Sorted by residual: chirality pdb=" C12 B12 B 301 " pdb=" C11 B12 B 301 " pdb=" C46 B12 B 301 " pdb=" C47 B12 B 301 " both_signs ideal model delta sigma weight residual False -2.64 2.50 -5.14 2.00e-01 2.50e+01 6.60e+02 chirality pdb=" N24 B12 B 301 " pdb=" C16 B12 B 301 " pdb=" C19 B12 B 301 " pdb="CO B12 B 301 " both_signs ideal model delta sigma weight residual False -2.93 1.49 -4.42 2.00e-01 2.50e+01 4.89e+02 chirality pdb=" N21 B12 B 301 " pdb=" C1 B12 B 301 " pdb=" C4 B12 B 301 " pdb="CO B12 B 301 " both_signs ideal model delta sigma weight residual False -3.05 -0.04 -3.00 2.00e-01 2.50e+01 2.26e+02 ... (remaining 1695 not shown) Planarity restraints: 1935 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 B12 B 301 " -0.132 2.00e-02 2.50e+03 2.12e-01 4.50e+02 pdb=" C18 B12 B 301 " -0.123 2.00e-02 2.50e+03 pdb=" C19 B12 B 301 " 0.367 2.00e-02 2.50e+03 pdb=" N24 B12 B 301 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 B12 B 301 " 0.140 2.00e-02 2.50e+03 1.07e-01 1.42e+02 pdb=" C11 B12 B 301 " 0.094 2.00e-02 2.50e+03 pdb=" C12 B12 B 301 " -0.112 2.00e-02 2.50e+03 pdb=" C9 B12 B 301 " -0.125 2.00e-02 2.50e+03 pdb=" N23 B12 B 301 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C35 B12 B 301 " -0.110 2.00e-02 2.50e+03 8.72e-02 1.14e+02 pdb=" C4 B12 B 301 " 0.097 2.00e-02 2.50e+03 pdb=" C5 B12 B 301 " 0.005 2.00e-02 2.50e+03 pdb=" C6 B12 B 301 " 0.034 2.00e-02 2.50e+03 pdb=" C7 B12 B 301 " 0.094 2.00e-02 2.50e+03 pdb=" N22 B12 B 301 " -0.120 2.00e-02 2.50e+03 ... (remaining 1932 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 97 2.60 - 3.17: 9249 3.17 - 3.75: 16244 3.75 - 4.32: 24597 4.32 - 4.90: 41162 Nonbonded interactions: 91349 Sorted by model distance: nonbonded pdb=" NH2 ARG D 185 " pdb=" O SER D 239 " model vdw 2.020 3.120 nonbonded pdb=" O4 B12 B 301 " pdb=" O7R B12 B 301 " model vdw 2.028 3.040 nonbonded pdb=" OD1 ASN D 162 " pdb=" OG1 THR D 201 " model vdw 2.059 3.040 nonbonded pdb=" OG1 THR C 296 " pdb=" OE1 GLU C 298 " model vdw 2.066 3.040 nonbonded pdb=" OG SER C 4 " pdb=" OE1 GLU C 363 " model vdw 2.066 3.040 ... (remaining 91344 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and resid 2 through 518) } 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: 1.070 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.470 Find NCS groups from input model: 0.160 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:9.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.006 0.214 11091 Z= 0.307 Angle : 0.833 22.917 15010 Z= 0.337 Chirality : 0.198 5.139 1698 Planarity : 0.007 0.212 1935 Dihedral : 19.059 175.098 4204 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 24.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.20 % Allowed : 25.04 % Favored : 70.75 % 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: 0.22 (0.24), residues: 1365 helix: 0.43 (0.20), residues: 716 sheet: -0.56 (0.41), residues: 180 loop : 0.29 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.000 ARG D 185 TYR 0.008 0.001 TYR D 237 PHE 0.009 0.001 PHE C 341 TRP 0.004 0.001 TRP C 10 HIS 0.003 0.001 HIS C 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.31 (11090) covalent geometry : angle 0.83263 / 0.34 (15010) hydrogen bonds : bond 0.26076 / 17.20 ( 552) hydrogen bonds : angle 7.92683 / 5.66 ( 1617) Misc. bond : bond 0.21399 / 11.26 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 0.476 Fit side-chains REVERT: D 184 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7922 (mm) outliers start: 48 outliers final: 42 residues processed: 184 average time/residue: 0.5373 time to fit residues: 107.1696 Evaluate side-chains 181 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 512 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 387 HIS Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 430 LYS Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 94 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN C 295 ASN C 357 GLN ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN D 480 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.171541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.139724 restraints weight = 10800.742| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.24 r_work: 0.3229 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 11091 Z= 0.180 Angle : 0.847 32.221 15010 Z= 0.365 Chirality : 0.079 2.473 1698 Planarity : 0.005 0.054 1935 Dihedral : 10.617 128.516 1650 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.99 % Allowed : 21.80 % Favored : 73.20 % 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: 0.77 (0.23), residues: 1365 helix: 1.16 (0.19), residues: 735 sheet: -0.69 (0.39), residues: 188 loop : 0.19 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 233 TYR 0.016 0.002 TYR D 237 PHE 0.019 0.001 PHE C 341 TRP 0.003 0.001 TRP D 10 HIS 0.004 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (11090) covalent geometry : angle 0.84667 / 0.37 (15010) hydrogen bonds : bond 0.06206 / 4.08 ( 552) hydrogen bonds : angle 4.98475 / 3.57 ( 1617) Misc. bond : bond 0.07912 / 4.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 159 time to evaluate : 0.383 Fit side-chains REVERT: B 74 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7482 (ttpp) REVERT: B 100 GLU cc_start: 0.5994 (mt-10) cc_final: 0.5772 (mt-10) REVERT: B 119 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.6333 (ptt90) REVERT: B 200 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6124 (mt) REVERT: C 80 TYR cc_start: 0.7831 (m-10) cc_final: 0.7597 (m-80) REVERT: C 127 LYS cc_start: 0.8007 (mptt) cc_final: 0.7500 (tmtt) REVERT: C 514 MET cc_start: 0.8517 (mtp) cc_final: 0.8238 (mtt) REVERT: D 260 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8577 (t0) REVERT: D 427 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7993 (pt0) REVERT: D 443 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8295 (mp) outliers start: 57 outliers final: 18 residues processed: 199 average time/residue: 0.5477 time to fit residues: 117.6580 Evaluate side-chains 166 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 37 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 107 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 126 optimal weight: 0.0370 chunk 38 optimal weight: 4.9990 chunk 108 optimal weight: 0.1980 chunk 1 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.0464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 247 HIS ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN D 236 ASN D 321 ASN A 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.182192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.155714 restraints weight = 10758.105| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 0.90 r_work: 0.3372 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 11091 Z= 0.163 Angle : 0.815 30.444 15010 Z= 0.348 Chirality : 0.075 2.386 1698 Planarity : 0.004 0.059 1935 Dihedral : 9.345 108.561 1588 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.25 % Allowed : 22.59 % Favored : 72.15 % 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: 1.01 (0.23), residues: 1365 helix: 1.47 (0.19), residues: 734 sheet: -0.70 (0.39), residues: 186 loop : 0.13 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 139 TYR 0.015 0.001 TYR C 237 PHE 0.018 0.001 PHE C 341 TRP 0.004 0.001 TRP D 10 HIS 0.004 0.001 HIS D 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (11090) covalent geometry : angle 0.81457 / 0.35 (15010) hydrogen bonds : bond 0.05476 / 3.60 ( 552) hydrogen bonds : angle 4.64225 / 3.33 ( 1617) Misc. bond : bond 0.07355 / 3.87 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 151 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: B 74 LYS cc_start: 0.8009 (pttp) cc_final: 0.7521 (tttp) REVERT: B 119 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.6424 (ptt90) REVERT: B 200 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.5976 (mt) REVERT: B 208 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6770 (mm-30) REVERT: B 224 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6679 (mtm180) REVERT: C 5 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6971 (mttt) REVERT: C 18 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: C 80 TYR cc_start: 0.7804 (m-10) cc_final: 0.7542 (m-80) REVERT: C 127 LYS cc_start: 0.7882 (mptt) cc_final: 0.7434 (tmtt) REVERT: C 192 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7428 (mp) REVERT: D 202 GLU cc_start: 0.5998 (OUTLIER) cc_final: 0.5770 (pm20) REVERT: D 427 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: D 443 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8272 (mp) REVERT: D 494 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7495 (mtpp) REVERT: A 35 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.8027 (tm-30) outliers start: 60 outliers final: 22 residues processed: 189 average time/residue: 0.5735 time to fit residues: 116.4841 Evaluate side-chains 176 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 37 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 40 optimal weight: 0.1980 chunk 60 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN D 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.179541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.142847 restraints weight = 10895.505| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.41 r_work: 0.3308 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 11091 Z= 0.133 Angle : 0.785 30.394 15010 Z= 0.332 Chirality : 0.074 2.379 1698 Planarity : 0.004 0.059 1935 Dihedral : 8.781 99.241 1580 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.73 % Allowed : 22.94 % Favored : 72.33 % 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 (0.23), residues: 1365 helix: 1.67 (0.19), residues: 734 sheet: -0.64 (0.39), residues: 186 loop : 0.15 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 488 TYR 0.012 0.001 TYR C 237 PHE 0.016 0.001 PHE C 341 TRP 0.004 0.001 TRP D 10 HIS 0.005 0.001 HIS D 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (11090) covalent geometry : angle 0.78478 / 0.33 (15010) hydrogen bonds : bond 0.04682 / 3.08 ( 552) hydrogen bonds : angle 4.45006 / 3.19 ( 1617) Misc. bond : bond 0.09809 / 5.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 151 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 LYS cc_start: 0.8077 (pttp) cc_final: 0.7481 (tttp) REVERT: B 111 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6803 (pt0) REVERT: B 119 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.6332 (ptt90) REVERT: B 200 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5931 (mt) REVERT: B 208 GLU cc_start: 0.7184 (tt0) cc_final: 0.6814 (tp30) REVERT: B 224 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6576 (mtm180) REVERT: C 5 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7097 (mttt) REVERT: C 18 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: C 127 LYS cc_start: 0.7734 (mptt) cc_final: 0.7255 (tmtt) REVERT: C 192 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7424 (mp) REVERT: D 202 GLU cc_start: 0.5932 (OUTLIER) cc_final: 0.5657 (pm20) REVERT: D 427 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7988 (pt0) REVERT: D 494 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7613 (mtpp) outliers start: 54 outliers final: 24 residues processed: 188 average time/residue: 0.5414 time to fit residues: 109.3798 Evaluate side-chains 178 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 494 LYS Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain A residue 37 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 109 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.177046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.140053 restraints weight = 10860.663| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.46 r_work: 0.3241 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11091 Z= 0.196 Angle : 0.841 30.652 15010 Z= 0.360 Chirality : 0.076 2.391 1698 Planarity : 0.005 0.061 1935 Dihedral : 8.758 97.597 1578 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.82 % Allowed : 23.38 % Favored : 71.80 % 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: 0.97 (0.23), residues: 1365 helix: 1.46 (0.19), residues: 734 sheet: -0.59 (0.40), residues: 177 loop : -0.02 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 139 TYR 0.017 0.002 TYR C 237 PHE 0.019 0.002 PHE C 341 TRP 0.004 0.001 TRP D 10 HIS 0.006 0.002 HIS D 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (11090) covalent geometry : angle 0.84124 / 0.36 (15010) hydrogen bonds : bond 0.05612 / 3.70 ( 552) hydrogen bonds : angle 4.51110 / 3.22 ( 1617) Misc. bond : bond 0.03810 / 2.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 153 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 LYS cc_start: 0.8132 (pttp) cc_final: 0.7485 (tttp) REVERT: B 111 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6741 (pt0) REVERT: B 119 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6379 (ptt90) REVERT: B 200 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.5932 (mt) REVERT: B 208 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6810 (tp30) REVERT: B 224 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6567 (mtm180) REVERT: C 5 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7037 (mttt) REVERT: C 18 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: C 127 LYS cc_start: 0.7749 (mptt) cc_final: 0.7285 (tmtt) REVERT: D 202 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5836 (pm20) REVERT: D 280 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: D 427 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7990 (pt0) REVERT: A 74 LYS cc_start: 0.8227 (pttt) cc_final: 0.7903 (tttt) outliers start: 55 outliers final: 25 residues processed: 190 average time/residue: 0.5022 time to fit residues: 103.0016 Evaluate side-chains 181 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 387 HIS Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 55 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 25 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 106 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN C 435 ASN A 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.187406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.159512 restraints weight = 10619.234| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 0.94 r_work: 0.3354 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11091 Z= 0.169 Angle : 0.817 30.581 15010 Z= 0.348 Chirality : 0.075 2.390 1698 Planarity : 0.004 0.061 1935 Dihedral : 8.635 93.394 1578 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.17 % Allowed : 22.77 % Favored : 72.07 % 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: 0.99 (0.23), residues: 1365 helix: 1.49 (0.19), residues: 734 sheet: -0.65 (0.39), residues: 177 loop : -0.04 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 139 TYR 0.015 0.001 TYR C 237 PHE 0.018 0.001 PHE C 341 TRP 0.004 0.001 TRP D 10 HIS 0.005 0.001 HIS D 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (11090) covalent geometry : angle 0.81700 / 0.35 (15010) hydrogen bonds : bond 0.05149 / 3.39 ( 552) hydrogen bonds : angle 4.42090 / 3.16 ( 1617) Misc. bond : bond 0.04867 / 2.56 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 149 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 LYS cc_start: 0.8016 (pttp) cc_final: 0.7452 (tttp) REVERT: B 111 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6710 (pt0) REVERT: B 119 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6533 (ptt90) REVERT: B 200 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.5898 (mt) REVERT: B 208 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6842 (tp30) REVERT: B 224 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6488 (mtm180) REVERT: C 5 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6876 (mttt) REVERT: C 18 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6950 (tm-30) REVERT: C 127 LYS cc_start: 0.7776 (mptt) cc_final: 0.7298 (tmtt) REVERT: D 29 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7699 (mttm) REVERT: D 427 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7914 (pt0) REVERT: A 74 LYS cc_start: 0.8118 (pttt) cc_final: 0.7900 (tttt) outliers start: 59 outliers final: 28 residues processed: 193 average time/residue: 0.5215 time to fit residues: 108.3789 Evaluate side-chains 179 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain A residue 37 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 50 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 75 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN A 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.185989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.157620 restraints weight = 10616.124| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 0.95 r_work: 0.3397 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11091 Z= 0.160 Angle : 0.808 30.619 15010 Z= 0.344 Chirality : 0.075 2.388 1698 Planarity : 0.004 0.060 1935 Dihedral : 8.551 96.938 1578 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.47 % Allowed : 23.91 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.23), residues: 1365 helix: 1.54 (0.19), residues: 734 sheet: -0.63 (0.39), residues: 177 loop : -0.04 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 139 TYR 0.016 0.001 TYR C 237 PHE 0.017 0.001 PHE C 341 TRP 0.004 0.001 TRP D 10 HIS 0.005 0.001 HIS D 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (11090) covalent geometry : angle 0.80832 / 0.34 (15010) hydrogen bonds : bond 0.04968 / 3.27 ( 552) hydrogen bonds : angle 4.36741 / 3.13 ( 1617) Misc. bond : bond 0.05473 / 2.88 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 LYS cc_start: 0.8037 (pttp) cc_final: 0.7520 (tttp) REVERT: B 111 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6664 (pt0) REVERT: B 119 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6535 (ptt90) REVERT: B 171 GLU cc_start: 0.6216 (tp30) cc_final: 0.5624 (mp0) REVERT: B 200 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.5970 (mt) REVERT: B 208 GLU cc_start: 0.7127 (tt0) cc_final: 0.6834 (tp30) REVERT: B 224 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6394 (mtm180) REVERT: C 5 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7037 (mttt) REVERT: C 18 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7126 (tm-30) REVERT: C 127 LYS cc_start: 0.7825 (mptt) cc_final: 0.7383 (tmtt) REVERT: C 217 MET cc_start: 0.8089 (tpt) cc_final: 0.7819 (mmm) REVERT: D 280 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: D 427 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7948 (pt0) outliers start: 51 outliers final: 27 residues processed: 184 average time/residue: 0.5186 time to fit residues: 103.1616 Evaluate side-chains 179 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain A residue 37 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN A 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.183494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.153868 restraints weight = 10660.395| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.20 r_work: 0.3322 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11091 Z= 0.163 Angle : 0.811 30.677 15010 Z= 0.345 Chirality : 0.075 2.388 1698 Planarity : 0.004 0.060 1935 Dihedral : 8.512 108.642 1577 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.12 % Allowed : 24.17 % Favored : 71.72 % 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 (0.23), residues: 1365 helix: 1.55 (0.19), residues: 734 sheet: -0.66 (0.39), residues: 177 loop : -0.04 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 139 TYR 0.016 0.001 TYR C 237 PHE 0.017 0.001 PHE C 341 TRP 0.004 0.001 TRP D 10 HIS 0.006 0.001 HIS D 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (11090) covalent geometry : angle 0.81080 / 0.35 (15010) hydrogen bonds : bond 0.05009 / 3.29 ( 552) hydrogen bonds : angle 4.34768 / 3.11 ( 1617) Misc. bond : bond 0.05057 / 2.66 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: B 74 LYS cc_start: 0.8073 (pttp) cc_final: 0.7464 (tttp) REVERT: B 111 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6705 (pt0) REVERT: B 119 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.6404 (ptt90) REVERT: B 200 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.5885 (mt) REVERT: B 208 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6826 (tp30) REVERT: B 224 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6383 (mtm180) REVERT: C 5 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7050 (mttt) REVERT: C 18 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: C 80 TYR cc_start: 0.7654 (m-10) cc_final: 0.7371 (m-80) REVERT: C 127 LYS cc_start: 0.7750 (mptt) cc_final: 0.7271 (tmtt) REVERT: C 217 MET cc_start: 0.7989 (tpt) cc_final: 0.7737 (mmm) REVERT: D 140 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.5794 (mp0) REVERT: D 280 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7734 (pt0) REVERT: D 427 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7962 (pt0) REVERT: A 90 ASP cc_start: 0.7838 (t0) cc_final: 0.7579 (t0) outliers start: 47 outliers final: 32 residues processed: 183 average time/residue: 0.5697 time to fit residues: 112.2802 Evaluate side-chains 186 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 387 HIS Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 55 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 55 optimal weight: 0.0570 chunk 127 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN A 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.186630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.160660 restraints weight = 10614.267| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 0.88 r_work: 0.3464 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11091 Z= 0.140 Angle : 0.798 30.567 15010 Z= 0.339 Chirality : 0.074 2.391 1698 Planarity : 0.004 0.060 1935 Dihedral : 8.349 111.014 1577 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.77 % Allowed : 24.61 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.23), residues: 1365 helix: 1.68 (0.19), residues: 734 sheet: -0.62 (0.39), residues: 177 loop : 0.01 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 185 TYR 0.019 0.001 TYR C 237 PHE 0.016 0.001 PHE D 341 TRP 0.004 0.001 TRP D 10 HIS 0.005 0.001 HIS D 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (11090) covalent geometry : angle 0.79841 / 0.34 (15010) hydrogen bonds : bond 0.04590 / 3.02 ( 552) hydrogen bonds : angle 4.27858 / 3.07 ( 1617) Misc. bond : bond 0.06755 / 3.56 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: B 74 LYS cc_start: 0.8031 (pttp) cc_final: 0.7585 (tttp) REVERT: B 111 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6731 (pt0) REVERT: B 119 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6533 (ptt90) REVERT: B 171 GLU cc_start: 0.6294 (tp30) cc_final: 0.5601 (mp0) REVERT: B 200 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6041 (mt) REVERT: B 208 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6888 (tp30) REVERT: B 224 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6404 (mtm180) REVERT: C 5 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7049 (mttt) REVERT: C 18 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: C 80 TYR cc_start: 0.7723 (m-10) cc_final: 0.7415 (m-80) REVERT: C 127 LYS cc_start: 0.7834 (mptt) cc_final: 0.7425 (tmtt) REVERT: D 140 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.5856 (mp0) REVERT: D 280 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7616 (pt0) REVERT: D 427 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7942 (pt0) REVERT: A 90 ASP cc_start: 0.7878 (t0) cc_final: 0.7662 (t0) outliers start: 43 outliers final: 27 residues processed: 183 average time/residue: 0.5349 time to fit residues: 105.6820 Evaluate side-chains 185 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain A residue 37 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 81 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 0.0670 chunk 28 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.182551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.158480 restraints weight = 10702.354| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 0.94 r_work: 0.3400 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11091 Z= 0.152 Angle : 0.811 30.666 15010 Z= 0.345 Chirality : 0.074 2.391 1698 Planarity : 0.004 0.060 1935 Dihedral : 8.180 114.857 1577 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.24 % Allowed : 25.83 % Favored : 70.93 % 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: 1.17 (0.23), residues: 1365 helix: 1.67 (0.19), residues: 734 sheet: -0.58 (0.39), residues: 177 loop : 0.01 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 139 TYR 0.020 0.001 TYR C 237 PHE 0.016 0.001 PHE C 341 TRP 0.004 0.001 TRP D 10 HIS 0.006 0.001 HIS D 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (11090) covalent geometry : angle 0.81076 / 0.34 (15010) hydrogen bonds : bond 0.04755 / 3.13 ( 552) hydrogen bonds : angle 4.28308 / 3.08 ( 1617) Misc. bond : bond 0.05833 / 3.07 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: B 74 LYS cc_start: 0.8077 (pttp) cc_final: 0.7535 (tttp) REVERT: B 111 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6860 (pt0) REVERT: B 119 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6488 (ptt90) REVERT: B 124 VAL cc_start: 0.7282 (t) cc_final: 0.7072 (p) REVERT: B 171 GLU cc_start: 0.6325 (tp30) cc_final: 0.5666 (mp0) REVERT: B 200 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5948 (mt) REVERT: B 208 GLU cc_start: 0.6984 (tt0) cc_final: 0.6728 (tp30) REVERT: B 224 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6293 (mtm180) REVERT: C 5 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7076 (mttt) REVERT: C 18 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: C 80 TYR cc_start: 0.7709 (m-10) cc_final: 0.7422 (m-80) REVERT: C 111 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.5616 (tpt) REVERT: C 127 LYS cc_start: 0.7763 (mptt) cc_final: 0.7334 (tmtt) REVERT: D 140 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.5791 (mp0) REVERT: D 280 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7665 (pt0) REVERT: D 427 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: A 21 ARG cc_start: 0.6870 (mtp-110) cc_final: 0.6661 (mtm110) REVERT: A 90 ASP cc_start: 0.7865 (t0) cc_final: 0.7585 (t0) outliers start: 37 outliers final: 27 residues processed: 178 average time/residue: 0.5700 time to fit residues: 109.2407 Evaluate side-chains 184 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain A residue 37 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 131 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.197851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.176438 restraints weight = 10356.540| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 0.88 r_work: 0.3469 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11091 Z= 0.135 Angle : 0.786 30.580 15010 Z= 0.333 Chirality : 0.073 2.390 1698 Planarity : 0.004 0.060 1935 Dihedral : 8.181 117.025 1577 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.98 % Allowed : 25.83 % Favored : 71.19 % 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: 1.31 (0.23), residues: 1365 helix: 1.78 (0.19), residues: 734 sheet: -0.53 (0.39), residues: 178 loop : 0.08 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 139 TYR 0.020 0.001 TYR C 237 PHE 0.016 0.001 PHE D 341 TRP 0.004 0.001 TRP D 10 HIS 0.005 0.001 HIS D 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (11090) covalent geometry : angle 0.78600 / 0.33 (15010) hydrogen bonds : bond 0.04384 / 2.89 ( 552) hydrogen bonds : angle 4.22098 / 3.04 ( 1617) Misc. bond : bond 0.06358 / 3.35 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3768.49 seconds wall clock time: 64 minutes 57.13 seconds (3897.13 seconds total)