Starting phenix.real_space_refine on Sun Oct 25 01:57:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xby_66714/10_2026/9xby_66714.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xby_66714/10_2026/9xby_66714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xby_66714/10_2026/9xby_66714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xby_66714/10_2026/9xby_66714.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xby_66714/10_2026/9xby_66714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xby_66714/10_2026/9xby_66714.map" } resolution = 3.9 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= 0.002 sd= 0.029 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 48 5.16 5 C 9374 2.51 5 N 2592 2.21 5 O 2939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14953 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6179 Classifications: {'peptide': 782} Link IDs: {'PTRANS': 29, 'TRANS': 752} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2752 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 11, 'TRANS': 354} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1440 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 10, 'TRANS': 179} Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1761 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 5, 'TRANS': 84} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2119 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 7, 'TRANS': 263} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 3.09, per 1000 atoms: 0.21 Number of scatterers: 14953 At special positions: 0 Unit cell: (126.336, 133.104, 148.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2939 8.00 N 2592 7.00 C 9374 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: 1.12 Conformation dependent library (CDL) restraints added in 582.9 milliseconds 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3520 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 22 sheets defined 30.7% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.961A pdb=" N MET A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 107 through 117 Processing helix chain 'A' and resid 129 through 145 removed outlier: 3.621A pdb=" N SER A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 144 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.851A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 233 removed outlier: 3.946A pdb=" N ARG A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.513A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.723A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.584A pdb=" N ASP A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.698A pdb=" N GLU A 650 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 removed outlier: 4.236A pdb=" N TYR A 686 " --> pdb=" O ASP A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'C' and resid 29 through 34 removed outlier: 4.076A pdb=" N ARG C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.954A pdb=" N ALA C 79 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 115 through 128 removed outlier: 3.500A pdb=" N GLN C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 214 removed outlier: 3.566A pdb=" N MET C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.834A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 83 removed outlier: 3.967A pdb=" N TYR D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 removed outlier: 3.761A pdb=" N ALA D 90 " --> pdb=" O PRO D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.646A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.727A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 removed outlier: 4.633A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 56 Processing helix chain 'F' and resid 62 through 86 removed outlier: 3.953A pdb=" N MET F 83 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 108 Processing helix chain 'F' and resid 110 through 122 Processing helix chain 'F' and resid 124 through 149 Processing helix chain 'F' and resid 153 through 160 Processing helix chain 'F' and resid 190 through 209 removed outlier: 3.754A pdb=" N GLU F 194 " --> pdb=" O ASP F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 219 removed outlier: 3.644A pdb=" N HIS F 219 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 228 removed outlier: 4.161A pdb=" N LEU F 226 " --> pdb=" O GLN F 223 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY F 228 " --> pdb=" O ALA F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 249 removed outlier: 3.957A pdb=" N GLN F 245 " --> pdb=" O GLY F 241 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ALA F 246 " --> pdb=" O ILE F 242 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR F 249 " --> pdb=" O GLN F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 420 removed outlier: 4.087A pdb=" N ARG F 404 " --> pdb=" O MET F 400 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 5.765A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 98 removed outlier: 7.294A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 5.477A pdb=" N ILE A 254 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 256 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 260 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 271 removed outlier: 7.342A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 343 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 271 removed outlier: 7.342A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355 removed outlier: 4.150A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 427 removed outlier: 3.932A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 671 through 674 removed outlier: 4.770A pdb=" N ALA A 672 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.004A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 removed outlier: 5.824A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.458A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 7.514A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.416A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.434A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 378 through 381 removed outlier: 3.730A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.542A pdb=" N VAL C 108 " --> pdb=" O GLN C 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL C 174 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS C 166 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL C 176 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N SER C 164 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU C 178 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN C 162 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN C 180 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLY C 159 " --> pdb=" O TRP C 145 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP C 145 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR C 140 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG C 134 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR C 142 " --> pdb=" O THR C 132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.542A pdb=" N VAL C 108 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 33 removed outlier: 3.587A pdb=" N PHE E 74 " --> pdb=" O MET E 64 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AC3, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC4, first strand: chain 'F' and resid 230 through 234 removed outlier: 5.394A pdb=" N GLN F 230 " --> pdb=" O HIS F 178 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N HIS F 178 " --> pdb=" O GLN F 230 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY F 232 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU F 176 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASN F 175 " --> pdb=" O ASN F 271 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N HIS F 266 " --> pdb=" O PRO F 258 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU F 268 " --> pdb=" O VAL F 256 " (cutoff:3.500A) 712 hydrogen bonds defined for protein. 1992 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: 2.52 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5070 1.34 - 1.46: 3271 1.46 - 1.58: 6812 1.58 - 1.70: 0 1.70 - 1.81: 93 Bond restraints: 15246 Sorted by residual: bond pdb=" N VAL F 89 " pdb=" CA VAL F 89 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.24e+00 bond pdb=" N ILE F 103 " pdb=" CA ILE F 103 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.17e+00 bond pdb=" N VAL F 36 " pdb=" CA VAL F 36 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.08e-02 8.57e+03 8.14e+00 bond pdb=" N ASN F 108 " pdb=" CA ASN F 108 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.59e+00 bond pdb=" N VAL F 157 " pdb=" CA VAL F 157 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.48e+00 ... (remaining 15241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 20433 2.67 - 5.33: 226 5.33 - 8.00: 30 8.00 - 10.66: 5 10.66 - 13.33: 3 Bond angle restraints: 20697 Sorted by residual: angle pdb=" N ASN F 34 " pdb=" CA ASN F 34 " pdb=" C ASN F 34 " ideal model delta sigma weight residual 113.97 105.47 8.50 1.28e+00 6.10e-01 4.41e+01 angle pdb=" CA MET A 304 " pdb=" CB MET A 304 " pdb=" CG MET A 304 " ideal model delta sigma weight residual 114.10 123.41 -9.31 2.00e+00 2.50e-01 2.17e+01 angle pdb=" CB MET F 402 " pdb=" CG MET F 402 " pdb=" SD MET F 402 " ideal model delta sigma weight residual 112.70 126.03 -13.33 3.00e+00 1.11e-01 1.97e+01 angle pdb=" CA MET F 71 " pdb=" CB MET F 71 " pdb=" CG MET F 71 " ideal model delta sigma weight residual 114.10 121.40 -7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" N ASN F 107 " pdb=" CA ASN F 107 " pdb=" C ASN F 107 " ideal model delta sigma weight residual 113.18 108.76 4.42 1.21e+00 6.83e-01 1.33e+01 ... (remaining 20692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8038 17.96 - 35.91: 840 35.91 - 53.87: 170 53.87 - 71.82: 38 71.82 - 89.78: 15 Dihedral angle restraints: 9101 sinusoidal: 3584 harmonic: 5517 Sorted by residual: dihedral pdb=" CA MET B 189 " pdb=" C MET B 189 " pdb=" N PRO B 190 " pdb=" CA PRO B 190 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ASN C 128 " pdb=" C ASN C 128 " pdb=" N TYR C 129 " pdb=" CA TYR C 129 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLN F 82 " pdb=" C GLN F 82 " pdb=" N MET F 83 " pdb=" CA MET F 83 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 9098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1958 0.067 - 0.134: 288 0.134 - 0.202: 30 0.202 - 0.269: 1 0.269 - 0.336: 1 Chirality restraints: 2278 Sorted by residual: chirality pdb=" CG LEU A 137 " pdb=" CB LEU A 137 " pdb=" CD1 LEU A 137 " pdb=" CD2 LEU A 137 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA VAL F 28 " pdb=" N VAL F 28 " pdb=" C VAL F 28 " pdb=" CB VAL F 28 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA VAL F 37 " pdb=" N VAL F 37 " pdb=" C VAL F 37 " pdb=" CB VAL F 37 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2275 not shown) Planarity restraints: 2734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 129 " -0.317 9.50e-02 1.11e+02 1.42e-01 1.25e+01 pdb=" NE ARG F 129 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG F 129 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG F 129 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 129 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 133 " -0.204 9.50e-02 1.11e+02 9.17e-02 5.20e+00 pdb=" NE ARG F 133 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG F 133 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG F 133 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 133 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 104 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.82e+00 pdb=" C PHE B 104 " 0.034 2.00e-02 2.50e+03 pdb=" O PHE B 104 " -0.013 2.00e-02 2.50e+03 pdb=" N SER B 105 " -0.011 2.00e-02 2.50e+03 ... (remaining 2731 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 15 2.57 - 3.15: 13118 3.15 - 3.74: 24303 3.74 - 4.32: 32008 4.32 - 4.90: 51818 Nonbonded interactions: 121262 Sorted by model distance: nonbonded pdb=" O GLU F 156 " pdb=" CD2 LEU F 160 " model vdw 1.990 3.460 nonbonded pdb=" O GLN F 85 " pdb=" NZ LYS F 90 " model vdw 2.050 3.120 nonbonded pdb=" CB LEU F 153 " pdb=" NE2 GLN F 155 " model vdw 2.115 2.816 nonbonded pdb=" C GLN F 85 " pdb=" NZ LYS F 90 " model vdw 2.322 3.350 nonbonded pdb=" CA GLN F 85 " pdb=" NZ LYS F 90 " model vdw 2.384 3.550 ... (remaining 121257 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.420 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.005 0.225 15247 Z= 0.310 Angle : 0.732 13.330 20697 Z= 0.420 Chirality : 0.047 0.336 2278 Planarity : 0.005 0.142 2734 Dihedral : 15.333 89.775 5581 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.37 % Allowed : 19.07 % Favored : 78.57 % 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: -0.42 (0.19), residues: 1901 helix: 1.06 (0.22), residues: 532 sheet: 0.08 (0.25), residues: 461 loop : -1.29 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 158 TYR 0.014 0.001 TYR E 57 PHE 0.011 0.001 PHE A 394 TRP 0.024 0.001 TRP C 148 HIS 0.003 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.25 (15246) covalent geometry : angle 0.73169 / 0.42 (20697) hydrogen bonds : bond 0.11382 / 7.35 ( 701) hydrogen bonds : angle 5.91875 / 4.17 ( 1992) Misc. bond : bond 0.22470 / 11.83 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8839 (tp) cc_final: 0.8383 (mt) REVERT: A 85 LEU cc_start: 0.9139 (tt) cc_final: 0.8825 (tt) REVERT: A 128 THR cc_start: 0.8407 (m) cc_final: 0.8083 (p) REVERT: A 396 GLU cc_start: 0.7736 (tp30) cc_final: 0.7479 (tp30) REVERT: A 626 LYS cc_start: 0.9194 (mmtp) cc_final: 0.8970 (mtmt) REVERT: A 661 ARG cc_start: 0.8304 (mtt90) cc_final: 0.8088 (mtm-85) REVERT: B 103 TRP cc_start: 0.7543 (OUTLIER) cc_final: 0.7122 (t60) REVERT: B 127 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7627 (mp0) REVERT: B 367 PHE cc_start: 0.8330 (m-80) cc_final: 0.8105 (m-80) REVERT: C 32 LYS cc_start: 0.8441 (mmtp) cc_final: 0.8168 (mmtm) REVERT: C 182 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8116 (mm-30) REVERT: C 190 ASP cc_start: 0.8944 (t0) cc_final: 0.8651 (t0) REVERT: C 194 MET cc_start: 0.7505 (ppp) cc_final: 0.7049 (mpp) REVERT: C 201 MET cc_start: 0.8715 (mmp) cc_final: 0.8196 (mtp) REVERT: C 202 MET cc_start: 0.8436 (tmm) cc_final: 0.7850 (ttp) REVERT: D 55 LEU cc_start: 0.9577 (mm) cc_final: 0.9349 (mm) REVERT: D 178 GLU cc_start: 0.9005 (tp30) cc_final: 0.8670 (tp30) REVERT: E 50 MET cc_start: 0.6904 (mpp) cc_final: 0.6606 (mpp) REVERT: F 60 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7994 (pp) outliers start: 38 outliers final: 21 residues processed: 207 average time/residue: 0.1334 time to fit residues: 39.9276 Evaluate side-chains 155 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 103 TRP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 425 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 50.0000 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN C 133 GLN C 183 GLN D 50 GLN E 52 GLN F 47 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.068110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.048035 restraints weight = 97931.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.049489 restraints weight = 50368.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.050401 restraints weight = 33728.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.050859 restraints weight = 26485.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.051255 restraints weight = 23221.489| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15247 Z= 0.140 Angle : 0.592 8.845 20697 Z= 0.310 Chirality : 0.043 0.226 2278 Planarity : 0.004 0.051 2734 Dihedral : 5.247 55.639 2129 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.99 % Allowed : 18.32 % Favored : 78.69 % 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: -0.33 (0.20), residues: 1901 helix: 1.22 (0.22), residues: 538 sheet: 0.04 (0.24), residues: 490 loop : -1.29 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 158 TYR 0.024 0.001 TYR F 125 PHE 0.013 0.001 PHE A 675 TRP 0.011 0.001 TRP C 148 HIS 0.003 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (15246) covalent geometry : angle 0.59179 / 0.31 (20697) hydrogen bonds : bond 0.03724 / 2.46 ( 701) hydrogen bonds : angle 4.91120 / 3.45 ( 1992) Misc. bond : bond 0.00144 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.9310 (mmm) cc_final: 0.9018 (mmm) REVERT: A 768 MET cc_start: 0.8335 (mmm) cc_final: 0.8021 (mmm) REVERT: A 777 MET cc_start: 0.9328 (mpp) cc_final: 0.8892 (mpp) REVERT: B 67 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8209 (pp) REVERT: B 103 TRP cc_start: 0.7469 (OUTLIER) cc_final: 0.7242 (t60) REVERT: B 127 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7569 (mp0) REVERT: B 367 PHE cc_start: 0.8349 (m-80) cc_final: 0.8127 (m-80) REVERT: C 190 ASP cc_start: 0.8949 (t0) cc_final: 0.8643 (t0) REVERT: C 194 MET cc_start: 0.7854 (ppp) cc_final: 0.7476 (mpp) REVERT: C 201 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8417 (mtp) REVERT: C 202 MET cc_start: 0.8461 (tmm) cc_final: 0.8004 (ttp) REVERT: D 52 ILE cc_start: 0.9483 (pt) cc_final: 0.9150 (mt) REVERT: F 46 MET cc_start: 0.9282 (mmm) cc_final: 0.9011 (mmm) REVERT: F 70 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8847 (mm) REVERT: F 74 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8890 (mp) REVERT: F 402 MET cc_start: 0.9509 (tmm) cc_final: 0.9274 (tmm) outliers start: 48 outliers final: 21 residues processed: 183 average time/residue: 0.1055 time to fit residues: 29.7411 Evaluate side-chains 148 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 103 TRP Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 188 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [143, 110, 144, 63, 17, 120, 188, 21, 79, 127, 42] chunk 143 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 188 optimal weight: 40.0000 chunk 21 optimal weight: 4.9990 chunk 79 optimal weight: 0.0870 chunk 127 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 overall best weight: 3.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.067286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.046096 restraints weight = 96506.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.047449 restraints weight = 50410.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.048274 restraints weight = 34336.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.048747 restraints weight = 27409.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.049078 restraints weight = 24159.902| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15247 Z= 0.177 Angle : 0.590 8.395 20697 Z= 0.309 Chirality : 0.042 0.156 2278 Planarity : 0.004 0.049 2734 Dihedral : 5.009 52.927 2115 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.18 % Allowed : 19.38 % Favored : 77.45 % 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: -0.27 (0.19), residues: 1901 helix: 1.36 (0.22), residues: 537 sheet: 0.07 (0.24), residues: 480 loop : -1.30 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 158 TYR 0.043 0.002 TYR A 142 PHE 0.012 0.001 PHE A 394 TRP 0.010 0.001 TRP B 317 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (15246) covalent geometry : angle 0.59015 / 0.31 (20697) hydrogen bonds : bond 0.03543 / 2.36 ( 701) hydrogen bonds : angle 4.81613 / 3.39 ( 1992) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 122 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.9329 (mmm) cc_final: 0.8753 (tpp) REVERT: A 711 MET cc_start: 0.8958 (ppp) cc_final: 0.8549 (ppp) REVERT: A 741 MET cc_start: 0.7649 (tmm) cc_final: 0.7370 (tmm) REVERT: A 777 MET cc_start: 0.9251 (mpp) cc_final: 0.9011 (mpp) REVERT: B 67 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8299 (pp) REVERT: B 103 TRP cc_start: 0.7456 (OUTLIER) cc_final: 0.7239 (t60) REVERT: B 221 MET cc_start: 0.7285 (pmm) cc_final: 0.6913 (pmm) REVERT: B 331 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8597 (m) REVERT: B 367 PHE cc_start: 0.8341 (m-80) cc_final: 0.8097 (m-80) REVERT: C 127 LYS cc_start: 0.8883 (tptm) cc_final: 0.8589 (mmtm) REVERT: C 182 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7797 (mm-30) REVERT: C 190 ASP cc_start: 0.9016 (t0) cc_final: 0.8800 (t0) REVERT: C 201 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8285 (mtp) REVERT: C 202 MET cc_start: 0.8379 (tmm) cc_final: 0.7917 (ttp) REVERT: D 52 ILE cc_start: 0.9525 (pt) cc_final: 0.9214 (mt) REVERT: F 74 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8871 (mp) REVERT: F 402 MET cc_start: 0.9576 (tmm) cc_final: 0.9375 (tmm) outliers start: 51 outliers final: 36 residues processed: 168 average time/residue: 0.1023 time to fit residues: 26.8497 Evaluate side-chains 154 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 103 TRP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 425 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [11, 169, 43, 175, 145, 10, 126, 30, 172, 92, 20] chunk 11 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 172 optimal weight: 50.0000 chunk 92 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 88 GLN F 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.065717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.044467 restraints weight = 96358.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.045745 restraints weight = 50029.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.046538 restraints weight = 34056.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.047033 restraints weight = 27280.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.047286 restraints weight = 24028.800| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15247 Z= 0.234 Angle : 0.621 7.062 20697 Z= 0.328 Chirality : 0.042 0.163 2278 Planarity : 0.004 0.053 2734 Dihedral : 5.131 51.505 2115 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.30 % Allowed : 19.31 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.19), residues: 1901 helix: 1.36 (0.22), residues: 541 sheet: -0.08 (0.24), residues: 481 loop : -1.33 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 160 TYR 0.037 0.002 TYR A 142 PHE 0.022 0.002 PHE D 147 TRP 0.015 0.002 TRP C 148 HIS 0.005 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (15246) covalent geometry : angle 0.62082 / 0.33 (20697) hydrogen bonds : bond 0.03611 / 2.41 ( 701) hydrogen bonds : angle 4.88236 / 3.43 ( 1992) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 118 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.9364 (mmm) cc_final: 0.9035 (mmm) REVERT: A 552 MET cc_start: 0.8929 (tpp) cc_final: 0.8714 (tpp) REVERT: A 711 MET cc_start: 0.9023 (ppp) cc_final: 0.8537 (ppp) REVERT: A 768 MET cc_start: 0.8171 (mmm) cc_final: 0.7890 (mmm) REVERT: B 67 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8314 (pp) REVERT: B 103 TRP cc_start: 0.7518 (OUTLIER) cc_final: 0.6651 (t60) REVERT: B 221 MET cc_start: 0.7457 (pmm) cc_final: 0.7195 (pmm) REVERT: B 331 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8625 (m) REVERT: B 367 PHE cc_start: 0.8362 (m-80) cc_final: 0.8140 (m-80) REVERT: C 157 TYR cc_start: 0.8922 (m-10) cc_final: 0.8483 (m-10) REVERT: C 190 ASP cc_start: 0.8910 (t0) cc_final: 0.8637 (p0) REVERT: C 197 TYR cc_start: 0.8842 (m-80) cc_final: 0.8431 (m-80) REVERT: C 201 MET cc_start: 0.8978 (mmp) cc_final: 0.8372 (mtp) REVERT: D 52 ILE cc_start: 0.9570 (pt) cc_final: 0.9268 (mt) REVERT: D 109 MET cc_start: 0.9123 (mtp) cc_final: 0.8762 (ttm) REVERT: D 201 MET cc_start: 0.8863 (ttm) cc_final: 0.8472 (ttm) REVERT: E 50 MET cc_start: 0.7546 (mpp) cc_final: 0.7332 (mpp) REVERT: F 46 MET cc_start: 0.9351 (mmm) cc_final: 0.9049 (mmm) REVERT: F 70 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8907 (mm) REVERT: F 74 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8975 (mp) REVERT: F 114 MET cc_start: 0.8917 (ptp) cc_final: 0.8626 (ptp) outliers start: 69 outliers final: 45 residues processed: 181 average time/residue: 0.1019 time to fit residues: 29.2621 Evaluate side-chains 162 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 112 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 103 TRP Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 425 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [114, 168, 130, 166, 65, 135, 156, 105, 152, 127, 109] chunk 114 optimal weight: 20.0000 chunk 168 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 166 optimal weight: 40.0000 chunk 65 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 109 optimal weight: 0.4980 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN B 170 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.065791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.044667 restraints weight = 96333.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.045950 restraints weight = 50640.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.046762 restraints weight = 34594.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.047228 restraints weight = 27687.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.047525 restraints weight = 24462.636| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15247 Z= 0.172 Angle : 0.583 11.428 20697 Z= 0.305 Chirality : 0.042 0.159 2278 Planarity : 0.004 0.052 2734 Dihedral : 4.972 52.029 2113 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.86 % Allowed : 20.06 % Favored : 76.07 % 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: -0.26 (0.19), residues: 1901 helix: 1.50 (0.22), residues: 540 sheet: -0.14 (0.24), residues: 488 loop : -1.27 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 188 TYR 0.012 0.001 TYR D 184 PHE 0.013 0.001 PHE A 394 TRP 0.022 0.001 TRP C 148 HIS 0.003 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (15246) covalent geometry : angle 0.58284 / 0.30 (20697) hydrogen bonds : bond 0.03353 / 2.23 ( 701) hydrogen bonds : angle 4.70962 / 3.32 ( 1992) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 123 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.9394 (mmm) cc_final: 0.8904 (tpp) REVERT: A 552 MET cc_start: 0.8986 (tpp) cc_final: 0.8751 (tpp) REVERT: A 711 MET cc_start: 0.9055 (ppp) cc_final: 0.8535 (ppp) REVERT: A 768 MET cc_start: 0.8187 (mmm) cc_final: 0.7955 (mmm) REVERT: A 777 MET cc_start: 0.9238 (mpp) cc_final: 0.9027 (mpp) REVERT: B 67 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8413 (pp) REVERT: B 103 TRP cc_start: 0.7539 (OUTLIER) cc_final: 0.6661 (t60) REVERT: B 157 VAL cc_start: 0.9260 (OUTLIER) cc_final: 0.8933 (t) REVERT: B 221 MET cc_start: 0.7384 (pmm) cc_final: 0.7181 (pmm) REVERT: B 367 PHE cc_start: 0.8468 (m-80) cc_final: 0.8226 (m-80) REVERT: C 32 LYS cc_start: 0.8544 (mmtp) cc_final: 0.8237 (mmtt) REVERT: C 182 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7568 (mm-30) REVERT: C 190 ASP cc_start: 0.8916 (t0) cc_final: 0.8619 (p0) REVERT: C 201 MET cc_start: 0.8917 (mmp) cc_final: 0.8576 (mtp) REVERT: D 52 ILE cc_start: 0.9587 (pt) cc_final: 0.9295 (mt) REVERT: D 109 MET cc_start: 0.9186 (mtp) cc_final: 0.8801 (ptm) REVERT: F 46 MET cc_start: 0.9347 (mmm) cc_final: 0.9134 (mmm) REVERT: F 74 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8936 (mp) REVERT: F 114 MET cc_start: 0.8831 (ptp) cc_final: 0.8559 (ptp) outliers start: 62 outliers final: 43 residues processed: 179 average time/residue: 0.1119 time to fit residues: 30.6232 Evaluate side-chains 155 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 108 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 734 ARG Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 103 TRP Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 425 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [126, 49, 138, 173, 53, 162, 184, 115, 187, 157, 33] chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 chunk 53 optimal weight: 0.3980 chunk 162 optimal weight: 7.9990 chunk 184 optimal weight: 0.0070 chunk 115 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 overall best weight: 2.0804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN B 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.066376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.045261 restraints weight = 95095.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.046587 restraints weight = 49809.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.047389 restraints weight = 34067.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.047885 restraints weight = 27243.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.048159 restraints weight = 23984.197| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15247 Z= 0.123 Angle : 0.578 9.482 20697 Z= 0.299 Chirality : 0.042 0.149 2278 Planarity : 0.003 0.051 2734 Dihedral : 4.776 52.520 2111 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.49 % Allowed : 21.25 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 1901 helix: 1.54 (0.23), residues: 536 sheet: 0.02 (0.24), residues: 481 loop : -1.24 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 188 TYR 0.018 0.001 TYR C 197 PHE 0.010 0.001 PHE A 738 TRP 0.020 0.001 TRP C 148 HIS 0.003 0.001 HIS F 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15246) covalent geometry : angle 0.57833 / 0.30 (20697) hydrogen bonds : bond 0.03186 / 2.13 ( 701) hydrogen bonds : angle 4.57774 / 3.21 ( 1992) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 120 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.9382 (mmm) cc_final: 0.8906 (tpp) REVERT: A 552 MET cc_start: 0.9030 (tpp) cc_final: 0.8759 (tpp) REVERT: A 711 MET cc_start: 0.9066 (ppp) cc_final: 0.8518 (ppp) REVERT: B 67 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8431 (pp) REVERT: B 103 TRP cc_start: 0.7545 (OUTLIER) cc_final: 0.6698 (t60) REVERT: B 157 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.8900 (t) REVERT: B 197 GLU cc_start: 0.8605 (mp0) cc_final: 0.6977 (mp0) REVERT: B 221 MET cc_start: 0.7358 (pmm) cc_final: 0.6989 (pmm) REVERT: B 331 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8560 (m) REVERT: B 367 PHE cc_start: 0.8505 (m-80) cc_final: 0.8246 (m-80) REVERT: C 32 LYS cc_start: 0.8619 (mmtp) cc_final: 0.8232 (mmtm) REVERT: C 190 ASP cc_start: 0.9000 (t0) cc_final: 0.8728 (p0) REVERT: C 197 TYR cc_start: 0.8887 (m-80) cc_final: 0.8660 (m-80) REVERT: C 201 MET cc_start: 0.8940 (mmp) cc_final: 0.8455 (mtp) REVERT: D 52 ILE cc_start: 0.9585 (pt) cc_final: 0.9293 (mt) REVERT: D 109 MET cc_start: 0.9205 (mtp) cc_final: 0.8814 (ptm) REVERT: F 46 MET cc_start: 0.9438 (mmm) cc_final: 0.9188 (mmm) REVERT: F 74 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9023 (mp) REVERT: F 269 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8810 (tptt) outliers start: 56 outliers final: 39 residues processed: 168 average time/residue: 0.1135 time to fit residues: 29.1870 Evaluate side-chains 156 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 111 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 734 ARG Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 103 TRP Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 422 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [36, 77, 33, 30, 18, 10, 164, 168, 175, 137, 86] chunk 36 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 18 optimal weight: 0.1980 chunk 10 optimal weight: 0.2980 chunk 164 optimal weight: 30.0000 chunk 168 optimal weight: 7.9990 chunk 175 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.065220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.043903 restraints weight = 94501.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.045220 restraints weight = 48979.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.046039 restraints weight = 33215.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.046518 restraints weight = 26450.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.046783 restraints weight = 23245.121| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15247 Z= 0.196 Angle : 0.618 8.896 20697 Z= 0.321 Chirality : 0.042 0.151 2278 Planarity : 0.004 0.052 2734 Dihedral : 4.868 53.258 2111 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.61 % Allowed : 21.31 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.19), residues: 1901 helix: 1.58 (0.22), residues: 537 sheet: -0.07 (0.24), residues: 476 loop : -1.32 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 47 TYR 0.021 0.002 TYR F 398 PHE 0.014 0.001 PHE A 394 TRP 0.024 0.001 TRP C 148 HIS 0.004 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (15246) covalent geometry : angle 0.61828 / 0.32 (20697) hydrogen bonds : bond 0.03411 / 2.28 ( 701) hydrogen bonds : angle 4.68449 / 3.28 ( 1992) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 113 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.9346 (mmm) cc_final: 0.8921 (tpp) REVERT: A 552 MET cc_start: 0.9006 (tpp) cc_final: 0.8738 (tpp) REVERT: A 711 MET cc_start: 0.9092 (ppp) cc_final: 0.8616 (ppp) REVERT: A 777 MET cc_start: 0.9189 (mpp) cc_final: 0.8722 (mpp) REVERT: B 67 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8366 (pp) REVERT: B 103 TRP cc_start: 0.7553 (OUTLIER) cc_final: 0.6729 (t60) REVERT: B 367 PHE cc_start: 0.8420 (m-80) cc_final: 0.8202 (m-80) REVERT: C 32 LYS cc_start: 0.8720 (mmtp) cc_final: 0.8344 (mmtt) REVERT: C 157 TYR cc_start: 0.8761 (m-80) cc_final: 0.8516 (m-80) REVERT: C 190 ASP cc_start: 0.8975 (t0) cc_final: 0.8644 (p0) REVERT: C 201 MET cc_start: 0.9013 (mmp) cc_final: 0.8462 (mtp) REVERT: D 52 ILE cc_start: 0.9585 (pt) cc_final: 0.9295 (mt) REVERT: F 46 MET cc_start: 0.9478 (mmm) cc_final: 0.9233 (mmm) REVERT: F 71 MET cc_start: 0.9215 (ppp) cc_final: 0.9000 (ppp) REVERT: F 74 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9040 (mp) REVERT: F 114 MET cc_start: 0.8862 (ptp) cc_final: 0.8621 (ptp) REVERT: F 269 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8747 (ptpp) REVERT: F 402 MET cc_start: 0.9603 (tmm) cc_final: 0.9372 (tmm) outliers start: 58 outliers final: 46 residues processed: 165 average time/residue: 0.1116 time to fit residues: 28.2674 Evaluate side-chains 159 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 109 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 734 ARG Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 103 TRP Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 425 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [100, 171, 118, 162, 98, 33, 90, 109, 153, 119, 149] chunk 100 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 162 optimal weight: 0.0770 chunk 98 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 162 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.065145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.044050 restraints weight = 94659.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.045344 restraints weight = 48367.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.046139 restraints weight = 32742.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.046604 restraints weight = 26017.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.046896 restraints weight = 22880.582| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15247 Z= 0.185 Angle : 0.609 9.034 20697 Z= 0.317 Chirality : 0.042 0.157 2278 Planarity : 0.004 0.052 2734 Dihedral : 4.851 53.475 2111 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.05 % Allowed : 21.81 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.19), residues: 1901 helix: 1.55 (0.22), residues: 539 sheet: -0.05 (0.24), residues: 476 loop : -1.32 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 47 TYR 0.015 0.001 TYR F 398 PHE 0.017 0.001 PHE A 197 TRP 0.019 0.001 TRP C 148 HIS 0.004 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (15246) covalent geometry : angle 0.60908 / 0.32 (20697) hydrogen bonds : bond 0.03343 / 2.22 ( 701) hydrogen bonds : angle 4.67553 / 3.27 ( 1992) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 112 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.9364 (mmm) cc_final: 0.8942 (tpp) REVERT: A 552 MET cc_start: 0.9024 (tpp) cc_final: 0.8765 (tpp) REVERT: A 711 MET cc_start: 0.9102 (ppp) cc_final: 0.8611 (ppp) REVERT: A 768 MET cc_start: 0.8449 (mmm) cc_final: 0.8154 (mmm) REVERT: A 777 MET cc_start: 0.9161 (mpp) cc_final: 0.8669 (mpp) REVERT: B 32 MET cc_start: 0.8889 (tmm) cc_final: 0.8687 (tmm) REVERT: B 67 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8420 (pp) REVERT: B 103 TRP cc_start: 0.7556 (OUTLIER) cc_final: 0.6680 (t60) REVERT: B 221 MET cc_start: 0.7016 (pmm) cc_final: 0.6740 (pmm) REVERT: C 32 LYS cc_start: 0.8741 (mmtp) cc_final: 0.8345 (mmtt) REVERT: C 190 ASP cc_start: 0.8957 (t0) cc_final: 0.8681 (p0) REVERT: C 201 MET cc_start: 0.9061 (mmp) cc_final: 0.8482 (mtp) REVERT: D 52 ILE cc_start: 0.9594 (pt) cc_final: 0.9322 (mt) REVERT: F 46 MET cc_start: 0.9476 (mmm) cc_final: 0.9224 (mmm) REVERT: F 74 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9070 (mp) REVERT: F 114 MET cc_start: 0.8826 (ptp) cc_final: 0.8577 (ptp) REVERT: F 219 HIS cc_start: 0.9118 (m-70) cc_final: 0.8849 (m-70) REVERT: F 269 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8726 (ptpp) outliers start: 49 outliers final: 45 residues processed: 157 average time/residue: 0.1115 time to fit residues: 27.0066 Evaluate side-chains 158 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 109 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 734 ARG Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 103 TRP Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 425 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [31, 110, 26, 167, 34, 180, 49, 153, 152, 52, 57] chunk 31 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 180 optimal weight: 50.0000 chunk 49 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.065063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.044143 restraints weight = 95678.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.045365 restraints weight = 49783.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.046133 restraints weight = 34052.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.046548 restraints weight = 27300.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 72)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.046824 restraints weight = 24247.073| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15247 Z= 0.179 Angle : 0.619 9.386 20697 Z= 0.320 Chirality : 0.043 0.191 2278 Planarity : 0.004 0.051 2734 Dihedral : 4.852 54.077 2111 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.49 % Allowed : 21.62 % Favored : 74.89 % 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: -0.24 (0.19), residues: 1901 helix: 1.51 (0.22), residues: 539 sheet: -0.03 (0.24), residues: 468 loop : -1.29 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 47 TYR 0.030 0.002 TYR C 197 PHE 0.014 0.001 PHE A 197 TRP 0.036 0.002 TRP F 413 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (15246) covalent geometry : angle 0.61901 / 0.32 (20697) hydrogen bonds : bond 0.03363 / 2.23 ( 701) hydrogen bonds : angle 4.65434 / 3.25 ( 1992) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 113 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.9410 (mmm) cc_final: 0.8995 (tpp) REVERT: A 552 MET cc_start: 0.9114 (tpp) cc_final: 0.8837 (tpp) REVERT: A 711 MET cc_start: 0.9098 (ppp) cc_final: 0.8567 (ppp) REVERT: A 768 MET cc_start: 0.8448 (mmm) cc_final: 0.8171 (mmm) REVERT: A 777 MET cc_start: 0.9132 (mpp) cc_final: 0.8707 (mpp) REVERT: B 103 TRP cc_start: 0.7547 (OUTLIER) cc_final: 0.6685 (t60) REVERT: B 194 LEU cc_start: 0.9227 (tp) cc_final: 0.9017 (tp) REVERT: B 221 MET cc_start: 0.7049 (pmm) cc_final: 0.6787 (pmm) REVERT: C 32 LYS cc_start: 0.8742 (mmtp) cc_final: 0.8371 (mmtt) REVERT: C 190 ASP cc_start: 0.9006 (t0) cc_final: 0.8663 (p0) REVERT: C 201 MET cc_start: 0.9055 (mmp) cc_final: 0.8421 (mtp) REVERT: D 52 ILE cc_start: 0.9618 (pt) cc_final: 0.9355 (mt) REVERT: F 46 MET cc_start: 0.9471 (mmm) cc_final: 0.9207 (mmm) REVERT: F 74 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9038 (mp) REVERT: F 114 MET cc_start: 0.8802 (ptp) cc_final: 0.8555 (ptp) REVERT: F 219 HIS cc_start: 0.9127 (m-70) cc_final: 0.8883 (m-70) REVERT: F 269 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8744 (ptpp) outliers start: 56 outliers final: 50 residues processed: 163 average time/residue: 0.1089 time to fit residues: 27.2487 Evaluate side-chains 163 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 110 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 734 ARG Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 103 TRP Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 425 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [133, 113, 100, 70, 47, 10, 105, 11, 3, 54, 40] chunk 133 optimal weight: 0.4980 chunk 113 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 47 optimal weight: 0.0670 chunk 10 optimal weight: 0.1980 chunk 105 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 overall best weight: 1.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.065846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.044871 restraints weight = 94582.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.046183 restraints weight = 49323.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.046974 restraints weight = 33523.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.047465 restraints weight = 26875.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.047708 restraints weight = 23571.138| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15247 Z= 0.117 Angle : 0.618 10.054 20697 Z= 0.316 Chirality : 0.043 0.168 2278 Planarity : 0.003 0.053 2734 Dihedral : 4.704 54.412 2111 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.49 % Allowed : 22.43 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.19), residues: 1901 helix: 1.60 (0.23), residues: 537 sheet: 0.10 (0.24), residues: 470 loop : -1.24 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 47 TYR 0.031 0.001 TYR C 197 PHE 0.012 0.001 PHE A 197 TRP 0.057 0.002 TRP F 413 HIS 0.003 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (15246) covalent geometry : angle 0.61758 / 0.32 (20697) hydrogen bonds : bond 0.03190 / 2.13 ( 701) hydrogen bonds : angle 4.50515 / 3.15 ( 1992) Misc. bond : bond 0.00038 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.9380 (mmm) cc_final: 0.8956 (tpp) REVERT: A 552 MET cc_start: 0.9081 (tpp) cc_final: 0.8790 (tpp) REVERT: A 711 MET cc_start: 0.9085 (ppp) cc_final: 0.8556 (ppp) REVERT: A 768 MET cc_start: 0.8436 (mmm) cc_final: 0.8169 (mmm) REVERT: A 777 MET cc_start: 0.9134 (mpp) cc_final: 0.8578 (mpp) REVERT: B 32 MET cc_start: 0.8947 (tmm) cc_final: 0.8740 (tmm) REVERT: B 157 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.8913 (t) REVERT: B 194 LEU cc_start: 0.9185 (tp) cc_final: 0.8981 (tp) REVERT: B 221 MET cc_start: 0.6948 (pmm) cc_final: 0.6705 (pmm) REVERT: C 32 LYS cc_start: 0.8759 (mmtp) cc_final: 0.8373 (mmtt) REVERT: C 129 TYR cc_start: 0.7611 (m-80) cc_final: 0.5855 (m-80) REVERT: C 190 ASP cc_start: 0.9030 (t0) cc_final: 0.8685 (p0) REVERT: C 201 MET cc_start: 0.9049 (mmp) cc_final: 0.8110 (mtp) REVERT: D 52 ILE cc_start: 0.9620 (pt) cc_final: 0.9360 (mt) REVERT: F 46 MET cc_start: 0.9466 (mmm) cc_final: 0.9197 (mmm) REVERT: F 74 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9034 (mp) REVERT: F 114 MET cc_start: 0.8772 (ptp) cc_final: 0.8535 (ptp) REVERT: F 219 HIS cc_start: 0.9105 (m-70) cc_final: 0.8552 (m90) REVERT: F 269 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8846 (tptt) outliers start: 40 outliers final: 37 residues processed: 162 average time/residue: 0.1251 time to fit residues: 30.4802 Evaluate side-chains 158 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 734 ARG Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 425 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [131, 25, 40, 37, 124, 78, 142, 18, 93, 94, 19] chunk 131 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 chunk 37 optimal weight: 4.9990 chunk 124 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.065295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.044431 restraints weight = 96138.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.045808 restraints weight = 50267.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.046667 restraints weight = 33960.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.047184 restraints weight = 26940.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.047532 restraints weight = 23440.458| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15247 Z= 0.165 Angle : 0.647 10.979 20697 Z= 0.332 Chirality : 0.043 0.167 2278 Planarity : 0.004 0.052 2734 Dihedral : 4.642 54.777 2108 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.68 % Allowed : 22.74 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 1901 helix: 1.53 (0.22), residues: 536 sheet: 0.05 (0.24), residues: 471 loop : -1.25 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 47 TYR 0.029 0.001 TYR C 197 PHE 0.011 0.001 PHE A 394 TRP 0.044 0.002 TRP F 413 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (15246) covalent geometry : angle 0.64671 / 0.33 (20697) hydrogen bonds : bond 0.03293 / 2.21 ( 701) hydrogen bonds : angle 4.57661 / 3.19 ( 1992) Misc. bond : bond 0.00042 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3281.35 seconds wall clock time: 57 minutes 5.72 seconds (3425.72 seconds total)