Starting phenix.real_space_refine on Tue Aug 4 23:49:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21vm_68037/08_2026/21vm_68037.cif Found real_map, /net/cci-nas-00/data/ceres_data/21vm_68037/08_2026/21vm_68037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21vm_68037/08_2026/21vm_68037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21vm_68037/08_2026/21vm_68037.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21vm_68037/08_2026/21vm_68037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21vm_68037/08_2026/21vm_68037.map" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= -0.014 sd= 0.975 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 4823 2.51 5 N 1223 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7564 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3509 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 11, 'TRANS': 443} Chain breaks: 1 Chain: "C" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1110 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "D" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1728 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 9, 'TRANS': 203} Chain: "A" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1217 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Time building chain proxies: 1.28, per 1000 atoms: 0.17 Number of scatterers: 7564 At special positions: 0 Unit cell: (146.3, 169.4, 209, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1492 8.00 N 1223 7.00 C 4823 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 355.5 milliseconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1804 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 14 sheets defined 23.8% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 46 through 54 removed outlier: 4.128A pdb=" N LEU B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 52 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 70 removed outlier: 3.570A pdb=" N ASP B 70 " --> pdb=" O LYS B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 136 removed outlier: 4.182A pdb=" N ILE B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 removed outlier: 3.597A pdb=" N ASP B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 217 removed outlier: 3.542A pdb=" N GLU B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS B 217 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.550A pdb=" N ASP B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 264 through 273 removed outlier: 4.418A pdb=" N VAL B 268 " --> pdb=" O PRO B 264 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 306 Processing helix chain 'B' and resid 330 through 358 removed outlier: 4.076A pdb=" N VAL B 334 " --> pdb=" O TYR B 330 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 348 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 358 " --> pdb=" O GLN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 379 removed outlier: 4.065A pdb=" N LEU B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 4.022A pdb=" N VAL B 383 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN B 386 " --> pdb=" O GLN B 382 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 387 " --> pdb=" O VAL B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'C' and resid 2 through 6 removed outlier: 3.575A pdb=" N PHE C 6 " --> pdb=" O LEU C 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 27 removed outlier: 3.660A pdb=" N ILE D 15 " --> pdb=" O TYR D 11 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 26 " --> pdb=" O PHE D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 105 through 111 removed outlier: 3.558A pdb=" N GLN D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 16 removed outlier: 3.775A pdb=" N VAL A 16 " --> pdb=" O PRO A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 4.099A pdb=" N LEU A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 44 removed outlier: 7.802A pdb=" N GLY B 81 " --> pdb=" O PRO B 28 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 30 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 222 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N SER B 199 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N SER B 224 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR B 221 " --> pdb=" O CYS B 251 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA B 253 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N PHE B 223 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N TRP B 255 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR B 225 " --> pdb=" O TRP B 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 145 through 146 removed outlier: 3.792A pdb=" N THR B 154 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 155 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 110 through 115 removed outlier: 3.500A pdb=" N TYR B 100 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 103 " --> pdb=" O ASP B 166 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 105 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 164 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AA5, first strand: chain 'B' and resid 393 through 396 removed outlier: 3.772A pdb=" N GLU B 393 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 409 through 411 removed outlier: 3.727A pdb=" N THR B 409 " --> pdb=" O GLU B 434 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU B 434 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 432 " --> pdb=" O TYR B 411 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 54 through 58 removed outlier: 7.133A pdb=" N ALA C 67 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU C 121 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE C 71 " --> pdb=" O CYS C 117 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N HIS C 114 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ASP C 105 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N HIS C 116 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU C 103 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL C 118 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 100 " --> pdb=" O ASP C 89 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP C 89 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 11.597A pdb=" N SER C 102 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 13.725A pdb=" N LEU C 87 " --> pdb=" O SER C 102 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 87 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG C 19 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASP C 89 " --> pdb=" O ARG C 17 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG C 17 " --> pdb=" O ASP C 89 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE C 91 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLN C 15 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N ILE C 93 " --> pdb=" O THR C 13 " (cutoff:3.500A) removed outlier: 13.934A pdb=" N THR C 13 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR C 12 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C 45 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 37 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 35 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 31 through 33 removed outlier: 3.511A pdb=" N TYR D 32 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU D 46 " --> pdb=" O PHE D 85 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE D 85 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU D 48 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N MET D 83 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE D 50 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLU D 81 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER D 52 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR D 78 " --> pdb=" O PHE D 146 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N PHE D 143 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA D 121 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR D 145 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER D 117 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 31 through 33 removed outlier: 3.511A pdb=" N TYR D 32 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU D 46 " --> pdb=" O PHE D 85 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE D 85 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU D 48 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N MET D 83 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE D 50 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLU D 81 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER D 52 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR D 78 " --> pdb=" O PHE D 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 151 through 156 removed outlier: 5.089A pdb=" N PHE D 70 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA D 69 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE D 65 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER D 71 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 65 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 196 " --> pdb=" O PHE D 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 129 through 131 removed outlier: 3.610A pdb=" N THR D 129 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 164 through 169 removed outlier: 3.645A pdb=" N MET D 165 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 184 " --> pdb=" O MET D 165 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 17 through 20 removed outlier: 3.504A pdb=" N PHE A 94 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 130 " --> pdb=" O GLN A 113 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 63 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 43 through 47 removed outlier: 3.539A pdb=" N ALA A 56 " --> pdb=" O ASN A 44 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 672 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: 0.99 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2444 1.34 - 1.46: 1669 1.46 - 1.58: 3554 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 7716 Sorted by residual: bond pdb=" N ASP B 420 " pdb=" CA ASP B 420 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.27e-02 6.20e+03 4.52e+00 bond pdb=" N THR B 37 " pdb=" CA THR B 37 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.12e+00 bond pdb=" CB ASN A 148 " pdb=" CG ASN A 148 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.71e+00 bond pdb=" CA ASN A 148 " pdb=" CB ASN A 148 " ideal model delta sigma weight residual 1.532 1.551 -0.019 1.36e-02 5.41e+03 1.96e+00 bond pdb=" CB PRO B 277 " pdb=" CG PRO B 277 " ideal model delta sigma weight residual 1.492 1.559 -0.067 5.00e-02 4.00e+02 1.80e+00 ... (remaining 7711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 10037 1.44 - 2.88: 381 2.88 - 4.31: 62 4.31 - 5.75: 11 5.75 - 7.19: 6 Bond angle restraints: 10497 Sorted by residual: angle pdb=" N ASP B 420 " pdb=" CA ASP B 420 " pdb=" C ASP B 420 " ideal model delta sigma weight residual 114.75 109.09 5.66 1.26e+00 6.30e-01 2.02e+01 angle pdb=" CA ASP B 420 " pdb=" CB ASP B 420 " pdb=" CG ASP B 420 " ideal model delta sigma weight residual 112.60 115.98 -3.38 1.00e+00 1.00e+00 1.14e+01 angle pdb=" C GLU D 161 " pdb=" N ALA D 162 " pdb=" CA ALA D 162 " ideal model delta sigma weight residual 122.56 117.50 5.06 1.50e+00 4.44e-01 1.14e+01 angle pdb=" N MET B 133 " pdb=" CA MET B 133 " pdb=" C MET B 133 " ideal model delta sigma weight residual 113.19 109.20 3.99 1.19e+00 7.06e-01 1.13e+01 angle pdb=" C ALA D 103 " pdb=" N ASP D 104 " pdb=" CA ASP D 104 " ideal model delta sigma weight residual 121.54 127.94 -6.40 1.91e+00 2.74e-01 1.12e+01 ... (remaining 10492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3996 18.00 - 35.99: 455 35.99 - 53.99: 93 53.99 - 71.98: 10 71.98 - 89.98: 9 Dihedral angle restraints: 4563 sinusoidal: 1749 harmonic: 2814 Sorted by residual: dihedral pdb=" CA MET B 245 " pdb=" C MET B 245 " pdb=" N GLY B 246 " pdb=" CA GLY B 246 " ideal model delta harmonic sigma weight residual -180.00 -161.47 -18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ARG D 171 " pdb=" C ARG D 171 " pdb=" N ASP D 172 " pdb=" CA ASP D 172 " ideal model delta harmonic sigma weight residual 180.00 -161.89 -18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA LEU D 73 " pdb=" C LEU D 73 " pdb=" N MET D 74 " pdb=" CA MET D 74 " ideal model delta harmonic sigma weight residual 180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 4560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 949 0.046 - 0.092: 188 0.092 - 0.139: 74 0.139 - 0.185: 4 0.185 - 0.231: 1 Chirality restraints: 1216 Sorted by residual: chirality pdb=" CA PRO B 277 " pdb=" N PRO B 277 " pdb=" C PRO B 277 " pdb=" CB PRO B 277 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB VAL B 128 " pdb=" CA VAL B 128 " pdb=" CG1 VAL B 128 " pdb=" CG2 VAL B 128 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA ILE B 20 " pdb=" N ILE B 20 " pdb=" C ILE B 20 " pdb=" CB ILE B 20 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 1213 not shown) Planarity restraints: 1339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 276 " -0.058 5.00e-02 4.00e+02 8.75e-02 1.22e+01 pdb=" N PRO B 277 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 277 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 277 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 148 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.97e+00 pdb=" C ASN A 148 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN A 148 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 149 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 73 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 74 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.022 5.00e-02 4.00e+02 ... (remaining 1336 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 808 2.75 - 3.29: 6731 3.29 - 3.82: 10514 3.82 - 4.36: 11123 4.36 - 4.90: 20835 Nonbonded interactions: 50011 Sorted by model distance: nonbonded pdb=" OH TYR A 97 " pdb=" OE1 GLU A 99 " model vdw 2.210 3.040 nonbonded pdb=" N GLU D 6 " pdb=" OE1 GLU D 6 " model vdw 2.247 3.120 nonbonded pdb=" O THR D 14 " pdb=" ND2 ASN D 18 " model vdw 2.296 3.120 nonbonded pdb=" OG SER B 397 " pdb=" OE1 GLU B 399 " model vdw 2.304 3.040 nonbonded pdb=" O ARG B 373 " pdb=" OG1 THR B 377 " model vdw 2.313 3.040 ... (remaining 50006 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.330 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.810 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.003 0.067 7716 Z= 0.170 Angle : 0.664 7.191 10497 Z= 0.392 Chirality : 0.044 0.231 1216 Planarity : 0.004 0.087 1339 Dihedral : 15.883 89.978 2759 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.91 % Favored : 92.57 % Rotamer: Outliers : 0.36 % Allowed : 21.39 % Favored : 78.25 % 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: -1.25 (0.25), residues: 955 helix: 1.33 (0.38), residues: 179 sheet: 0.27 (0.35), residues: 228 loop : -2.21 (0.22), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 25 TYR 0.014 0.001 TYR B 333 PHE 0.014 0.001 PHE B 170 TRP 0.008 0.001 TRP C 106 HIS 0.003 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 ( 7716) covalent geometry : angle 0.66355 / 0.39 (10497) hydrogen bonds : bond 0.28012 / 18.82 ( 228) hydrogen bonds : angle 7.64489 / 5.29 ( 672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.206 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 112 average time/residue: 0.0725 time to fit residues: 11.2988 Evaluate side-chains 107 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 120 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.109617 restraints weight = 15993.075| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.52 r_work: 0.3041 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7716 Z= 0.151 Angle : 0.609 7.033 10497 Z= 0.337 Chirality : 0.046 0.237 1216 Planarity : 0.004 0.082 1339 Dihedral : 5.145 40.885 1047 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.33 % Favored : 92.25 % Rotamer: Outliers : 2.52 % Allowed : 19.59 % Favored : 77.88 % 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 (0.26), residues: 955 helix: 1.52 (0.39), residues: 184 sheet: 0.39 (0.36), residues: 223 loop : -2.25 (0.23), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 25 TYR 0.014 0.001 TYR C 21 PHE 0.010 0.001 PHE D 143 TRP 0.008 0.001 TRP C 106 HIS 0.004 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 7716) covalent geometry : angle 0.60906 / 0.34 (10497) hydrogen bonds : bond 0.05602 / 3.70 ( 228) hydrogen bonds : angle 5.24719 / 3.64 ( 672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.247 Fit side-chains REVERT: B 144 PHE cc_start: 0.7454 (t80) cc_final: 0.6841 (t80) REVERT: B 170 PHE cc_start: 0.6114 (OUTLIER) cc_final: 0.5431 (p90) REVERT: B 434 GLU cc_start: 0.5726 (mm-30) cc_final: 0.5158 (mm-30) REVERT: D 128 ASN cc_start: 0.9364 (m110) cc_final: 0.9154 (m-40) REVERT: D 173 ASP cc_start: 0.7309 (p0) cc_final: 0.7081 (p0) REVERT: A 157 THR cc_start: 0.8765 (p) cc_final: 0.8459 (p) outliers start: 21 outliers final: 12 residues processed: 137 average time/residue: 0.0598 time to fit residues: 11.7769 Evaluate side-chains 129 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain A residue 32 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 217 HIS C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.105047 restraints weight = 15775.172| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.50 r_work: 0.3002 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7716 Z= 0.220 Angle : 0.704 7.705 10497 Z= 0.390 Chirality : 0.048 0.231 1216 Planarity : 0.005 0.075 1339 Dihedral : 5.531 38.055 1044 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.06 % Favored : 91.52 % Rotamer: Outliers : 3.49 % Allowed : 19.83 % Favored : 76.68 % 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: -1.54 (0.26), residues: 955 helix: 1.12 (0.38), residues: 188 sheet: 0.22 (0.38), residues: 212 loop : -2.47 (0.22), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 90 TYR 0.016 0.002 TYR D 63 PHE 0.017 0.002 PHE B 113 TRP 0.009 0.001 TRP C 106 HIS 0.006 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 ( 7716) covalent geometry : angle 0.70378 / 0.39 (10497) hydrogen bonds : bond 0.06890 / 4.56 ( 228) hydrogen bonds : angle 5.23127 / 3.61 ( 672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.167 Fit side-chains REVERT: B 132 GLU cc_start: 0.8225 (tt0) cc_final: 0.7976 (pp20) REVERT: B 170 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.5522 (p90) REVERT: B 434 GLU cc_start: 0.5894 (mm-30) cc_final: 0.4177 (pt0) REVERT: D 12 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6669 (pt0) REVERT: D 126 GLN cc_start: 0.8828 (pp30) cc_final: 0.8204 (pp30) REVERT: D 128 ASN cc_start: 0.9381 (m-40) cc_final: 0.8951 (m-40) REVERT: A 148 ASN cc_start: 0.7956 (t0) cc_final: 0.7552 (t0) outliers start: 29 outliers final: 19 residues processed: 129 average time/residue: 0.0588 time to fit residues: 10.8682 Evaluate side-chains 125 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 70 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.105949 restraints weight = 15968.774| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.52 r_work: 0.2995 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7716 Z= 0.198 Angle : 0.663 7.257 10497 Z= 0.368 Chirality : 0.047 0.226 1216 Planarity : 0.004 0.063 1339 Dihedral : 5.453 37.270 1044 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.06 % Favored : 91.52 % Rotamer: Outliers : 4.21 % Allowed : 19.11 % Favored : 76.68 % 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: -1.63 (0.26), residues: 955 helix: 1.10 (0.38), residues: 189 sheet: 0.20 (0.38), residues: 214 loop : -2.58 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 90 TYR 0.014 0.002 TYR C 21 PHE 0.014 0.002 PHE B 113 TRP 0.010 0.001 TRP B 255 HIS 0.005 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 ( 7716) covalent geometry : angle 0.66317 / 0.37 (10497) hydrogen bonds : bond 0.06114 / 4.03 ( 228) hydrogen bonds : angle 5.03497 / 3.47 ( 672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.254 Fit side-chains REVERT: B 132 GLU cc_start: 0.8235 (tt0) cc_final: 0.8001 (pp20) REVERT: B 144 PHE cc_start: 0.7705 (t80) cc_final: 0.7401 (t80) REVERT: B 170 PHE cc_start: 0.6862 (OUTLIER) cc_final: 0.5495 (p90) REVERT: B 209 ASP cc_start: 0.8600 (m-30) cc_final: 0.8307 (m-30) REVERT: B 434 GLU cc_start: 0.5938 (mm-30) cc_final: 0.4715 (mm-30) REVERT: D 12 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6942 (tt0) REVERT: A 148 ASN cc_start: 0.7893 (t0) cc_final: 0.7452 (t0) outliers start: 35 outliers final: 26 residues processed: 136 average time/residue: 0.0631 time to fit residues: 12.5589 Evaluate side-chains 136 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 114 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 9 optimal weight: 0.0970 chunk 34 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 86 optimal weight: 0.2980 chunk 32 optimal weight: 0.1980 chunk 89 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 overall best weight: 1.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.131067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.108840 restraints weight = 15901.757| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.55 r_work: 0.3058 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7716 Z= 0.119 Angle : 0.553 6.083 10497 Z= 0.306 Chirality : 0.044 0.161 1216 Planarity : 0.003 0.040 1339 Dihedral : 4.929 34.799 1044 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.54 % Favored : 92.15 % Rotamer: Outliers : 3.61 % Allowed : 20.43 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.26), residues: 955 helix: 1.50 (0.39), residues: 188 sheet: 0.13 (0.35), residues: 241 loop : -2.61 (0.23), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 25 TYR 0.011 0.001 TYR B 333 PHE 0.010 0.001 PHE B 113 TRP 0.011 0.001 TRP B 255 HIS 0.002 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 ( 7716) covalent geometry : angle 0.55254 / 0.31 (10497) hydrogen bonds : bond 0.04180 / 2.76 ( 228) hydrogen bonds : angle 4.65493 / 3.20 ( 672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.210 Fit side-chains REVERT: B 170 PHE cc_start: 0.6649 (OUTLIER) cc_final: 0.5264 (p90) REVERT: B 434 GLU cc_start: 0.5800 (mm-30) cc_final: 0.4090 (mm-30) REVERT: D 12 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6861 (tt0) REVERT: D 126 GLN cc_start: 0.8696 (pp30) cc_final: 0.8317 (pp30) REVERT: D 139 ARG cc_start: 0.9362 (mtt180) cc_final: 0.9114 (mtt-85) REVERT: D 173 ASP cc_start: 0.7432 (p0) cc_final: 0.7172 (p0) REVERT: A 1 MET cc_start: 0.8336 (mtm) cc_final: 0.8060 (mtm) REVERT: A 148 ASN cc_start: 0.7939 (t0) cc_final: 0.7459 (t0) outliers start: 30 outliers final: 20 residues processed: 138 average time/residue: 0.0648 time to fit residues: 12.7091 Evaluate side-chains 140 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 114 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 18 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 57 optimal weight: 0.0370 chunk 91 optimal weight: 9.9990 overall best weight: 2.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.108010 restraints weight = 16024.612| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.58 r_work: 0.3044 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7716 Z= 0.130 Angle : 0.568 7.293 10497 Z= 0.312 Chirality : 0.044 0.169 1216 Planarity : 0.003 0.041 1339 Dihedral : 4.860 33.772 1044 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.96 % Favored : 91.73 % Rotamer: Outliers : 4.21 % Allowed : 19.95 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.46 (0.26), residues: 955 helix: 1.47 (0.39), residues: 188 sheet: 0.13 (0.35), residues: 241 loop : -2.59 (0.23), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 25 TYR 0.011 0.001 TYR B 333 PHE 0.009 0.001 PHE B 113 TRP 0.008 0.001 TRP B 255 HIS 0.002 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 7716) covalent geometry : angle 0.56846 / 0.31 (10497) hydrogen bonds : bond 0.04530 / 2.99 ( 228) hydrogen bonds : angle 4.60610 / 3.16 ( 672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.229 Fit side-chains REVERT: B 144 PHE cc_start: 0.7535 (t80) cc_final: 0.7186 (t80) REVERT: B 170 PHE cc_start: 0.6710 (OUTLIER) cc_final: 0.5243 (p90) REVERT: B 209 ASP cc_start: 0.8590 (m-30) cc_final: 0.8292 (m-30) REVERT: B 434 GLU cc_start: 0.5762 (mm-30) cc_final: 0.3851 (mm-30) REVERT: D 12 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6882 (tt0) REVERT: D 173 ASP cc_start: 0.7462 (p0) cc_final: 0.7201 (p0) REVERT: A 1 MET cc_start: 0.8420 (mtm) cc_final: 0.8156 (mtm) REVERT: A 148 ASN cc_start: 0.8151 (t0) cc_final: 0.7624 (t0) outliers start: 35 outliers final: 29 residues processed: 138 average time/residue: 0.0623 time to fit residues: 12.2735 Evaluate side-chains 141 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 59 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.129215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.106936 restraints weight = 15822.949| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.53 r_work: 0.3023 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 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 : 0.003 0.033 7716 Z= 0.155 Angle : 0.604 6.702 10497 Z= 0.332 Chirality : 0.045 0.175 1216 Planarity : 0.004 0.042 1339 Dihedral : 5.014 33.686 1044 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.06 % Favored : 91.62 % Rotamer: Outliers : 4.45 % Allowed : 19.59 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.26), residues: 955 helix: 1.34 (0.39), residues: 189 sheet: 0.14 (0.35), residues: 231 loop : -2.60 (0.23), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 90 TYR 0.011 0.001 TYR B 333 PHE 0.010 0.001 PHE B 349 TRP 0.008 0.001 TRP C 106 HIS 0.003 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 7716) covalent geometry : angle 0.60351 / 0.33 (10497) hydrogen bonds : bond 0.05163 / 3.42 ( 228) hydrogen bonds : angle 4.70588 / 3.24 ( 672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.277 Fit side-chains REVERT: B 144 PHE cc_start: 0.7562 (t80) cc_final: 0.7223 (t80) REVERT: B 170 PHE cc_start: 0.6852 (OUTLIER) cc_final: 0.5390 (p90) REVERT: B 209 ASP cc_start: 0.8570 (m-30) cc_final: 0.8275 (m-30) REVERT: B 434 GLU cc_start: 0.5841 (mm-30) cc_final: 0.4074 (mm-30) REVERT: D 12 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6916 (tt0) outliers start: 37 outliers final: 32 residues processed: 135 average time/residue: 0.0625 time to fit residues: 12.1615 Evaluate side-chains 145 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 7 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.106237 restraints weight = 16114.553| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.55 r_work: 0.3014 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7716 Z= 0.165 Angle : 0.616 6.860 10497 Z= 0.340 Chirality : 0.045 0.176 1216 Planarity : 0.004 0.042 1339 Dihedral : 4.983 20.631 1042 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.17 % Favored : 91.52 % Rotamer: Outliers : 4.57 % Allowed : 19.23 % Favored : 76.20 % 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: -1.57 (0.26), residues: 955 helix: 1.28 (0.39), residues: 189 sheet: 0.09 (0.35), residues: 238 loop : -2.64 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 90 TYR 0.011 0.001 TYR C 21 PHE 0.010 0.001 PHE B 349 TRP 0.008 0.001 TRP B 255 HIS 0.003 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 ( 7716) covalent geometry : angle 0.61638 / 0.34 (10497) hydrogen bonds : bond 0.05354 / 3.54 ( 228) hydrogen bonds : angle 4.76260 / 3.28 ( 672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.303 Fit side-chains REVERT: B 144 PHE cc_start: 0.7616 (t80) cc_final: 0.7308 (t80) REVERT: B 170 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.5449 (p90) REVERT: B 209 ASP cc_start: 0.8602 (m-30) cc_final: 0.8316 (m-30) REVERT: B 434 GLU cc_start: 0.5876 (mm-30) cc_final: 0.4100 (mm-30) REVERT: D 12 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6912 (tt0) REVERT: A 148 ASN cc_start: 0.7565 (t0) cc_final: 0.7097 (t0) outliers start: 38 outliers final: 33 residues processed: 134 average time/residue: 0.0567 time to fit residues: 11.0241 Evaluate side-chains 143 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 82 optimal weight: 0.0570 chunk 48 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 overall best weight: 6.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.125732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.103352 restraints weight = 16048.473| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.53 r_work: 0.2969 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 7716 Z= 0.249 Angle : 0.723 7.761 10497 Z= 0.398 Chirality : 0.049 0.181 1216 Planarity : 0.004 0.046 1339 Dihedral : 5.479 22.203 1042 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.21 % Favored : 90.47 % Rotamer: Outliers : 4.45 % Allowed : 19.47 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.26), residues: 955 helix: 0.97 (0.38), residues: 188 sheet: 0.07 (0.36), residues: 222 loop : -2.67 (0.22), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 171 TYR 0.014 0.002 TYR C 21 PHE 0.016 0.002 PHE B 143 TRP 0.008 0.001 TRP C 106 HIS 0.005 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.25 ( 7716) covalent geometry : angle 0.72279 / 0.40 (10497) hydrogen bonds : bond 0.06891 / 4.57 ( 228) hydrogen bonds : angle 5.00726 / 3.47 ( 672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.178 Fit side-chains REVERT: B 144 PHE cc_start: 0.7614 (t80) cc_final: 0.7294 (t80) REVERT: B 170 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.5749 (p90) REVERT: B 209 ASP cc_start: 0.8600 (m-30) cc_final: 0.8319 (m-30) REVERT: B 434 GLU cc_start: 0.5956 (mm-30) cc_final: 0.4261 (mm-30) REVERT: C 111 PHE cc_start: 0.8919 (m-10) cc_final: 0.8679 (m-80) REVERT: D 12 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6727 (pt0) REVERT: A 148 ASN cc_start: 0.7804 (t0) cc_final: 0.7395 (t0) outliers start: 37 outliers final: 34 residues processed: 131 average time/residue: 0.0632 time to fit residues: 11.7306 Evaluate side-chains 140 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 68 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.128986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.106679 restraints weight = 15944.212| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.56 r_work: 0.3021 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7716 Z= 0.147 Angle : 0.602 6.592 10497 Z= 0.332 Chirality : 0.045 0.170 1216 Planarity : 0.004 0.046 1339 Dihedral : 5.058 20.332 1042 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.64 % Favored : 92.04 % Rotamer: Outliers : 3.97 % Allowed : 19.71 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.26), residues: 955 helix: 1.27 (0.39), residues: 188 sheet: 0.10 (0.36), residues: 223 loop : -2.62 (0.23), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 90 TYR 0.012 0.001 TYR B 333 PHE 0.018 0.001 PHE B 143 TRP 0.010 0.001 TRP B 255 HIS 0.003 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 ( 7716) covalent geometry : angle 0.60182 / 0.33 (10497) hydrogen bonds : bond 0.04951 / 3.27 ( 228) hydrogen bonds : angle 4.69510 / 3.25 ( 672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.303 Fit side-chains REVERT: B 144 PHE cc_start: 0.7670 (t80) cc_final: 0.7366 (t80) REVERT: B 170 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.5585 (p90) REVERT: B 209 ASP cc_start: 0.8613 (m-30) cc_final: 0.8332 (m-30) REVERT: B 434 GLU cc_start: 0.5884 (mm-30) cc_final: 0.4181 (mm-30) REVERT: D 12 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6904 (tt0) REVERT: A 148 ASN cc_start: 0.7642 (t0) cc_final: 0.7175 (t0) outliers start: 33 outliers final: 31 residues processed: 131 average time/residue: 0.0605 time to fit residues: 11.3944 Evaluate side-chains 142 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 74 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.105751 restraints weight = 15865.087| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.54 r_work: 0.3007 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7716 Z= 0.169 Angle : 0.626 7.083 10497 Z= 0.345 Chirality : 0.046 0.177 1216 Planarity : 0.004 0.050 1339 Dihedral : 5.099 20.653 1042 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.38 % Favored : 91.31 % Rotamer: Outliers : 3.97 % Allowed : 19.95 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.26), residues: 955 helix: 1.20 (0.38), residues: 188 sheet: -0.05 (0.35), residues: 233 loop : -2.58 (0.23), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 90 TYR 0.011 0.001 TYR C 21 PHE 0.011 0.001 PHE B 349 TRP 0.008 0.001 TRP C 106 HIS 0.003 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 7716) covalent geometry : angle 0.62611 / 0.34 (10497) hydrogen bonds : bond 0.05414 / 3.58 ( 228) hydrogen bonds : angle 4.71819 / 3.27 ( 672) =============================================================================== Job complete usr+sys time: 2576.72 seconds wall clock time: 44 minutes 26.06 seconds (2666.06 seconds total)