Starting phenix.real_space_refine on Sat Jul 4 13:59:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyl_71025/07_2026/9oyl_71025.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyl_71025/07_2026/9oyl_71025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oyl_71025/07_2026/9oyl_71025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyl_71025/07_2026/9oyl_71025.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oyl_71025/07_2026/9oyl_71025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyl_71025/07_2026/9oyl_71025.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 55 5.49 5 Mg 3 5.21 5 S 112 5.16 5 C 12929 2.51 5 N 3720 2.21 5 O 3976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20799 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2725 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "B" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2840 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 16, 'TRANS': 348} Chain: "C" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2865 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "D" Number of atoms: 2807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2807 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 14, 'TRANS': 346} Chain: "E" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2601 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "F" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2835 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 20, 'TRANS': 344} Chain: "G" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2843 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 20, 'TRANS': 345} Chain: "H" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 529 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "I" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 243 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3208 SG CYS B 64 75.086 86.065 113.386 1.00105.37 S ATOM 3268 SG CYS B 73 78.754 85.160 113.612 1.00115.97 S ATOM 3285 SG CYS B 76 76.272 82.438 114.308 1.00121.32 S ATOM 3307 SG CYS B 79 76.512 83.730 110.816 1.00112.59 S ATOM 6048 SG CYS C 64 99.364 55.880 85.670 1.00104.05 S ATOM 6108 SG CYS C 73 100.639 52.991 83.584 1.00116.50 S ATOM 6125 SG CYS C 76 97.883 52.307 85.960 1.00108.95 S ATOM 6147 SG CYS C 79 97.022 54.356 83.021 1.00 96.62 S ATOM 8921 SG CYS D 64 76.603 28.148 55.188 1.00116.64 S ATOM 8981 SG CYS D 73 74.662 25.584 53.237 1.00134.13 S ATOM 8998 SG CYS D 76 73.458 26.368 56.715 1.00125.58 S ATOM 9020 SG CYS D 79 73.080 29.012 54.170 1.00120.88 S ATOM 11644 SG CYS E 50 28.370 35.856 48.852 1.00126.59 S ATOM 11713 SG CYS E 59 24.780 35.350 50.030 1.00141.95 S ATOM 11733 SG CYS E 62 27.453 35.300 52.598 1.00136.87 S ATOM 11754 SG CYS E 65 26.690 38.580 50.779 1.00121.05 S Time building chain proxies: 4.21, per 1000 atoms: 0.20 Number of scatterers: 20799 At special positions: 0 Unit cell: (111.78, 122.544, 146.556, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 112 16.00 P 55 15.00 Mg 3 11.99 O 3976 8.00 N 3720 7.00 C 12929 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 831.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 79 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 64 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 76 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 76 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 79 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 64 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 79 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 76 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 64 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 73 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 59 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 65 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 62 " Number of angles added : 24 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 15 sheets defined 53.9% alpha, 14.8% beta 19 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 removed outlier: 4.435A pdb=" N ARG A 10 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.566A pdb=" N ILE A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.843A pdb=" N GLU A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 removed outlier: 3.604A pdb=" N ASN A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 146 through 159 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.816A pdb=" N GLN A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 225 through 240 Processing helix chain 'A' and resid 242 through 264 removed outlier: 3.588A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.532A pdb=" N LEU A 272 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 319 through 332 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 21 through 34 removed outlier: 4.396A pdb=" N ALA B 27 " --> pdb=" O HIS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.848A pdb=" N ASP B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 131 Processing helix chain 'B' and resid 132 through 145 removed outlier: 3.620A pdb=" N ASN B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 199 through 211 removed outlier: 4.079A pdb=" N GLU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 228 removed outlier: 3.659A pdb=" N ALA B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.646A pdb=" N THR B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 244 " --> pdb=" O MET B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 277 through 296 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.622A pdb=" N ALA B 307 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 321 through 338 Processing helix chain 'B' and resid 339 through 342 Processing helix chain 'B' and resid 344 through 358 Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.789A pdb=" N VAL C 18 " --> pdb=" O PHE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 35 Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 100 through 110 removed outlier: 3.827A pdb=" N ASN C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.618A pdb=" N LEU C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.559A pdb=" N LEU C 162 " --> pdb=" O PRO C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 169 removed outlier: 3.790A pdb=" N ARG C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 194 Processing helix chain 'C' and resid 199 through 210 Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.676A pdb=" N ALA C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 245 through 259 Processing helix chain 'C' and resid 260 through 274 Processing helix chain 'C' and resid 277 through 298 removed outlier: 3.688A pdb=" N LEU C 282 " --> pdb=" O TRP C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 308 removed outlier: 4.513A pdb=" N ALA C 308 " --> pdb=" O ASP C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 321 through 339 removed outlier: 3.664A pdb=" N LEU C 327 " --> pdb=" O THR C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 21 through 35 removed outlier: 3.923A pdb=" N ALA D 27 " --> pdb=" O HIS D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 132 through 145 removed outlier: 3.512A pdb=" N LEU D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 Processing helix chain 'D' and resid 179 through 195 Processing helix chain 'D' and resid 199 through 210 Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 247 through 259 Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 277 through 298 Processing helix chain 'D' and resid 299 through 302 removed outlier: 4.039A pdb=" N LEU D 302 " --> pdb=" O PRO D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 299 through 302' Processing helix chain 'D' and resid 303 through 308 removed outlier: 4.306A pdb=" N ALA D 308 " --> pdb=" O ASP D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 321 through 338 removed outlier: 3.695A pdb=" N GLN D 326 " --> pdb=" O PRO D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'E' and resid 6 through 20 removed outlier: 4.551A pdb=" N ASP E 10 " --> pdb=" O TRP E 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 49 Processing helix chain 'E' and resid 62 through 70 removed outlier: 3.614A pdb=" N LEU E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA E 70 " --> pdb=" O GLN E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 100 removed outlier: 3.829A pdb=" N VAL E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 121 through 134 removed outlier: 4.403A pdb=" N LYS E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 152 through 158 removed outlier: 3.558A pdb=" N SER E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 178 Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 197 through 204 Processing helix chain 'E' and resid 208 through 227 Proline residue: E 225 - end of helix Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 240 through 260 Processing helix chain 'E' and resid 270 through 280 Processing helix chain 'E' and resid 282 through 303 Processing helix chain 'E' and resid 307 through 323 Processing helix chain 'F' and resid 6 through 19 removed outlier: 4.378A pdb=" N LYS F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) Proline residue: F 13 - end of helix Processing helix chain 'F' and resid 72 through 82 removed outlier: 3.644A pdb=" N LEU F 82 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 116 Processing helix chain 'F' and resid 131 through 141 Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 152 through 155 Processing helix chain 'F' and resid 197 through 207 Processing helix chain 'F' and resid 260 through 273 removed outlier: 3.618A pdb=" N ILE F 272 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 332 Processing helix chain 'G' and resid 7 through 19 removed outlier: 4.753A pdb=" N LYS G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) Proline residue: G 13 - end of helix Processing helix chain 'G' and resid 72 through 82 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 131 through 141 Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 197 through 207 Processing helix chain 'G' and resid 243 through 248 removed outlier: 3.957A pdb=" N VAL G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 274 removed outlier: 4.138A pdb=" N LEU G 273 " --> pdb=" O ARG G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 332 removed outlier: 3.601A pdb=" N LYS G 332 " --> pdb=" O LEU G 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 13 Processing helix chain 'J' and resid 21 through 25 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 7.386A pdb=" N LEU A 4 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN A 78 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE A 111 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU A 80 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ARG A 113 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU A 82 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLU A 49 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU A 81 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS A 51 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU A 83 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE A 53 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.452A pdb=" N GLU A 161 " --> pdb=" O LEU A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.127A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA B 40 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE B 173 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 42 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.564A pdb=" N LYS C 151 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR C 41 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N THR C 156 " --> pdb=" O TYR C 41 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE C 43 " --> pdb=" O THR C 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 90 through 94 removed outlier: 5.927A pdb=" N LYS D 121 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU D 153 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA D 155 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE D 125 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY D 45 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 76 through 79 removed outlier: 6.628A pdb=" N TYR E 77 " --> pdb=" O TRP E 113 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL E 112 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ALA E 144 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL E 114 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 2 through 5 removed outlier: 3.555A pdb=" N ARG F 96 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU G 301 " --> pdb=" O SER F 107 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN G 295 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY G 280 " --> pdb=" O ASN G 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 66 through 71 removed outlier: 3.796A pdb=" N GLY F 66 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN F 32 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR F 47 " --> pdb=" O ASN F 32 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 309 through 311 removed outlier: 4.175A pdb=" N SER F 311 " --> pdb=" O HIS F 255 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N HIS F 255 " --> pdb=" O SER F 311 " (cutoff:3.500A) removed outlier: 15.596A pdb=" N SER F 181 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 15.815A pdb=" N THR F 172 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 14.925A pdb=" N VAL F 170 " --> pdb=" O PRO F 183 " (cutoff:3.500A) removed outlier: 13.124A pdb=" N GLY F 185 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 13.348A pdb=" N ARG F 168 " --> pdb=" O GLY F 185 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N SER F 187 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLU F 166 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY F 164 " --> pdb=" O PRO F 189 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS F 191 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR F 162 " --> pdb=" O HIS F 191 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 315 through 320 removed outlier: 3.590A pdb=" N MET F 315 " --> pdb=" O VAL F 285 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLY F 280 " --> pdb=" O ASN F 295 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASN F 295 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU F 301 " --> pdb=" O SER G 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'G' and resid 32 through 36 Processing sheet with id=AB5, first strand: chain 'G' and resid 41 through 47 Processing sheet with id=AB6, first strand: chain 'G' and resid 254 through 259 removed outlier: 5.120A pdb=" N GLU G 165 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N GLN G 186 " --> pdb=" O GLU G 163 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N GLU G 163 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N LEU G 188 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 10.499A pdb=" N GLU G 161 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 13.784A pdb=" N SER G 190 " --> pdb=" O LEU G 159 " (cutoff:3.500A) removed outlier: 14.595A pdb=" N LEU G 159 " --> pdb=" O SER G 190 " (cutoff:3.500A) removed outlier: 13.304A pdb=" N SER G 192 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 12.807A pdb=" N GLY G 157 " --> pdb=" O SER G 192 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3066 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7117 1.36 - 1.51: 5531 1.51 - 1.66: 8430 1.66 - 1.80: 142 1.80 - 1.95: 44 Bond restraints: 21264 Sorted by residual: bond pdb=" N ASP A 56 " pdb=" CA ASP A 56 " ideal model delta sigma weight residual 1.455 1.489 -0.034 7.00e-03 2.04e+04 2.33e+01 bond pdb=" O3B AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.05e+01 bond pdb=" O3B AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sigma weight residual 1.673 1.586 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" O3B AGS B 402 " pdb=" PB AGS B 402 " ideal model delta sigma weight residual 1.673 1.588 0.085 2.00e-02 2.50e+03 1.83e+01 bond pdb=" O3A AGS C 402 " pdb=" PA AGS C 402 " ideal model delta sigma weight residual 1.664 1.582 0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 21259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 28609 2.04 - 4.09: 391 4.09 - 6.13: 40 6.13 - 8.18: 10 8.18 - 10.22: 11 Bond angle restraints: 29061 Sorted by residual: angle pdb=" N TYR C 3 " pdb=" CA TYR C 3 " pdb=" C TYR C 3 " ideal model delta sigma weight residual 111.11 105.22 5.89 1.20e+00 6.94e-01 2.41e+01 angle pdb=" N3 DT I 14 " pdb=" C4 DT I 14 " pdb=" O4 DT I 14 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT I 8 " pdb=" C4 DT I 8 " pdb=" O4 DT I 8 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT H 28 " pdb=" C4 DT H 28 " pdb=" O4 DT H 28 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT I 16 " pdb=" C4 DT I 16 " pdb=" O4 DT I 16 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 ... (remaining 29056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.60: 12319 30.60 - 61.20: 543 61.20 - 91.80: 40 91.80 - 122.40: 1 122.40 - 152.99: 5 Dihedral angle restraints: 12908 sinusoidal: 5573 harmonic: 7335 Sorted by residual: dihedral pdb=" O1B AGS C 402 " pdb=" O3B AGS C 402 " pdb=" PB AGS C 402 " pdb=" PG AGS C 402 " ideal model delta sinusoidal sigma weight residual 138.55 -14.44 152.99 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" O2B AGS C 402 " pdb=" O3B AGS C 402 " pdb=" PB AGS C 402 " pdb=" PG AGS C 402 " ideal model delta sinusoidal sigma weight residual 7.37 -137.81 145.18 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" O3A AGS C 402 " pdb=" O3B AGS C 402 " pdb=" PB AGS C 402 " pdb=" PG AGS C 402 " ideal model delta sinusoidal sigma weight residual 252.61 108.22 144.39 1 3.00e+01 1.11e-03 1.93e+01 ... (remaining 12905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2958 0.058 - 0.116: 363 0.116 - 0.174: 25 0.174 - 0.232: 1 0.232 - 0.290: 3 Chirality restraints: 3350 Sorted by residual: chirality pdb=" C3' AGS B 402 " pdb=" C2' AGS B 402 " pdb=" C4' AGS B 402 " pdb=" O3' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' AGS C 402 " pdb=" C2' AGS C 402 " pdb=" C4' AGS C 402 " pdb=" O3' AGS C 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C3' AGS D 402 " pdb=" C2' AGS D 402 " pdb=" C4' AGS D 402 " pdb=" O3' AGS D 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3347 not shown) Planarity restraints: 3612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 27 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO A 28 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 28 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 28 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 296 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO G 297 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO G 297 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 297 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 282 " -0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO E 283 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO E 283 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 283 " -0.017 5.00e-02 4.00e+02 ... (remaining 3609 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 118 2.51 - 3.11: 14814 3.11 - 3.71: 33083 3.71 - 4.30: 45846 4.30 - 4.90: 77790 Nonbonded interactions: 171651 Sorted by model distance: nonbonded pdb=" O2G AGS B 402 " pdb="MG MG B 403 " model vdw 1.918 2.170 nonbonded pdb=" O2G AGS D 402 " pdb="MG MG D 403 " model vdw 1.926 2.170 nonbonded pdb=" OG1 THR B 52 " pdb="MG MG B 403 " model vdw 1.938 2.170 nonbonded pdb=" OG1 THR D 52 " pdb="MG MG D 403 " model vdw 1.969 2.170 nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 403 " model vdw 2.009 2.170 ... (remaining 171646 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 361 or resid 401 through 403)) selection = (chain 'C' and (resid 2 through 361 or resid 401 through 403)) selection = (chain 'D' and resid 2 through 403) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 365) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.260 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 21280 Z= 0.243 Angle : 0.598 10.225 29085 Z= 0.335 Chirality : 0.040 0.290 3350 Planarity : 0.003 0.038 3612 Dihedral : 16.243 152.994 8148 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.38 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.17), residues: 2516 helix: 1.50 (0.15), residues: 1246 sheet: 0.46 (0.26), residues: 437 loop : 0.24 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 246 TYR 0.007 0.001 TYR E 47 PHE 0.018 0.001 PHE B 136 TRP 0.012 0.001 TRP B 278 HIS 0.008 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.24 (21264) covalent geometry : angle 0.59086 / 0.33 (29061) hydrogen bonds : bond 0.15423 / 10.31 ( 1122) hydrogen bonds : angle 5.57209 / 4.04 ( 3166) metal coordination : bond 0.00346 / 0.22 ( 16) metal coordination : angle 3.17174 / 1.96 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 617 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.5337 (tt0) cc_final: 0.5129 (tt0) REVERT: A 126 TRP cc_start: 0.6854 (p-90) cc_final: 0.6562 (p-90) REVERT: A 175 GLU cc_start: 0.7520 (tm-30) cc_final: 0.6456 (mt-10) REVERT: A 211 HIS cc_start: 0.7093 (t70) cc_final: 0.6630 (m170) REVERT: A 234 GLN cc_start: 0.7591 (mt0) cc_final: 0.7330 (pt0) REVERT: A 286 MET cc_start: 0.7209 (mmm) cc_final: 0.6556 (mmt) REVERT: A 338 ASP cc_start: 0.7399 (m-30) cc_final: 0.6929 (t0) REVERT: B 77 ASP cc_start: 0.7060 (m-30) cc_final: 0.6416 (m-30) REVERT: B 80 ARG cc_start: 0.7011 (mtm110) cc_final: 0.6662 (ttp80) REVERT: B 81 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6508 (mp0) REVERT: B 133 ARG cc_start: 0.7431 (tpp80) cc_final: 0.7190 (ttp80) REVERT: B 188 GLU cc_start: 0.7724 (tt0) cc_final: 0.7497 (tt0) REVERT: B 192 ASN cc_start: 0.7917 (m-40) cc_final: 0.7712 (m-40) REVERT: B 231 GLN cc_start: 0.7053 (mt0) cc_final: 0.6848 (mt0) REVERT: B 311 LEU cc_start: 0.6744 (tp) cc_final: 0.6294 (mm) REVERT: B 338 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7345 (pt0) REVERT: C 22 GLU cc_start: 0.7373 (tp30) cc_final: 0.6847 (mp0) REVERT: C 77 ASP cc_start: 0.7029 (t70) cc_final: 0.6819 (t0) REVERT: C 80 ARG cc_start: 0.7521 (mmm-85) cc_final: 0.7288 (mmm-85) REVERT: C 94 ASP cc_start: 0.7519 (p0) cc_final: 0.7245 (p0) REVERT: C 98 ARG cc_start: 0.7917 (mtp-110) cc_final: 0.7676 (mtp-110) REVERT: C 106 ASP cc_start: 0.7657 (m-30) cc_final: 0.7332 (m-30) REVERT: C 130 MET cc_start: 0.8436 (mmp) cc_final: 0.8178 (mmp) REVERT: C 133 ARG cc_start: 0.7372 (ttp80) cc_final: 0.7156 (ttp80) REVERT: C 176 LYS cc_start: 0.7939 (mtpp) cc_final: 0.7396 (mmtt) REVERT: C 192 ASN cc_start: 0.7946 (t0) cc_final: 0.7671 (t0) REVERT: C 193 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7711 (mm-30) REVERT: C 211 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7552 (mm-30) REVERT: C 231 GLN cc_start: 0.7652 (pt0) cc_final: 0.7110 (pp30) REVERT: C 254 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7407 (mt-10) REVERT: C 258 GLU cc_start: 0.6609 (mt-10) cc_final: 0.6357 (tt0) REVERT: C 262 GLU cc_start: 0.7780 (pp20) cc_final: 0.7516 (mm-30) REVERT: C 318 ARG cc_start: 0.7298 (ptm-80) cc_final: 0.6594 (ttm110) REVERT: C 337 LYS cc_start: 0.8281 (mtmt) cc_final: 0.7977 (mtmm) REVERT: D 17 ASP cc_start: 0.7387 (t0) cc_final: 0.7012 (m-30) REVERT: D 106 ASP cc_start: 0.6557 (m-30) cc_final: 0.6276 (m-30) REVERT: D 174 HIS cc_start: 0.7579 (m90) cc_final: 0.7333 (m90) REVERT: D 176 LYS cc_start: 0.8454 (mttm) cc_final: 0.8225 (mtpp) REVERT: D 211 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7709 (mm-30) REVERT: D 263 ARG cc_start: 0.7972 (tpp80) cc_final: 0.7601 (tpp80) REVERT: D 291 ARG cc_start: 0.8060 (tpp80) cc_final: 0.7836 (tpp80) REVERT: E 134 GLU cc_start: 0.7952 (tt0) cc_final: 0.7332 (pt0) REVERT: E 170 GLN cc_start: 0.6907 (tp40) cc_final: 0.6456 (tp-100) REVERT: E 258 ARG cc_start: 0.7102 (tpm170) cc_final: 0.6637 (tmt170) REVERT: E 298 GLU cc_start: 0.7725 (tp30) cc_final: 0.7064 (mm-30) REVERT: F 36 GLN cc_start: 0.8087 (mt0) cc_final: 0.7773 (mt0) REVERT: F 73 ARG cc_start: 0.7105 (mmt180) cc_final: 0.6612 (mmt-90) REVERT: F 87 GLU cc_start: 0.6858 (tt0) cc_final: 0.6624 (pp20) REVERT: F 91 GLN cc_start: 0.6983 (tt0) cc_final: 0.6521 (tm130) REVERT: F 95 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6427 (pp20) REVERT: F 105 ARG cc_start: 0.8045 (ttt180) cc_final: 0.7550 (ttp-170) REVERT: F 152 ARG cc_start: 0.6648 (mpp80) cc_final: 0.6113 (mtm180) REVERT: F 161 GLU cc_start: 0.6886 (pt0) cc_final: 0.6662 (pt0) REVERT: F 166 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6774 (mt-10) REVERT: F 205 ARG cc_start: 0.7248 (mtp-110) cc_final: 0.6896 (mtm-85) REVERT: F 221 ASN cc_start: 0.7683 (m-40) cc_final: 0.7381 (m-40) REVERT: F 309 THR cc_start: 0.7903 (m) cc_final: 0.7468 (p) REVERT: F 326 ASP cc_start: 0.7783 (m-30) cc_final: 0.7539 (m-30) REVERT: F 335 ASN cc_start: 0.8107 (m-40) cc_final: 0.7639 (m-40) REVERT: F 343 SER cc_start: 0.8414 (p) cc_final: 0.8081 (t) REVERT: G 14 LEU cc_start: 0.7697 (mt) cc_final: 0.7328 (mt) REVERT: G 50 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6526 (mm-30) REVERT: G 52 GLU cc_start: 0.8280 (pt0) cc_final: 0.8068 (pt0) REVERT: G 79 CYS cc_start: 0.7420 (m) cc_final: 0.6998 (m) REVERT: G 91 GLN cc_start: 0.6851 (mt0) cc_final: 0.6525 (pp30) REVERT: G 153 TYR cc_start: 0.7049 (p90) cc_final: 0.6701 (p90) REVERT: G 161 GLU cc_start: 0.7131 (tt0) cc_final: 0.6594 (tt0) REVERT: G 215 ARG cc_start: 0.7488 (ttp-170) cc_final: 0.7040 (mtm110) REVERT: G 217 GLN cc_start: 0.6285 (tt0) cc_final: 0.5744 (mm110) REVERT: G 254 LYS cc_start: 0.7467 (mmtp) cc_final: 0.7183 (mttp) REVERT: G 282 ARG cc_start: 0.8640 (mtt90) cc_final: 0.8419 (mtt-85) REVERT: G 299 GLN cc_start: 0.7282 (mm110) cc_final: 0.7019 (tm-30) REVERT: G 301 GLU cc_start: 0.7768 (pt0) cc_final: 0.7106 (mm-30) outliers start: 0 outliers final: 2 residues processed: 617 average time/residue: 0.6768 time to fit residues: 465.3596 Evaluate side-chains 398 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 396 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain E residue 138 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN A 157 GLN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS B 38 HIS B 182 GLN B 185 HIS C 4 GLN C 38 HIS C 39 HIS C 269 ASN D 4 GLN D 110 ASN E 101 ASN F 148 HIS F 288 ASN F 320 ASN F 355 GLN G 143 GLN G 221 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.190578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.158444 restraints weight = 23285.165| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.05 r_work: 0.3815 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21280 Z= 0.135 Angle : 0.595 9.243 29085 Z= 0.303 Chirality : 0.039 0.183 3350 Planarity : 0.004 0.046 3612 Dihedral : 15.057 142.353 3357 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.79 % Allowed : 14.00 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.17), residues: 2516 helix: 1.69 (0.15), residues: 1262 sheet: 0.26 (0.24), residues: 442 loop : 0.30 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 208 TYR 0.020 0.001 TYR G 310 PHE 0.021 0.001 PHE G 75 TRP 0.012 0.001 TRP D 10 HIS 0.007 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (21264) covalent geometry : angle 0.58006 / 0.30 (29061) hydrogen bonds : bond 0.04220 / 2.82 ( 1122) hydrogen bonds : angle 4.45778 / 3.22 ( 3166) metal coordination : bond 0.00353 / 0.17 ( 16) metal coordination : angle 4.69137 / 2.98 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 425 time to evaluate : 0.591 Fit side-chains REVERT: A 66 SER cc_start: 0.6455 (OUTLIER) cc_final: 0.6197 (p) REVERT: A 71 MET cc_start: 0.7459 (mtp) cc_final: 0.7145 (ptp) REVERT: A 126 TRP cc_start: 0.6546 (p-90) cc_final: 0.6156 (p-90) REVERT: A 211 HIS cc_start: 0.7099 (t70) cc_final: 0.6496 (m170) REVERT: A 234 GLN cc_start: 0.7572 (mt0) cc_final: 0.7308 (pt0) REVERT: A 286 MET cc_start: 0.7281 (mmm) cc_final: 0.6479 (mmt) REVERT: A 325 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: A 338 ASP cc_start: 0.7430 (m-30) cc_final: 0.6823 (t0) REVERT: B 80 ARG cc_start: 0.6737 (mtm110) cc_final: 0.6528 (ttm110) REVERT: B 81 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6378 (mp0) REVERT: B 92 GLU cc_start: 0.7735 (tt0) cc_final: 0.7312 (tm-30) REVERT: B 133 ARG cc_start: 0.7493 (tpp80) cc_final: 0.7200 (ttp80) REVERT: B 185 HIS cc_start: 0.7286 (OUTLIER) cc_final: 0.6769 (t-90) REVERT: B 231 GLN cc_start: 0.6942 (mt0) cc_final: 0.6714 (mt0) REVERT: B 274 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6505 (ptm160) REVERT: B 311 LEU cc_start: 0.6724 (tp) cc_final: 0.6467 (mm) REVERT: B 338 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7380 (pt0) REVERT: C 22 GLU cc_start: 0.7414 (tp30) cc_final: 0.7183 (mp0) REVERT: C 44 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8519 (t) REVERT: C 77 ASP cc_start: 0.6803 (t70) cc_final: 0.6241 (t0) REVERT: C 94 ASP cc_start: 0.7536 (p0) cc_final: 0.7318 (p0) REVERT: C 106 ASP cc_start: 0.7592 (m-30) cc_final: 0.7319 (m-30) REVERT: C 130 MET cc_start: 0.8560 (mmp) cc_final: 0.8238 (mmp) REVERT: C 176 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7356 (mmtm) REVERT: C 192 ASN cc_start: 0.7746 (t0) cc_final: 0.7522 (t0) REVERT: C 193 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7620 (mp0) REVERT: C 231 GLN cc_start: 0.7640 (pt0) cc_final: 0.7129 (pp30) REVERT: C 254 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7502 (mt-10) REVERT: C 258 GLU cc_start: 0.6502 (mt-10) cc_final: 0.6075 (tt0) REVERT: C 318 ARG cc_start: 0.7180 (ptm-80) cc_final: 0.6574 (ttm110) REVERT: C 337 LYS cc_start: 0.8281 (mtmt) cc_final: 0.7874 (mtmm) REVERT: D 17 ASP cc_start: 0.7226 (t0) cc_final: 0.6910 (m-30) REVERT: D 106 ASP cc_start: 0.6597 (m-30) cc_final: 0.6306 (m-30) REVERT: D 110 ASN cc_start: 0.7935 (m-40) cc_final: 0.7633 (m110) REVERT: D 126 ASP cc_start: 0.8501 (t0) cc_final: 0.8185 (m-30) REVERT: D 127 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7371 (mt-10) REVERT: D 141 LYS cc_start: 0.8171 (tptt) cc_final: 0.7652 (tppp) REVERT: D 176 LYS cc_start: 0.8409 (mttm) cc_final: 0.8193 (mtpp) REVERT: D 211 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7427 (mm-30) REVERT: D 235 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7376 (tp40) REVERT: D 284 GLU cc_start: 0.7406 (tt0) cc_final: 0.6846 (mp0) REVERT: D 291 ARG cc_start: 0.7853 (tpp80) cc_final: 0.6959 (mmp80) REVERT: D 320 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7519 (mp) REVERT: E 134 GLU cc_start: 0.7749 (tt0) cc_final: 0.7228 (pt0) REVERT: E 147 GLU cc_start: 0.7813 (tp30) cc_final: 0.7483 (tp30) REVERT: E 170 GLN cc_start: 0.6654 (tp40) cc_final: 0.6129 (tp-100) REVERT: E 228 ASP cc_start: 0.7932 (t0) cc_final: 0.7535 (t0) REVERT: E 258 ARG cc_start: 0.6957 (tpm170) cc_final: 0.6441 (tmt170) REVERT: F 1 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.6999 (ptp) REVERT: F 36 GLN cc_start: 0.7768 (mt0) cc_final: 0.7383 (mt0) REVERT: F 87 GLU cc_start: 0.6715 (tt0) cc_final: 0.6448 (pp20) REVERT: F 95 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6435 (pp20) REVERT: F 105 ARG cc_start: 0.7847 (ttt180) cc_final: 0.7486 (ttp-170) REVERT: F 161 GLU cc_start: 0.6657 (pt0) cc_final: 0.6106 (pt0) REVERT: F 300 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6867 (mp0) REVERT: F 301 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7157 (mt-10) REVERT: F 343 SER cc_start: 0.8500 (p) cc_final: 0.8075 (t) REVERT: F 364 MET cc_start: 0.7802 (ttp) cc_final: 0.6893 (mmp) REVERT: G 4 THR cc_start: 0.8058 (m) cc_final: 0.7851 (m) REVERT: G 14 LEU cc_start: 0.7365 (mt) cc_final: 0.7088 (mt) REVERT: G 36 GLN cc_start: 0.6145 (OUTLIER) cc_final: 0.5885 (pp30) REVERT: G 48 ASP cc_start: 0.8132 (t0) cc_final: 0.7857 (t0) REVERT: G 50 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6309 (mm-30) REVERT: G 52 GLU cc_start: 0.8085 (pt0) cc_final: 0.7594 (pt0) REVERT: G 91 GLN cc_start: 0.6577 (mt0) cc_final: 0.6184 (pp30) REVERT: G 152 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6457 (mmt90) REVERT: G 153 TYR cc_start: 0.6960 (p90) cc_final: 0.6679 (p90) REVERT: G 161 GLU cc_start: 0.7159 (tt0) cc_final: 0.6415 (tt0) REVERT: G 217 GLN cc_start: 0.6101 (tt0) cc_final: 0.5732 (mm-40) REVERT: G 233 THR cc_start: 0.7064 (m) cc_final: 0.6744 (p) REVERT: G 299 GLN cc_start: 0.7207 (mm110) cc_final: 0.6872 (tm-30) REVERT: G 301 GLU cc_start: 0.7739 (pt0) cc_final: 0.7099 (tt0) REVERT: J 4 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6719 (tmt170) outliers start: 59 outliers final: 17 residues processed: 454 average time/residue: 0.6571 time to fit residues: 334.2364 Evaluate side-chains 400 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 373 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 152 ARG Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 138 optimal weight: 0.6980 chunk 191 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 139 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 HIS ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS C 269 ASN E 101 ASN E 126 ASN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.190311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.158237 restraints weight = 23122.782| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.03 r_work: 0.3810 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21280 Z= 0.129 Angle : 0.568 8.892 29085 Z= 0.288 Chirality : 0.039 0.229 3350 Planarity : 0.004 0.057 3612 Dihedral : 14.774 141.270 3352 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.97 % Allowed : 14.47 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.17), residues: 2516 helix: 1.75 (0.15), residues: 1258 sheet: 0.15 (0.23), residues: 447 loop : 0.24 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 168 TYR 0.014 0.001 TYR G 310 PHE 0.020 0.001 PHE G 75 TRP 0.011 0.001 TRP D 10 HIS 0.009 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (21264) covalent geometry : angle 0.55309 / 0.29 (29061) hydrogen bonds : bond 0.03576 / 2.40 ( 1122) hydrogen bonds : angle 4.19254 / 3.02 ( 3166) metal coordination : bond 0.01533 / 0.73 ( 16) metal coordination : angle 4.60964 / 3.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 395 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7236 (mtp) cc_final: 0.6965 (ptp) REVERT: A 126 TRP cc_start: 0.6593 (p-90) cc_final: 0.6004 (p-90) REVERT: A 211 HIS cc_start: 0.7030 (t70) cc_final: 0.6496 (m170) REVERT: A 226 SER cc_start: 0.8604 (t) cc_final: 0.7889 (m) REVERT: A 234 GLN cc_start: 0.7545 (mt0) cc_final: 0.7272 (pt0) REVERT: A 286 MET cc_start: 0.7311 (mmm) cc_final: 0.6470 (mmt) REVERT: A 325 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: A 338 ASP cc_start: 0.7438 (m-30) cc_final: 0.6793 (t0) REVERT: B 77 ASP cc_start: 0.7058 (m-30) cc_final: 0.6020 (m-30) REVERT: B 80 ARG cc_start: 0.6802 (mtm110) cc_final: 0.6561 (ttm110) REVERT: B 81 GLU cc_start: 0.6695 (mt-10) cc_final: 0.6352 (mp0) REVERT: B 92 GLU cc_start: 0.7752 (tt0) cc_final: 0.7342 (tm-30) REVERT: B 109 ASP cc_start: 0.7432 (t0) cc_final: 0.7050 (t0) REVERT: B 133 ARG cc_start: 0.7504 (tpp80) cc_final: 0.7196 (ttp80) REVERT: B 160 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: B 181 GLU cc_start: 0.7103 (tp30) cc_final: 0.6809 (tp30) REVERT: B 231 GLN cc_start: 0.6991 (mt0) cc_final: 0.6753 (mt0) REVERT: B 274 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6590 (ptm160) REVERT: B 338 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7344 (pt0) REVERT: C 22 GLU cc_start: 0.7428 (tp30) cc_final: 0.7086 (mp0) REVERT: C 44 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8557 (t) REVERT: C 81 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7417 (mt-10) REVERT: C 94 ASP cc_start: 0.7602 (p0) cc_final: 0.7264 (p0) REVERT: C 106 ASP cc_start: 0.7583 (m-30) cc_final: 0.7335 (m-30) REVERT: C 127 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: C 148 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8394 (mp0) REVERT: C 176 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7371 (mmtm) REVERT: C 192 ASN cc_start: 0.7767 (t0) cc_final: 0.7543 (t0) REVERT: C 231 GLN cc_start: 0.7683 (pt0) cc_final: 0.7264 (pp30) REVERT: C 318 ARG cc_start: 0.7182 (ptm-80) cc_final: 0.6579 (ttm110) REVERT: C 337 LYS cc_start: 0.8377 (mtmt) cc_final: 0.8048 (mtmm) REVERT: D 17 ASP cc_start: 0.7278 (t0) cc_final: 0.6935 (m-30) REVERT: D 92 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7891 (tp30) REVERT: D 106 ASP cc_start: 0.6556 (m-30) cc_final: 0.6290 (m-30) REVERT: D 126 ASP cc_start: 0.8510 (t0) cc_final: 0.8215 (m-30) REVERT: D 127 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7469 (mt-10) REVERT: D 141 LYS cc_start: 0.8181 (tptt) cc_final: 0.7641 (tppp) REVERT: D 176 LYS cc_start: 0.8423 (mttm) cc_final: 0.8173 (mtpp) REVERT: D 211 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7455 (mm-30) REVERT: D 235 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7376 (tp40) REVERT: D 284 GLU cc_start: 0.7407 (tt0) cc_final: 0.6858 (mp0) REVERT: D 291 ARG cc_start: 0.7827 (tpp80) cc_final: 0.7405 (tpp-160) REVERT: E 98 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: E 130 LYS cc_start: 0.7853 (tppp) cc_final: 0.7482 (tptp) REVERT: E 147 GLU cc_start: 0.7753 (tp30) cc_final: 0.7540 (tp30) REVERT: E 170 GLN cc_start: 0.6708 (tp40) cc_final: 0.6174 (mp10) REVERT: E 228 ASP cc_start: 0.7852 (t0) cc_final: 0.7651 (t0) REVERT: F 1 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7200 (ptp) REVERT: F 36 GLN cc_start: 0.7783 (mt0) cc_final: 0.7379 (mt0) REVERT: F 87 GLU cc_start: 0.6730 (tt0) cc_final: 0.6424 (pp20) REVERT: F 95 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6407 (pp20) REVERT: F 105 ARG cc_start: 0.7844 (ttt180) cc_final: 0.7406 (ttp-170) REVERT: F 136 LYS cc_start: 0.7426 (ttpt) cc_final: 0.6913 (tppt) REVERT: F 300 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6876 (mp0) REVERT: F 301 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7254 (mt-10) REVERT: F 343 SER cc_start: 0.8444 (p) cc_final: 0.7940 (t) REVERT: F 364 MET cc_start: 0.7760 (ttp) cc_final: 0.6893 (mmp) REVERT: G 4 THR cc_start: 0.7959 (m) cc_final: 0.7746 (m) REVERT: G 36 GLN cc_start: 0.6190 (OUTLIER) cc_final: 0.5879 (pp30) REVERT: G 48 ASP cc_start: 0.8097 (t0) cc_final: 0.7800 (t0) REVERT: G 50 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6299 (mm-30) REVERT: G 52 GLU cc_start: 0.8022 (pt0) cc_final: 0.7719 (pt0) REVERT: G 91 GLN cc_start: 0.6469 (mt0) cc_final: 0.6129 (pp30) REVERT: G 153 TYR cc_start: 0.6977 (p90) cc_final: 0.6705 (p90) REVERT: G 161 GLU cc_start: 0.7265 (tt0) cc_final: 0.6561 (tt0) REVERT: G 251 ASN cc_start: 0.7648 (p0) cc_final: 0.7290 (p0) REVERT: G 299 GLN cc_start: 0.7125 (mm110) cc_final: 0.6783 (tm-30) REVERT: G 301 GLU cc_start: 0.7706 (pt0) cc_final: 0.7010 (tt0) REVERT: G 339 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7060 (mpp) outliers start: 84 outliers final: 28 residues processed: 442 average time/residue: 0.6064 time to fit residues: 302.5421 Evaluate side-chains 398 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 361 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 364 MET Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 160 optimal weight: 5.9990 chunk 220 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN A 96 GLN A 281 ASN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS C 269 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN D 198 HIS ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN E 126 ASN G 212 ASN G 217 GLN G 299 GLN G 348 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.186428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.153330 restraints weight = 23277.731| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.22 r_work: 0.3719 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 21280 Z= 0.204 Angle : 0.632 8.346 29085 Z= 0.313 Chirality : 0.042 0.210 3350 Planarity : 0.005 0.070 3612 Dihedral : 14.964 142.082 3352 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.54 % Allowed : 16.26 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.17), residues: 2516 helix: 1.37 (0.15), residues: 1270 sheet: 0.12 (0.25), residues: 393 loop : 0.02 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 11 TYR 0.022 0.002 TYR G 310 PHE 0.017 0.002 PHE B 136 TRP 0.011 0.002 TRP B 10 HIS 0.005 0.001 HIS E 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (21264) covalent geometry : angle 0.61972 / 0.31 (29061) hydrogen bonds : bond 0.03889 / 2.63 ( 1122) hydrogen bonds : angle 4.20590 / 3.02 ( 3166) metal coordination : bond 0.00734 / 0.32 ( 16) metal coordination : angle 4.28796 / 2.72 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 384 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 108 LEU cc_start: 0.5302 (OUTLIER) cc_final: 0.5002 (tp) REVERT: A 126 TRP cc_start: 0.6470 (p-90) cc_final: 0.6041 (p-90) REVERT: A 211 HIS cc_start: 0.7143 (t70) cc_final: 0.6426 (m170) REVERT: A 234 GLN cc_start: 0.7575 (mt0) cc_final: 0.7276 (pt0) REVERT: A 286 MET cc_start: 0.7347 (mmm) cc_final: 0.6468 (mmt) REVERT: B 77 ASP cc_start: 0.7112 (m-30) cc_final: 0.6228 (m-30) REVERT: B 80 ARG cc_start: 0.6986 (mtm110) cc_final: 0.6733 (ttm110) REVERT: B 81 GLU cc_start: 0.6747 (mt-10) cc_final: 0.6404 (mt-10) REVERT: B 92 GLU cc_start: 0.7800 (tt0) cc_final: 0.7327 (tm-30) REVERT: B 102 GLU cc_start: 0.6580 (tt0) cc_final: 0.6216 (tp30) REVERT: B 133 ARG cc_start: 0.7540 (tpp80) cc_final: 0.7187 (ttp80) REVERT: B 160 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7427 (mp10) REVERT: B 185 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.6858 (t70) REVERT: B 231 GLN cc_start: 0.7297 (mt0) cc_final: 0.7009 (mt0) REVERT: B 314 ARG cc_start: 0.7711 (mmt-90) cc_final: 0.7347 (mmm-85) REVERT: B 338 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7429 (pt0) REVERT: C 22 GLU cc_start: 0.7587 (tp30) cc_final: 0.7135 (mp0) REVERT: C 81 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7486 (mt-10) REVERT: C 94 ASP cc_start: 0.7596 (p0) cc_final: 0.7290 (p0) REVERT: C 106 ASP cc_start: 0.7605 (m-30) cc_final: 0.7334 (m-30) REVERT: C 127 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7542 (tp30) REVERT: C 148 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8419 (mp0) REVERT: C 176 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7360 (mmtm) REVERT: C 192 ASN cc_start: 0.7872 (t0) cc_final: 0.7334 (t0) REVERT: C 193 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.5780 (mp0) REVERT: C 231 GLN cc_start: 0.7762 (pt0) cc_final: 0.7275 (pp30) REVERT: C 250 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6896 (mt) REVERT: C 258 GLU cc_start: 0.6782 (mt-10) cc_final: 0.6231 (tt0) REVERT: C 316 LEU cc_start: 0.7877 (mt) cc_final: 0.7633 (mp) REVERT: C 318 ARG cc_start: 0.7200 (ptm-80) cc_final: 0.6576 (ttm110) REVERT: C 337 LYS cc_start: 0.8452 (mtmt) cc_final: 0.8193 (ttmm) REVERT: D 17 ASP cc_start: 0.7344 (t0) cc_final: 0.6921 (m-30) REVERT: D 92 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7934 (tp30) REVERT: D 106 ASP cc_start: 0.6702 (m-30) cc_final: 0.6428 (m-30) REVERT: D 126 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8337 (m-30) REVERT: D 127 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7591 (mt-10) REVERT: D 141 LYS cc_start: 0.8336 (tptt) cc_final: 0.7748 (tppt) REVERT: D 154 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8167 (mt) REVERT: D 176 LYS cc_start: 0.8391 (mttm) cc_final: 0.8043 (mtpp) REVERT: D 211 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7500 (mm-30) REVERT: D 262 GLU cc_start: 0.7732 (mp0) cc_final: 0.7406 (mp0) REVERT: D 284 GLU cc_start: 0.7580 (tt0) cc_final: 0.6863 (mp0) REVERT: D 291 ARG cc_start: 0.7945 (tpp80) cc_final: 0.7637 (tpp80) REVERT: E 72 THR cc_start: 0.7139 (OUTLIER) cc_final: 0.6800 (t) REVERT: E 78 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8523 (p) REVERT: E 85 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.5907 (mptm) REVERT: E 98 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: E 130 LYS cc_start: 0.7807 (tppp) cc_final: 0.7429 (tptp) REVERT: E 147 GLU cc_start: 0.7846 (tp30) cc_final: 0.7450 (tp30) REVERT: E 149 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: E 170 GLN cc_start: 0.6830 (tp40) cc_final: 0.6229 (mp10) REVERT: E 258 ARG cc_start: 0.7733 (mmm160) cc_final: 0.7472 (mmm-85) REVERT: E 322 TYR cc_start: 0.7894 (m-10) cc_final: 0.7428 (m-10) REVERT: F 36 GLN cc_start: 0.7819 (mt0) cc_final: 0.7415 (mt0) REVERT: F 50 GLU cc_start: 0.7231 (mt-10) cc_final: 0.7011 (tt0) REVERT: F 73 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7005 (pmt170) REVERT: F 87 GLU cc_start: 0.6783 (tt0) cc_final: 0.6451 (pp20) REVERT: F 95 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6297 (pp20) REVERT: F 105 ARG cc_start: 0.7991 (ttt180) cc_final: 0.7523 (ttp-170) REVERT: F 136 LYS cc_start: 0.7519 (ttpt) cc_final: 0.6959 (tppt) REVERT: F 205 ARG cc_start: 0.7376 (mtm-85) cc_final: 0.6982 (mtm-85) REVERT: F 300 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6869 (mp0) REVERT: F 301 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7337 (mt-10) REVERT: F 305 ILE cc_start: 0.8520 (mt) cc_final: 0.8228 (mp) REVERT: F 343 SER cc_start: 0.8426 (p) cc_final: 0.8001 (t) REVERT: F 364 MET cc_start: 0.7839 (ttp) cc_final: 0.6913 (mmp) REVERT: G 14 LEU cc_start: 0.7250 (mt) cc_final: 0.6950 (mt) REVERT: G 36 GLN cc_start: 0.6251 (OUTLIER) cc_final: 0.5911 (pp30) REVERT: G 48 ASP cc_start: 0.8142 (t0) cc_final: 0.7902 (t0) REVERT: G 50 GLU cc_start: 0.6772 (mm-30) cc_final: 0.6304 (mm-30) REVERT: G 91 GLN cc_start: 0.6704 (mt0) cc_final: 0.6319 (pp30) REVERT: G 127 GLU cc_start: 0.7996 (pt0) cc_final: 0.7335 (pt0) REVERT: G 153 TYR cc_start: 0.7139 (p90) cc_final: 0.6728 (p90) REVERT: G 161 GLU cc_start: 0.7492 (tt0) cc_final: 0.6552 (tt0) REVERT: G 217 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.6951 (mm110) REVERT: G 251 ASN cc_start: 0.7637 (p0) cc_final: 0.7288 (p0) REVERT: G 299 GLN cc_start: 0.7333 (mm-40) cc_final: 0.6921 (tm-30) REVERT: G 301 GLU cc_start: 0.7756 (pt0) cc_final: 0.7112 (tt0) outliers start: 96 outliers final: 43 residues processed: 440 average time/residue: 0.6082 time to fit residues: 302.5891 Evaluate side-chains 423 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 365 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 217 GLN Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 364 MET Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 246 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 chunk 91 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 237 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 35 GLN B 13 GLN C 13 GLN C 269 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN E 101 ASN E 211 GLN G 212 ASN G 217 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.188732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.155761 restraints weight = 23131.233| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.19 r_work: 0.3756 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21280 Z= 0.133 Angle : 0.572 8.153 29085 Z= 0.285 Chirality : 0.039 0.166 3350 Planarity : 0.004 0.073 3612 Dihedral : 14.696 150.660 3352 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.74 % Allowed : 18.39 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.17), residues: 2516 helix: 1.59 (0.15), residues: 1260 sheet: 0.06 (0.25), residues: 402 loop : 0.07 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 86 TYR 0.028 0.002 TYR B 341 PHE 0.013 0.001 PHE F 3 TRP 0.012 0.001 TRP B 278 HIS 0.007 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (21264) covalent geometry : angle 0.55964 / 0.28 (29061) hydrogen bonds : bond 0.03365 / 2.27 ( 1122) hydrogen bonds : angle 4.00220 / 2.87 ( 3166) metal coordination : bond 0.00303 / 0.15 ( 16) metal coordination : angle 4.21850 / 2.68 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 378 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7456 (ptp) cc_final: 0.6983 (ptp) REVERT: A 108 LEU cc_start: 0.5273 (OUTLIER) cc_final: 0.4929 (tp) REVERT: A 126 TRP cc_start: 0.6483 (p-90) cc_final: 0.5989 (p-90) REVERT: A 211 HIS cc_start: 0.7221 (t70) cc_final: 0.6471 (m170) REVERT: A 234 GLN cc_start: 0.7565 (mt0) cc_final: 0.7254 (pt0) REVERT: B 77 ASP cc_start: 0.7076 (m-30) cc_final: 0.6210 (m-30) REVERT: B 80 ARG cc_start: 0.6992 (mtm110) cc_final: 0.6710 (ttm110) REVERT: B 81 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6336 (mt-10) REVERT: B 92 GLU cc_start: 0.7745 (tt0) cc_final: 0.7296 (tm-30) REVERT: B 133 ARG cc_start: 0.7483 (tpp80) cc_final: 0.7164 (ttp80) REVERT: B 160 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: B 181 GLU cc_start: 0.7166 (tp30) cc_final: 0.6904 (tp30) REVERT: B 185 HIS cc_start: 0.7456 (m170) cc_final: 0.6907 (t-90) REVERT: B 231 GLN cc_start: 0.7264 (mt0) cc_final: 0.7005 (mt0) REVERT: B 314 ARG cc_start: 0.7827 (mmt-90) cc_final: 0.7494 (mmm-85) REVERT: B 338 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7384 (pt0) REVERT: C 9 LYS cc_start: 0.8496 (tttp) cc_final: 0.8265 (tttm) REVERT: C 22 GLU cc_start: 0.7513 (tp30) cc_final: 0.7121 (mp0) REVERT: C 81 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7425 (mt-10) REVERT: C 94 ASP cc_start: 0.7589 (p0) cc_final: 0.7258 (p0) REVERT: C 106 ASP cc_start: 0.7652 (m-30) cc_final: 0.7378 (m-30) REVERT: C 127 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7513 (tp30) REVERT: C 148 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8362 (mp0) REVERT: C 176 LYS cc_start: 0.8262 (mtpp) cc_final: 0.7375 (mmtm) REVERT: C 192 ASN cc_start: 0.7846 (t0) cc_final: 0.7308 (t0) REVERT: C 193 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.5870 (mp0) REVERT: C 231 GLN cc_start: 0.7749 (pt0) cc_final: 0.7251 (pp30) REVERT: C 274 ARG cc_start: 0.7851 (ttm-80) cc_final: 0.7623 (mtp-110) REVERT: C 318 ARG cc_start: 0.7237 (ptm-80) cc_final: 0.6620 (ttm110) REVERT: C 337 LYS cc_start: 0.8307 (mtmt) cc_final: 0.7957 (mtmm) REVERT: D 17 ASP cc_start: 0.7348 (t0) cc_final: 0.6951 (m-30) REVERT: D 92 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7937 (tp30) REVERT: D 106 ASP cc_start: 0.6612 (m-30) cc_final: 0.6373 (m-30) REVERT: D 126 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: D 127 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7546 (mt-10) REVERT: D 141 LYS cc_start: 0.8338 (tptt) cc_final: 0.7757 (tppt) REVERT: D 176 LYS cc_start: 0.8365 (mttm) cc_final: 0.7981 (mtpp) REVERT: D 211 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7476 (mm-30) REVERT: D 262 GLU cc_start: 0.7667 (mp0) cc_final: 0.7344 (mp0) REVERT: D 284 GLU cc_start: 0.7540 (tt0) cc_final: 0.6898 (mp0) REVERT: D 291 ARG cc_start: 0.7888 (tpp80) cc_final: 0.6949 (mmp80) REVERT: E 45 SER cc_start: 0.8167 (p) cc_final: 0.7958 (p) REVERT: E 72 THR cc_start: 0.7135 (OUTLIER) cc_final: 0.6811 (t) REVERT: E 78 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8547 (m) REVERT: E 85 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.5904 (mptm) REVERT: E 126 ASN cc_start: 0.8452 (m-40) cc_final: 0.8156 (m-40) REVERT: E 130 LYS cc_start: 0.7809 (tppp) cc_final: 0.7453 (tptp) REVERT: E 147 GLU cc_start: 0.7799 (tp30) cc_final: 0.7593 (tp30) REVERT: E 170 GLN cc_start: 0.6811 (tp40) cc_final: 0.6218 (mp10) REVERT: E 258 ARG cc_start: 0.7809 (mmm160) cc_final: 0.7573 (mmm-85) REVERT: E 277 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7101 (tt) REVERT: F 36 GLN cc_start: 0.7779 (mt0) cc_final: 0.7366 (mt0) REVERT: F 69 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7650 (p) REVERT: F 73 ARG cc_start: 0.7736 (tpp80) cc_final: 0.7044 (pmt170) REVERT: F 87 GLU cc_start: 0.6776 (tt0) cc_final: 0.6448 (pp20) REVERT: F 95 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6287 (pp20) REVERT: F 105 ARG cc_start: 0.7944 (ttt180) cc_final: 0.7486 (ttp-170) REVERT: F 136 LYS cc_start: 0.7543 (ttpt) cc_final: 0.6983 (tppt) REVERT: F 205 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.6926 (mtm-85) REVERT: F 300 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6827 (mp0) REVERT: F 301 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7516 (mt-10) REVERT: F 343 SER cc_start: 0.8406 (p) cc_final: 0.7869 (t) REVERT: G 14 LEU cc_start: 0.7207 (mt) cc_final: 0.6989 (mt) REVERT: G 27 LEU cc_start: 0.8101 (mm) cc_final: 0.7813 (tm) REVERT: G 34 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6910 (mt) REVERT: G 36 GLN cc_start: 0.6228 (OUTLIER) cc_final: 0.5774 (pp30) REVERT: G 48 ASP cc_start: 0.8122 (t0) cc_final: 0.7909 (t0) REVERT: G 50 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6290 (mm-30) REVERT: G 91 GLN cc_start: 0.6442 (mt0) cc_final: 0.6160 (pp30) REVERT: G 153 TYR cc_start: 0.7128 (p90) cc_final: 0.6696 (p90) REVERT: G 161 GLU cc_start: 0.7502 (tt0) cc_final: 0.6761 (tt0) REVERT: G 251 ASN cc_start: 0.7614 (p0) cc_final: 0.7295 (p0) REVERT: G 299 GLN cc_start: 0.7373 (mm-40) cc_final: 0.6919 (tm-30) outliers start: 79 outliers final: 35 residues processed: 427 average time/residue: 0.6268 time to fit residues: 302.0441 Evaluate side-chains 402 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 355 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 364 MET Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 247 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 208 optimal weight: 0.9990 chunk 225 optimal weight: 0.9980 chunk 246 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN B 185 HIS C 269 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.188437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.155839 restraints weight = 23034.661| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.16 r_work: 0.3857 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21280 Z= 0.138 Angle : 0.566 8.310 29085 Z= 0.282 Chirality : 0.039 0.159 3350 Planarity : 0.004 0.065 3612 Dihedral : 14.549 152.053 3352 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.55 % Allowed : 19.86 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.17), residues: 2516 helix: 1.63 (0.15), residues: 1259 sheet: 0.06 (0.25), residues: 402 loop : 0.08 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 244 TYR 0.024 0.002 TYR B 341 PHE 0.013 0.001 PHE F 3 TRP 0.011 0.001 TRP B 278 HIS 0.006 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (21264) covalent geometry : angle 0.55456 / 0.28 (29061) hydrogen bonds : bond 0.03322 / 2.25 ( 1122) hydrogen bonds : angle 3.94084 / 2.83 ( 3166) metal coordination : bond 0.00329 / 0.16 ( 16) metal coordination : angle 4.04334 / 2.58 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 365 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.7541 (ptp) cc_final: 0.7117 (ptp) REVERT: A 126 TRP cc_start: 0.6392 (p-90) cc_final: 0.5876 (p-90) REVERT: A 211 HIS cc_start: 0.7215 (t70) cc_final: 0.6471 (m170) REVERT: A 234 GLN cc_start: 0.7533 (mt0) cc_final: 0.7236 (pt0) REVERT: A 244 VAL cc_start: 0.7512 (OUTLIER) cc_final: 0.7237 (p) REVERT: A 325 GLU cc_start: 0.7668 (mp0) cc_final: 0.7276 (mm-30) REVERT: B 77 ASP cc_start: 0.7042 (m-30) cc_final: 0.6199 (m-30) REVERT: B 80 ARG cc_start: 0.6981 (mtm110) cc_final: 0.6728 (ttm110) REVERT: B 81 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6367 (mt-10) REVERT: B 92 GLU cc_start: 0.7697 (tt0) cc_final: 0.7251 (tm-30) REVERT: B 133 ARG cc_start: 0.7463 (tpp80) cc_final: 0.7150 (ttp80) REVERT: B 160 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: B 185 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.6899 (t70) REVERT: B 231 GLN cc_start: 0.7312 (mt0) cc_final: 0.7031 (mp10) REVERT: B 314 ARG cc_start: 0.7793 (mmt-90) cc_final: 0.7526 (mmm-85) REVERT: B 338 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7314 (pt0) REVERT: C 9 LYS cc_start: 0.8496 (tttp) cc_final: 0.8278 (tttm) REVERT: C 22 GLU cc_start: 0.7461 (tp30) cc_final: 0.7137 (mp0) REVERT: C 81 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7476 (mt-10) REVERT: C 94 ASP cc_start: 0.7599 (p0) cc_final: 0.7309 (p0) REVERT: C 106 ASP cc_start: 0.7635 (m-30) cc_final: 0.7390 (m-30) REVERT: C 127 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7567 (tp30) REVERT: C 176 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7369 (mmtm) REVERT: C 192 ASN cc_start: 0.7840 (t0) cc_final: 0.7356 (t0) REVERT: C 193 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.5911 (mp0) REVERT: C 231 GLN cc_start: 0.7798 (pt0) cc_final: 0.7315 (pp30) REVERT: C 258 GLU cc_start: 0.6492 (mt-10) cc_final: 0.5999 (tt0) REVERT: C 318 ARG cc_start: 0.7230 (ptm-80) cc_final: 0.6636 (ttm110) REVERT: C 337 LYS cc_start: 0.8323 (mtmt) cc_final: 0.7981 (mtmm) REVERT: D 17 ASP cc_start: 0.7345 (t0) cc_final: 0.6952 (m-30) REVERT: D 92 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7892 (tp30) REVERT: D 106 ASP cc_start: 0.6601 (m-30) cc_final: 0.6348 (m-30) REVERT: D 126 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8264 (m-30) REVERT: D 127 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7576 (mt-10) REVERT: D 141 LYS cc_start: 0.8348 (tptt) cc_final: 0.7770 (tppt) REVERT: D 154 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8231 (mt) REVERT: D 176 LYS cc_start: 0.8373 (mttm) cc_final: 0.7985 (mtpp) REVERT: D 211 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7491 (mm-30) REVERT: D 262 GLU cc_start: 0.7664 (mp0) cc_final: 0.7384 (mp0) REVERT: D 284 GLU cc_start: 0.7496 (tt0) cc_final: 0.6845 (mp0) REVERT: D 291 ARG cc_start: 0.7858 (tpp80) cc_final: 0.6904 (mmp80) REVERT: E 72 THR cc_start: 0.7161 (OUTLIER) cc_final: 0.6848 (t) REVERT: E 85 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.5894 (mptm) REVERT: E 98 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: E 126 ASN cc_start: 0.8450 (m-40) cc_final: 0.8135 (m-40) REVERT: E 130 LYS cc_start: 0.7833 (tppp) cc_final: 0.7486 (tptp) REVERT: E 170 GLN cc_start: 0.6796 (tp40) cc_final: 0.6210 (mp10) REVERT: E 258 ARG cc_start: 0.7738 (mmm160) cc_final: 0.7494 (mmm-85) REVERT: E 277 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7121 (tt) REVERT: F 1 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.7043 (ptt) REVERT: F 36 GLN cc_start: 0.7752 (mt0) cc_final: 0.7353 (mt0) REVERT: F 69 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7789 (p) REVERT: F 87 GLU cc_start: 0.6762 (tt0) cc_final: 0.6467 (pp20) REVERT: F 95 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6261 (pp20) REVERT: F 105 ARG cc_start: 0.7907 (ttt180) cc_final: 0.7462 (ttp-110) REVERT: F 136 LYS cc_start: 0.7550 (ttpt) cc_final: 0.7000 (tppt) REVERT: F 165 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.5954 (tm-30) REVERT: F 300 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6872 (mp0) REVERT: F 301 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7170 (mm-30) REVERT: F 343 SER cc_start: 0.8385 (p) cc_final: 0.7921 (t) REVERT: G 14 LEU cc_start: 0.7244 (mt) cc_final: 0.6982 (mt) REVERT: G 27 LEU cc_start: 0.8108 (mm) cc_final: 0.7817 (tm) REVERT: G 34 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6953 (mt) REVERT: G 36 GLN cc_start: 0.6159 (OUTLIER) cc_final: 0.5749 (pp30) REVERT: G 50 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6335 (mm-30) REVERT: G 51 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7536 (ptp) REVERT: G 91 GLN cc_start: 0.6501 (mt0) cc_final: 0.6222 (pp30) REVERT: G 127 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: G 153 TYR cc_start: 0.7131 (p90) cc_final: 0.6669 (p90) REVERT: G 161 GLU cc_start: 0.7520 (tt0) cc_final: 0.6516 (tt0) REVERT: G 251 ASN cc_start: 0.7588 (p0) cc_final: 0.7232 (p0) REVERT: G 299 GLN cc_start: 0.7375 (mm-40) cc_final: 0.6918 (tm-30) outliers start: 75 outliers final: 38 residues processed: 411 average time/residue: 0.6205 time to fit residues: 288.3800 Evaluate side-chains 402 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 347 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 364 MET Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 117 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 223 optimal weight: 0.0970 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 206 optimal weight: 0.0770 chunk 175 optimal weight: 3.9990 overall best weight: 1.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 269 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN E 211 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.187477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.155039 restraints weight = 23207.804| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.95 r_work: 0.3857 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21280 Z= 0.165 Angle : 0.596 7.760 29085 Z= 0.298 Chirality : 0.040 0.220 3350 Planarity : 0.005 0.097 3612 Dihedral : 14.576 148.648 3352 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.83 % Allowed : 20.14 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.17), residues: 2516 helix: 1.51 (0.15), residues: 1264 sheet: 0.11 (0.24), residues: 413 loop : 0.12 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 86 TYR 0.023 0.002 TYR B 341 PHE 0.012 0.001 PHE F 3 TRP 0.013 0.001 TRP E 140 HIS 0.006 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (21264) covalent geometry : angle 0.58559 / 0.30 (29061) hydrogen bonds : bond 0.03446 / 2.34 ( 1122) hydrogen bonds : angle 3.97044 / 2.84 ( 3166) metal coordination : bond 0.00373 / 0.19 ( 16) metal coordination : angle 3.89091 / 2.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 353 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.7604 (ptp) cc_final: 0.7203 (ptp) REVERT: A 126 TRP cc_start: 0.6266 (p-90) cc_final: 0.5788 (p-90) REVERT: A 211 HIS cc_start: 0.7220 (t70) cc_final: 0.6489 (m170) REVERT: A 234 GLN cc_start: 0.7516 (mt0) cc_final: 0.7247 (pt0) REVERT: A 244 VAL cc_start: 0.7516 (OUTLIER) cc_final: 0.7258 (p) REVERT: B 77 ASP cc_start: 0.7010 (m-30) cc_final: 0.6175 (m-30) REVERT: B 80 ARG cc_start: 0.6998 (mtm110) cc_final: 0.6759 (ttm110) REVERT: B 81 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6353 (mt-10) REVERT: B 92 GLU cc_start: 0.7660 (tt0) cc_final: 0.7228 (tm-30) REVERT: B 133 ARG cc_start: 0.7454 (tpp80) cc_final: 0.7148 (ttp80) REVERT: B 160 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: B 185 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.7028 (t70) REVERT: B 231 GLN cc_start: 0.7335 (mt0) cc_final: 0.7081 (mt0) REVERT: B 314 ARG cc_start: 0.7797 (mmt-90) cc_final: 0.7526 (mmm-85) REVERT: B 338 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7292 (pt0) REVERT: C 9 LYS cc_start: 0.8531 (tttp) cc_final: 0.8313 (tttm) REVERT: C 22 GLU cc_start: 0.7466 (tp30) cc_final: 0.7169 (mp0) REVERT: C 81 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7389 (mt-10) REVERT: C 86 ARG cc_start: 0.7437 (mtm110) cc_final: 0.7195 (mtm110) REVERT: C 94 ASP cc_start: 0.7501 (p0) cc_final: 0.7260 (p0) REVERT: C 106 ASP cc_start: 0.7605 (m-30) cc_final: 0.7345 (m-30) REVERT: C 127 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7534 (tp30) REVERT: C 176 LYS cc_start: 0.8291 (mtpp) cc_final: 0.7377 (mmtm) REVERT: C 192 ASN cc_start: 0.7842 (t0) cc_final: 0.7343 (t0) REVERT: C 193 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6085 (mp0) REVERT: C 231 GLN cc_start: 0.7780 (pt0) cc_final: 0.7298 (pp30) REVERT: C 258 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6169 (tt0) REVERT: C 318 ARG cc_start: 0.7162 (ptm-80) cc_final: 0.6553 (ttm110) REVERT: C 337 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7999 (mtmm) REVERT: D 17 ASP cc_start: 0.7396 (t0) cc_final: 0.6959 (m-30) REVERT: D 92 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7857 (tp30) REVERT: D 106 ASP cc_start: 0.6630 (m-30) cc_final: 0.6359 (m-30) REVERT: D 126 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8214 (m-30) REVERT: D 127 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7620 (mt-10) REVERT: D 141 LYS cc_start: 0.8348 (tptt) cc_final: 0.7766 (tppt) REVERT: D 154 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8125 (mt) REVERT: D 176 LYS cc_start: 0.8363 (mttm) cc_final: 0.7980 (mtpp) REVERT: D 211 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7471 (mm-30) REVERT: D 262 GLU cc_start: 0.7642 (mp0) cc_final: 0.7371 (mp0) REVERT: D 284 GLU cc_start: 0.7473 (tt0) cc_final: 0.6832 (mp0) REVERT: D 291 ARG cc_start: 0.7852 (tpp80) cc_final: 0.6897 (mmp80) REVERT: E 72 THR cc_start: 0.7144 (OUTLIER) cc_final: 0.6837 (t) REVERT: E 85 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.5926 (mptm) REVERT: E 98 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: E 101 ASN cc_start: 0.6717 (m-40) cc_final: 0.6514 (m110) REVERT: E 126 ASN cc_start: 0.8501 (m-40) cc_final: 0.8146 (m-40) REVERT: E 130 LYS cc_start: 0.7841 (tppp) cc_final: 0.7498 (tptp) REVERT: E 170 GLN cc_start: 0.6777 (tp40) cc_final: 0.6211 (mp10) REVERT: E 258 ARG cc_start: 0.7697 (mmm160) cc_final: 0.7466 (mmm-85) REVERT: F 69 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7743 (p) REVERT: F 73 ARG cc_start: 0.7746 (mpp80) cc_final: 0.7469 (mpp80) REVERT: F 87 GLU cc_start: 0.6717 (tt0) cc_final: 0.6443 (pp20) REVERT: F 95 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6224 (pp20) REVERT: F 105 ARG cc_start: 0.7919 (ttt180) cc_final: 0.7475 (ttp-110) REVERT: F 165 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.6037 (tm-30) REVERT: F 300 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6879 (mp0) REVERT: F 301 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7159 (mm-30) REVERT: F 343 SER cc_start: 0.8362 (p) cc_final: 0.7789 (t) REVERT: G 14 LEU cc_start: 0.7196 (mt) cc_final: 0.6945 (mt) REVERT: G 27 LEU cc_start: 0.8127 (mm) cc_final: 0.7844 (tm) REVERT: G 34 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6937 (mt) REVERT: G 36 GLN cc_start: 0.6153 (OUTLIER) cc_final: 0.5722 (pp30) REVERT: G 48 ASP cc_start: 0.8323 (t0) cc_final: 0.8087 (t0) REVERT: G 50 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6575 (mm-30) REVERT: G 51 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7590 (ptp) REVERT: G 91 GLN cc_start: 0.6503 (mt0) cc_final: 0.6276 (pp30) REVERT: G 161 GLU cc_start: 0.7612 (tt0) cc_final: 0.6705 (tt0) REVERT: G 207 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7189 (mm) REVERT: G 235 LYS cc_start: 0.7263 (mmtm) cc_final: 0.6876 (mtmt) REVERT: G 251 ASN cc_start: 0.7592 (p0) cc_final: 0.7241 (p0) REVERT: G 299 GLN cc_start: 0.7401 (mm-40) cc_final: 0.6917 (tm-30) outliers start: 81 outliers final: 40 residues processed: 400 average time/residue: 0.6080 time to fit residues: 275.7385 Evaluate side-chains 394 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 339 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 364 MET Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 75 optimal weight: 2.9990 chunk 245 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN B 185 HIS C 269 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.186292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.153228 restraints weight = 22960.953| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.19 r_work: 0.3821 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21280 Z= 0.189 Angle : 0.629 12.300 29085 Z= 0.312 Chirality : 0.041 0.183 3350 Planarity : 0.005 0.069 3612 Dihedral : 14.699 143.730 3352 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.92 % Allowed : 20.61 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2516 helix: 1.36 (0.15), residues: 1261 sheet: 0.02 (0.24), residues: 418 loop : 0.05 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 86 TYR 0.024 0.002 TYR B 341 PHE 0.013 0.002 PHE F 3 TRP 0.016 0.002 TRP E 140 HIS 0.010 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (21264) covalent geometry : angle 0.61996 / 0.31 (29061) hydrogen bonds : bond 0.03605 / 2.45 ( 1122) hydrogen bonds : angle 4.05632 / 2.90 ( 3166) metal coordination : bond 0.00397 / 0.20 ( 16) metal coordination : angle 3.70106 / 2.35 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 357 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7661 (ptp) cc_final: 0.7287 (ptp) REVERT: A 126 TRP cc_start: 0.6255 (p-90) cc_final: 0.5757 (p-90) REVERT: A 211 HIS cc_start: 0.7182 (t70) cc_final: 0.6383 (m170) REVERT: A 234 GLN cc_start: 0.7544 (mt0) cc_final: 0.7261 (pt0) REVERT: A 244 VAL cc_start: 0.7570 (OUTLIER) cc_final: 0.7305 (p) REVERT: A 286 MET cc_start: 0.7428 (mmm) cc_final: 0.6550 (mmt) REVERT: A 325 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7339 (mm-30) REVERT: B 77 ASP cc_start: 0.7042 (m-30) cc_final: 0.6207 (m-30) REVERT: B 80 ARG cc_start: 0.7071 (mtm110) cc_final: 0.6816 (ttm110) REVERT: B 81 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6306 (mt-10) REVERT: B 92 GLU cc_start: 0.7698 (tt0) cc_final: 0.7267 (tm-30) REVERT: B 133 ARG cc_start: 0.7507 (tpp80) cc_final: 0.7292 (mmm-85) REVERT: B 160 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7310 (mp10) REVERT: B 181 GLU cc_start: 0.7411 (tp30) cc_final: 0.7188 (mm-30) REVERT: B 185 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.6945 (t70) REVERT: B 231 GLN cc_start: 0.7381 (mt0) cc_final: 0.7072 (mt0) REVERT: B 314 ARG cc_start: 0.7815 (mmt-90) cc_final: 0.7385 (mmm-85) REVERT: B 338 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7394 (pt0) REVERT: C 9 LYS cc_start: 0.8552 (tttp) cc_final: 0.8327 (tttm) REVERT: C 22 GLU cc_start: 0.7486 (tp30) cc_final: 0.7140 (mp0) REVERT: C 106 ASP cc_start: 0.7733 (m-30) cc_final: 0.7413 (m-30) REVERT: C 176 LYS cc_start: 0.8328 (mtpp) cc_final: 0.7405 (mmtm) REVERT: C 192 ASN cc_start: 0.7886 (t0) cc_final: 0.7572 (t0) REVERT: C 231 GLN cc_start: 0.7797 (pt0) cc_final: 0.7279 (pp30) REVERT: C 258 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6384 (tt0) REVERT: C 318 ARG cc_start: 0.7239 (ptm-80) cc_final: 0.6614 (ttm110) REVERT: C 337 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8064 (mtmm) REVERT: D 17 ASP cc_start: 0.7461 (t0) cc_final: 0.6976 (m-30) REVERT: D 92 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7805 (tp30) REVERT: D 106 ASP cc_start: 0.6822 (m-30) cc_final: 0.6548 (m-30) REVERT: D 126 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8306 (m-30) REVERT: D 127 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7687 (mt-10) REVERT: D 141 LYS cc_start: 0.8349 (tptt) cc_final: 0.7767 (tppt) REVERT: D 154 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8126 (mt) REVERT: D 176 LYS cc_start: 0.8413 (mttm) cc_final: 0.7966 (mtpp) REVERT: D 262 GLU cc_start: 0.7653 (mp0) cc_final: 0.7385 (mp0) REVERT: D 291 ARG cc_start: 0.7881 (tpp80) cc_final: 0.6924 (mmp80) REVERT: E 72 THR cc_start: 0.7138 (OUTLIER) cc_final: 0.6836 (t) REVERT: E 85 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.5929 (mptm) REVERT: E 98 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: E 126 ASN cc_start: 0.8587 (m-40) cc_final: 0.8228 (m-40) REVERT: E 130 LYS cc_start: 0.7838 (tppp) cc_final: 0.7462 (tptp) REVERT: E 170 GLN cc_start: 0.6860 (tp40) cc_final: 0.6227 (mp10) REVERT: E 258 ARG cc_start: 0.7714 (mmm160) cc_final: 0.7487 (mmm-85) REVERT: E 277 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7017 (tt) REVERT: F 69 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7781 (p) REVERT: F 73 ARG cc_start: 0.7846 (mpp80) cc_final: 0.7076 (pmt170) REVERT: F 87 GLU cc_start: 0.6738 (tt0) cc_final: 0.6440 (pp20) REVERT: F 95 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6202 (pp20) REVERT: F 105 ARG cc_start: 0.8045 (ttt180) cc_final: 0.7552 (ttp-110) REVERT: F 165 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6121 (tm-30) REVERT: F 300 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6894 (mp0) REVERT: F 301 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7210 (mm-30) REVERT: F 343 SER cc_start: 0.8332 (p) cc_final: 0.7749 (t) REVERT: G 14 LEU cc_start: 0.7289 (mt) cc_final: 0.7012 (mt) REVERT: G 27 LEU cc_start: 0.8198 (mm) cc_final: 0.7841 (tm) REVERT: G 36 GLN cc_start: 0.6179 (OUTLIER) cc_final: 0.5593 (pp30) REVERT: G 48 ASP cc_start: 0.8281 (t0) cc_final: 0.7980 (t0) REVERT: G 50 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6646 (mm-30) REVERT: G 51 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7646 (ptp) REVERT: G 161 GLU cc_start: 0.7687 (tt0) cc_final: 0.7089 (tt0) REVERT: G 207 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7232 (mm) REVERT: G 235 LYS cc_start: 0.7286 (mmtm) cc_final: 0.6937 (mtmt) REVERT: G 251 ASN cc_start: 0.7584 (p0) cc_final: 0.7257 (p0) REVERT: G 299 GLN cc_start: 0.7486 (mm-40) cc_final: 0.6950 (tm-30) outliers start: 83 outliers final: 43 residues processed: 411 average time/residue: 0.5885 time to fit residues: 274.2019 Evaluate side-chains 397 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 339 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 22 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 210 optimal weight: 0.0270 chunk 219 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 198 optimal weight: 4.9990 chunk 182 optimal weight: 0.3980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 211 GLN F 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.188458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.155693 restraints weight = 22859.974| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.19 r_work: 0.3854 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21280 Z= 0.121 Angle : 0.584 13.217 29085 Z= 0.292 Chirality : 0.039 0.447 3350 Planarity : 0.004 0.058 3612 Dihedral : 14.582 141.820 3352 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.12 % Allowed : 21.84 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.17), residues: 2516 helix: 1.59 (0.15), residues: 1261 sheet: 0.06 (0.24), residues: 417 loop : 0.11 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 274 TYR 0.024 0.002 TYR G 153 PHE 0.015 0.001 PHE G 75 TRP 0.023 0.001 TRP E 140 HIS 0.019 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (21264) covalent geometry : angle 0.57417 / 0.29 (29061) hydrogen bonds : bond 0.03189 / 2.16 ( 1122) hydrogen bonds : angle 3.92629 / 2.82 ( 3166) metal coordination : bond 0.00263 / 0.13 ( 16) metal coordination : angle 3.72753 / 2.39 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 359 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 SER cc_start: 0.6733 (OUTLIER) cc_final: 0.6454 (p) REVERT: A 71 MET cc_start: 0.7654 (ptp) cc_final: 0.7407 (ptp) REVERT: A 126 TRP cc_start: 0.6212 (p-90) cc_final: 0.5715 (p-90) REVERT: A 211 HIS cc_start: 0.7159 (t70) cc_final: 0.6382 (m170) REVERT: A 234 GLN cc_start: 0.7523 (mt0) cc_final: 0.7228 (pt0) REVERT: A 244 VAL cc_start: 0.7459 (OUTLIER) cc_final: 0.7225 (p) REVERT: B 77 ASP cc_start: 0.6988 (m-30) cc_final: 0.6201 (m-30) REVERT: B 80 ARG cc_start: 0.7017 (mtm110) cc_final: 0.6751 (ttm110) REVERT: B 81 GLU cc_start: 0.6549 (mt-10) cc_final: 0.6255 (mt-10) REVERT: B 92 GLU cc_start: 0.7623 (tt0) cc_final: 0.7179 (tm-30) REVERT: B 133 ARG cc_start: 0.7457 (tpp80) cc_final: 0.7228 (mmm-85) REVERT: B 160 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: B 185 HIS cc_start: 0.7363 (OUTLIER) cc_final: 0.7046 (t-90) REVERT: B 231 GLN cc_start: 0.7297 (mt0) cc_final: 0.7040 (mt0) REVERT: B 314 ARG cc_start: 0.7803 (mmt-90) cc_final: 0.7379 (mmm-85) REVERT: B 338 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7285 (pt0) REVERT: B 351 MET cc_start: 0.8469 (mmt) cc_final: 0.8076 (mmt) REVERT: C 9 LYS cc_start: 0.8538 (tttp) cc_final: 0.8336 (tttm) REVERT: C 22 GLU cc_start: 0.7461 (tp30) cc_final: 0.7097 (mp0) REVERT: C 106 ASP cc_start: 0.7684 (m-30) cc_final: 0.7409 (m-30) REVERT: C 176 LYS cc_start: 0.8273 (mtpp) cc_final: 0.7329 (mmtm) REVERT: C 192 ASN cc_start: 0.7813 (t0) cc_final: 0.7270 (t0) REVERT: C 193 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.5690 (mp0) REVERT: C 231 GLN cc_start: 0.7782 (pt0) cc_final: 0.7254 (pp30) REVERT: C 318 ARG cc_start: 0.7158 (ptm-80) cc_final: 0.6562 (ttm110) REVERT: C 337 LYS cc_start: 0.8322 (mtmt) cc_final: 0.7986 (mtmm) REVERT: D 17 ASP cc_start: 0.7426 (t0) cc_final: 0.6977 (m-30) REVERT: D 92 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7835 (tp30) REVERT: D 106 ASP cc_start: 0.6646 (m-30) cc_final: 0.6368 (m-30) REVERT: D 126 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8260 (m-30) REVERT: D 127 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7622 (mt-10) REVERT: D 141 LYS cc_start: 0.8267 (tptt) cc_final: 0.7681 (tppt) REVERT: D 154 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8131 (mt) REVERT: D 176 LYS cc_start: 0.8365 (mttm) cc_final: 0.7957 (mtpp) REVERT: D 211 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7258 (mm-30) REVERT: D 262 GLU cc_start: 0.7627 (mp0) cc_final: 0.7360 (mp0) REVERT: D 291 ARG cc_start: 0.7802 (tpp80) cc_final: 0.6849 (mmp80) REVERT: E 72 THR cc_start: 0.7120 (OUTLIER) cc_final: 0.6844 (t) REVERT: E 85 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.5927 (mptm) REVERT: E 126 ASN cc_start: 0.8463 (m-40) cc_final: 0.8155 (m-40) REVERT: E 130 LYS cc_start: 0.7803 (tppp) cc_final: 0.7451 (tptp) REVERT: E 149 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: E 170 GLN cc_start: 0.6793 (tp40) cc_final: 0.6184 (mp10) REVERT: E 258 ARG cc_start: 0.7821 (mmm160) cc_final: 0.7593 (mmm-85) REVERT: E 277 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7025 (tt) REVERT: F 1 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6349 (ptt) REVERT: F 69 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7792 (p) REVERT: F 73 ARG cc_start: 0.7863 (mpp80) cc_final: 0.7112 (pmt170) REVERT: F 87 GLU cc_start: 0.6705 (tt0) cc_final: 0.6391 (pp20) REVERT: F 95 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6168 (pp20) REVERT: F 105 ARG cc_start: 0.8003 (ttt180) cc_final: 0.7518 (ttp-110) REVERT: F 162 THR cc_start: 0.7511 (m) cc_final: 0.6931 (p) REVERT: F 165 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.6008 (tm-30) REVERT: F 182 MET cc_start: 0.8111 (mmm) cc_final: 0.7627 (mtm) REVERT: F 300 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6851 (mp0) REVERT: F 301 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7209 (mm-30) REVERT: F 343 SER cc_start: 0.8286 (p) cc_final: 0.7721 (t) REVERT: G 14 LEU cc_start: 0.7157 (mt) cc_final: 0.6896 (mt) REVERT: G 27 LEU cc_start: 0.8190 (mm) cc_final: 0.7851 (tm) REVERT: G 34 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6950 (mt) REVERT: G 36 GLN cc_start: 0.6278 (OUTLIER) cc_final: 0.5698 (pp30) REVERT: G 48 ASP cc_start: 0.8318 (t0) cc_final: 0.8025 (t0) REVERT: G 50 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6568 (mm-30) REVERT: G 91 GLN cc_start: 0.6318 (mt0) cc_final: 0.6085 (pp30) REVERT: G 154 TYR cc_start: 0.7319 (p90) cc_final: 0.7045 (p90) REVERT: G 161 GLU cc_start: 0.7612 (tt0) cc_final: 0.6916 (tt0) REVERT: G 207 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7200 (mm) REVERT: G 235 LYS cc_start: 0.7238 (mmtm) cc_final: 0.6873 (mtmt) REVERT: G 251 ASN cc_start: 0.7631 (p0) cc_final: 0.7325 (p0) REVERT: G 299 GLN cc_start: 0.7444 (mm-40) cc_final: 0.6910 (tm-30) outliers start: 66 outliers final: 30 residues processed: 401 average time/residue: 0.5882 time to fit residues: 266.4817 Evaluate side-chains 386 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 339 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 196 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 222 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.188750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.155791 restraints weight = 22929.326| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.21 r_work: 0.3854 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21280 Z= 0.129 Angle : 0.593 13.659 29085 Z= 0.297 Chirality : 0.040 0.312 3350 Planarity : 0.004 0.057 3612 Dihedral : 14.558 141.489 3352 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.41 % Allowed : 22.98 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.17), residues: 2516 helix: 1.57 (0.15), residues: 1260 sheet: 0.09 (0.25), residues: 404 loop : 0.10 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 274 TYR 0.024 0.002 TYR G 153 PHE 0.012 0.001 PHE F 3 TRP 0.026 0.002 TRP E 140 HIS 0.010 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (21264) covalent geometry : angle 0.58439 / 0.30 (29061) hydrogen bonds : bond 0.03183 / 2.17 ( 1122) hydrogen bonds : angle 3.95241 / 2.85 ( 3166) metal coordination : bond 0.00301 / 0.14 ( 16) metal coordination : angle 3.63177 / 2.31 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 343 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 SER cc_start: 0.6786 (OUTLIER) cc_final: 0.6556 (p) REVERT: A 71 MET cc_start: 0.7672 (ptp) cc_final: 0.7419 (ptp) REVERT: A 126 TRP cc_start: 0.6182 (p-90) cc_final: 0.5685 (p-90) REVERT: A 211 HIS cc_start: 0.7194 (t70) cc_final: 0.6430 (m170) REVERT: A 234 GLN cc_start: 0.7539 (mt0) cc_final: 0.7244 (pt0) REVERT: A 244 VAL cc_start: 0.7439 (OUTLIER) cc_final: 0.7182 (p) REVERT: B 66 THR cc_start: 0.7429 (OUTLIER) cc_final: 0.7183 (t) REVERT: B 77 ASP cc_start: 0.6977 (m-30) cc_final: 0.6180 (m-30) REVERT: B 80 ARG cc_start: 0.7026 (mtm110) cc_final: 0.6755 (ttm110) REVERT: B 81 GLU cc_start: 0.6469 (mt-10) cc_final: 0.6189 (mt-10) REVERT: B 92 GLU cc_start: 0.7617 (tt0) cc_final: 0.7173 (tm-30) REVERT: B 133 ARG cc_start: 0.7437 (tpp80) cc_final: 0.7209 (mmm-85) REVERT: B 160 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: B 167 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7211 (mt) REVERT: B 231 GLN cc_start: 0.7327 (mt0) cc_final: 0.7068 (mt0) REVERT: B 314 ARG cc_start: 0.7735 (mmt-90) cc_final: 0.7254 (mmm160) REVERT: B 338 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7262 (pt0) REVERT: B 351 MET cc_start: 0.8481 (mmt) cc_final: 0.8090 (mmt) REVERT: C 22 GLU cc_start: 0.7426 (tp30) cc_final: 0.7021 (mp0) REVERT: C 44 SER cc_start: 0.9227 (m) cc_final: 0.8948 (t) REVERT: C 106 ASP cc_start: 0.7666 (m-30) cc_final: 0.7411 (m-30) REVERT: C 176 LYS cc_start: 0.8273 (mtpp) cc_final: 0.7336 (mmtm) REVERT: C 192 ASN cc_start: 0.7797 (t0) cc_final: 0.7256 (t0) REVERT: C 193 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.5702 (mp0) REVERT: C 231 GLN cc_start: 0.7794 (pt0) cc_final: 0.7266 (pp30) REVERT: C 258 GLU cc_start: 0.6667 (mt-10) cc_final: 0.6143 (tt0) REVERT: C 318 ARG cc_start: 0.7125 (ptm-80) cc_final: 0.6545 (ttm110) REVERT: C 337 LYS cc_start: 0.8328 (mtmt) cc_final: 0.7973 (mtmm) REVERT: C 351 MET cc_start: 0.8733 (mmt) cc_final: 0.8531 (mmt) REVERT: D 17 ASP cc_start: 0.7422 (t0) cc_final: 0.6968 (m-30) REVERT: D 92 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7783 (tp30) REVERT: D 106 ASP cc_start: 0.6448 (m-30) cc_final: 0.6192 (m-30) REVERT: D 126 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8284 (m-30) REVERT: D 127 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7655 (mt-10) REVERT: D 141 LYS cc_start: 0.8280 (tptt) cc_final: 0.7697 (tppt) REVERT: D 154 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8145 (mt) REVERT: D 176 LYS cc_start: 0.8380 (mttm) cc_final: 0.7982 (mtpp) REVERT: D 211 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7270 (mm-30) REVERT: D 262 GLU cc_start: 0.7623 (mp0) cc_final: 0.7363 (mp0) REVERT: D 291 ARG cc_start: 0.7779 (tpp80) cc_final: 0.7476 (tpp80) REVERT: E 72 THR cc_start: 0.7108 (OUTLIER) cc_final: 0.6825 (t) REVERT: E 85 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.5888 (mptm) REVERT: E 126 ASN cc_start: 0.8456 (m-40) cc_final: 0.8147 (m-40) REVERT: E 130 LYS cc_start: 0.7797 (tppp) cc_final: 0.7435 (tptp) REVERT: E 149 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: E 170 GLN cc_start: 0.6824 (tp40) cc_final: 0.6203 (mp10) REVERT: E 211 GLN cc_start: 0.7910 (tp40) cc_final: 0.7652 (tp-100) REVERT: E 258 ARG cc_start: 0.7814 (mmm160) cc_final: 0.7585 (mmm-85) REVERT: E 277 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7166 (tt) REVERT: F 1 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6365 (ptt) REVERT: F 69 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7791 (p) REVERT: F 73 ARG cc_start: 0.7879 (mpp80) cc_final: 0.7094 (pmt170) REVERT: F 87 GLU cc_start: 0.6716 (tt0) cc_final: 0.6376 (pp20) REVERT: F 95 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6116 (pp20) REVERT: F 105 ARG cc_start: 0.8027 (ttt180) cc_final: 0.7538 (ttp-110) REVERT: F 165 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5964 (tm-30) REVERT: F 182 MET cc_start: 0.8086 (mmm) cc_final: 0.7647 (mtm) REVERT: F 300 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6849 (mp0) REVERT: F 301 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7221 (mm-30) REVERT: F 343 SER cc_start: 0.8279 (p) cc_final: 0.7777 (t) REVERT: G 14 LEU cc_start: 0.7182 (mt) cc_final: 0.6932 (mt) REVERT: G 27 LEU cc_start: 0.8190 (mm) cc_final: 0.7853 (tm) REVERT: G 34 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6976 (mt) REVERT: G 36 GLN cc_start: 0.6331 (OUTLIER) cc_final: 0.5723 (pp30) REVERT: G 48 ASP cc_start: 0.8303 (t0) cc_final: 0.8071 (t0) REVERT: G 50 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6557 (mm-30) REVERT: G 154 TYR cc_start: 0.7324 (p90) cc_final: 0.7070 (p90) REVERT: G 161 GLU cc_start: 0.7616 (tt0) cc_final: 0.6862 (tt0) REVERT: G 207 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7182 (mm) REVERT: G 235 LYS cc_start: 0.7209 (mmtm) cc_final: 0.6853 (mtmt) REVERT: G 251 ASN cc_start: 0.7632 (p0) cc_final: 0.7319 (p0) REVERT: G 299 GLN cc_start: 0.7418 (mm-40) cc_final: 0.6890 (tm-30) REVERT: G 344 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7790 (p) outliers start: 51 outliers final: 25 residues processed: 379 average time/residue: 0.5727 time to fit residues: 246.4047 Evaluate side-chains 372 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 328 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 117 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 243 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 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 = 0.4226 r_free = 0.4226 target = 0.189950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.156983 restraints weight = 22934.245| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.21 r_work: 0.3866 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21280 Z= 0.127 Angle : 0.597 15.273 29085 Z= 0.294 Chirality : 0.039 0.300 3350 Planarity : 0.004 0.054 3612 Dihedral : 14.565 140.586 3352 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.60 % Allowed : 23.07 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.17), residues: 2516 helix: 1.63 (0.15), residues: 1262 sheet: 0.10 (0.25), residues: 404 loop : 0.13 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 274 TYR 0.023 0.002 TYR G 153 PHE 0.020 0.001 PHE G 75 TRP 0.029 0.001 TRP E 140 HIS 0.004 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (21264) covalent geometry : angle 0.57873 / 0.29 (29061) hydrogen bonds : bond 0.03124 / 2.12 ( 1122) hydrogen bonds : angle 3.91632 / 2.82 ( 3166) metal coordination : bond 0.00644 / 0.25 ( 16) metal coordination : angle 5.07068 / 3.31 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7891.06 seconds wall clock time: 134 minutes 55.12 seconds (8095.12 seconds total)