Starting phenix.real_space_refine on Fri Jun 5 13:51:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyl_71025/06_2026/9oyl_71025.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyl_71025/06_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_71025/06_2026/9oyl_71025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyl_71025/06_2026/9oyl_71025.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oyl_71025/06_2026/9oyl_71025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyl_71025/06_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-6079/lib/python3.9/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: 5.03, per 1000 atoms: 0.24 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: 1.79 Conformation dependent library (CDL) restraints added in 975.0 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: 2.46 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: 3.78 Time building geometry restraints manager: 2.36 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=" N ILE A 55 " pdb=" CA ILE A 55 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 8.99e+00 bond pdb=" N VAL C 5 " pdb=" CA VAL C 5 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.14e+00 bond pdb=" N ASN A 58 " pdb=" CA ASN A 58 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.19e-02 7.06e+03 7.10e+00 bond pdb=" N LYS B 100 " pdb=" CA LYS B 100 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.22e-02 6.72e+03 6.79e+00 ... (remaining 21259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 28110 1.18 - 2.36: 721 2.36 - 3.54: 189 3.54 - 4.72: 33 4.72 - 5.90: 8 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=" CA THR B 99 " pdb=" CB THR B 99 " pdb=" OG1 THR B 99 " ideal model delta sigma weight residual 109.60 103.83 5.77 1.50e+00 4.44e-01 1.48e+01 angle pdb=" CA ASP A 56 " pdb=" CB ASP A 56 " pdb=" CG ASP A 56 " ideal model delta sigma weight residual 112.60 116.29 -3.69 1.00e+00 1.00e+00 1.36e+01 angle pdb=" C ASP A 56 " pdb=" N PRO A 57 " pdb=" CA PRO A 57 " ideal model delta sigma weight residual 119.47 122.82 -3.35 1.16e+00 7.43e-01 8.34e+00 angle pdb=" C ASP A 56 " pdb=" CA ASP A 56 " pdb=" CB ASP A 56 " ideal model delta sigma weight residual 109.56 113.90 -4.34 1.51e+00 4.39e-01 8.25e+00 ... (remaining 29056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.18: 12311 32.18 - 64.36: 505 64.36 - 96.53: 35 96.53 - 128.71: 1 128.71 - 160.89: 2 Dihedral angle restraints: 12854 sinusoidal: 5519 harmonic: 7335 Sorted by residual: dihedral pdb=" O1A AGS D 402 " pdb=" O3A AGS D 402 " pdb=" PA AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sinusoidal sigma weight residual -67.73 93.16 -160.89 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" CA PHE F 319 " pdb=" C PHE F 319 " pdb=" N ASN F 320 " pdb=" CA ASN F 320 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" C4' DT H 30 " pdb=" C3' DT H 30 " pdb=" O3' DT H 30 " pdb=" P DC H 31 " ideal model delta sinusoidal sigma weight residual 220.00 76.73 143.27 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 12851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2404 0.035 - 0.070: 726 0.070 - 0.105: 165 0.105 - 0.141: 58 0.141 - 0.176: 3 Chirality restraints: 3356 Sorted by residual: chirality pdb=" CA ILE A 55 " pdb=" N ILE A 55 " pdb=" C ILE A 55 " pdb=" CB ILE A 55 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA TYR C 3 " pdb=" N TYR C 3 " pdb=" C TYR C 3 " pdb=" CB TYR C 3 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CA ARG B 98 " pdb=" N ARG B 98 " pdb=" C ARG B 98 " pdb=" CB ARG B 98 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 3353 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.740 Find NCS groups from input model: 0.380 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:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21280 Z= 0.161 Angle : 0.511 5.904 29085 Z= 0.270 Chirality : 0.037 0.176 3356 Planarity : 0.003 0.038 3612 Dihedral : 16.243 160.890 8094 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 0.00333 / 0.16 (21264) covalent geometry : angle 0.50330 / 0.27 (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 : 0.797 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: 0.7619 time to fit residues: 522.0193 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 : 0.827 ------------------------------------------------------------------------------- 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: 0.0070 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN D 4 GLN D 110 ASN D 290 HIS E 101 ASN F 148 HIS F 288 ASN F 320 ASN F 355 GLN G 143 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.190833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.157394 restraints weight = 23242.673| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.15 r_work: 0.3798 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21280 Z= 0.131 Angle : 0.578 10.046 29085 Z= 0.290 Chirality : 0.039 0.164 3356 Planarity : 0.004 0.046 3612 Dihedral : 14.732 140.693 3303 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.17 % Allowed : 13.57 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.17), residues: 2516 helix: 1.73 (0.15), residues: 1263 sheet: 0.30 (0.24), residues: 438 loop : 0.25 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 263 TYR 0.019 0.001 TYR G 310 PHE 0.020 0.001 PHE G 75 TRP 0.014 0.001 TRP D 10 HIS 0.007 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (21264) covalent geometry : angle 0.56247 / 0.29 (29061) hydrogen bonds : bond 0.03713 / 2.49 ( 1122) hydrogen bonds : angle 4.30222 / 3.10 ( 3166) metal coordination : bond 0.00264 / 0.16 ( 16) metal coordination : angle 4.72499 / 2.97 ( 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 502 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 435 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 TRP cc_start: 0.6640 (p-90) cc_final: 0.6195 (p-90) REVERT: A 211 HIS cc_start: 0.6980 (t70) cc_final: 0.6414 (m170) REVERT: A 226 SER cc_start: 0.8597 (t) cc_final: 0.7858 (m) REVERT: A 234 GLN cc_start: 0.7545 (mt0) cc_final: 0.7207 (pt0) REVERT: A 286 MET cc_start: 0.7261 (mmm) cc_final: 0.6413 (mmt) REVERT: A 325 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: A 338 ASP cc_start: 0.7413 (m-30) cc_final: 0.6735 (t0) REVERT: B 80 ARG cc_start: 0.6737 (mtm110) cc_final: 0.6493 (ttm110) REVERT: B 81 GLU cc_start: 0.6599 (mt-10) cc_final: 0.6240 (mp0) REVERT: B 92 GLU cc_start: 0.7767 (tt0) cc_final: 0.7310 (tm-30) REVERT: B 133 ARG cc_start: 0.7435 (tpp80) cc_final: 0.7085 (ttp80) REVERT: B 185 HIS cc_start: 0.7241 (OUTLIER) cc_final: 0.6698 (t-90) REVERT: B 231 GLN cc_start: 0.6885 (mt0) cc_final: 0.6622 (mt0) REVERT: B 274 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6438 (ptm160) REVERT: B 277 GLU cc_start: 0.7205 (tt0) cc_final: 0.6975 (tm-30) REVERT: B 338 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7315 (pt0) REVERT: C 22 GLU cc_start: 0.7448 (tp30) cc_final: 0.7141 (mp0) REVERT: C 44 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8501 (t) REVERT: C 77 ASP cc_start: 0.6778 (t70) cc_final: 0.6159 (t0) REVERT: C 80 ARG cc_start: 0.7357 (mmm-85) cc_final: 0.7119 (ptm-80) REVERT: C 94 ASP cc_start: 0.7485 (p0) cc_final: 0.7238 (p0) REVERT: C 106 ASP cc_start: 0.7598 (m-30) cc_final: 0.7312 (m-30) REVERT: C 127 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7452 (mp0) REVERT: C 130 MET cc_start: 0.8494 (mmp) cc_final: 0.8239 (mmp) REVERT: C 133 ARG cc_start: 0.7482 (ttp80) cc_final: 0.7273 (ttp80) REVERT: C 176 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7296 (mmtm) REVERT: C 192 ASN cc_start: 0.7697 (t0) cc_final: 0.7469 (t0) REVERT: C 211 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7268 (mm-30) REVERT: C 231 GLN cc_start: 0.7627 (pt0) cc_final: 0.7090 (pp30) REVERT: C 254 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7418 (mt-10) REVERT: C 258 GLU cc_start: 0.6457 (mt-10) cc_final: 0.5980 (tt0) REVERT: C 262 GLU cc_start: 0.7389 (pp20) cc_final: 0.7186 (mm-30) REVERT: C 318 ARG cc_start: 0.7109 (ptm-80) cc_final: 0.6483 (ttm110) REVERT: C 337 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7814 (mtmm) REVERT: C 363 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7287 (ptt) REVERT: D 17 ASP cc_start: 0.7211 (t0) cc_final: 0.6860 (m-30) REVERT: D 92 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7985 (tp30) REVERT: D 106 ASP cc_start: 0.6536 (m-30) cc_final: 0.6234 (m-30) REVERT: D 110 ASN cc_start: 0.7922 (m-40) cc_final: 0.7648 (m110) REVERT: D 126 ASP cc_start: 0.8541 (t0) cc_final: 0.8222 (m-30) REVERT: D 127 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7419 (mt-10) REVERT: D 141 LYS cc_start: 0.8151 (tptt) cc_final: 0.7617 (tppp) REVERT: D 176 LYS cc_start: 0.8343 (mttm) cc_final: 0.8082 (mtpp) REVERT: D 211 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7425 (mm-30) REVERT: D 235 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7303 (tp40) REVERT: D 263 ARG cc_start: 0.7575 (tpp80) cc_final: 0.7359 (tpp80) REVERT: D 284 GLU cc_start: 0.7411 (tt0) cc_final: 0.6782 (mp0) REVERT: D 291 ARG cc_start: 0.7774 (tpp80) cc_final: 0.7518 (tpp80) REVERT: E 130 LYS cc_start: 0.7811 (tppp) cc_final: 0.7419 (tptp) REVERT: E 147 GLU cc_start: 0.7807 (tp30) cc_final: 0.7467 (tp30) REVERT: E 170 GLN cc_start: 0.6594 (tp40) cc_final: 0.5991 (mp10) REVERT: E 228 ASP cc_start: 0.7964 (t0) cc_final: 0.7645 (t0) REVERT: E 258 ARG cc_start: 0.6946 (tpm170) cc_final: 0.6360 (tmt170) REVERT: F 1 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7245 (ptt) REVERT: F 36 GLN cc_start: 0.7762 (mt0) cc_final: 0.7319 (mt0) REVERT: F 73 ARG cc_start: 0.7095 (mmt180) cc_final: 0.6888 (tpp80) REVERT: F 87 GLU cc_start: 0.6707 (tt0) cc_final: 0.6375 (pp20) REVERT: F 95 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6380 (pp20) REVERT: F 105 ARG cc_start: 0.7859 (ttt180) cc_final: 0.7318 (ttp-170) REVERT: F 152 ARG cc_start: 0.6506 (mpp80) cc_final: 0.6149 (mtm180) REVERT: F 161 GLU cc_start: 0.6736 (pt0) cc_final: 0.6061 (pt0) REVERT: F 205 ARG cc_start: 0.7176 (mtp-110) cc_final: 0.6949 (ttm-80) REVERT: F 260 CYS cc_start: 0.6332 (t) cc_final: 0.6024 (p) REVERT: F 300 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6862 (mp0) REVERT: F 301 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7112 (mt-10) REVERT: F 343 SER cc_start: 0.8486 (p) cc_final: 0.8088 (t) REVERT: F 364 MET cc_start: 0.7829 (ttp) cc_final: 0.6686 (mmt) REVERT: G 14 LEU cc_start: 0.7235 (mt) cc_final: 0.6940 (mt) REVERT: G 36 GLN cc_start: 0.6209 (OUTLIER) cc_final: 0.5893 (pp30) REVERT: G 48 ASP cc_start: 0.8181 (t0) cc_final: 0.7903 (t0) REVERT: G 50 GLU cc_start: 0.6665 (mm-30) cc_final: 0.6273 (mm-30) REVERT: G 52 GLU cc_start: 0.8043 (pt0) cc_final: 0.7710 (pt0) REVERT: G 91 GLN cc_start: 0.6454 (mt0) cc_final: 0.6048 (pp30) REVERT: G 93 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6302 (mt-10) REVERT: G 153 TYR cc_start: 0.6944 (p90) cc_final: 0.6638 (p90) REVERT: G 161 GLU cc_start: 0.7291 (tt0) cc_final: 0.6595 (tt0) REVERT: G 217 GLN cc_start: 0.6075 (tt0) cc_final: 0.5629 (mm-40) REVERT: G 251 ASN cc_start: 0.7617 (p0) cc_final: 0.7289 (p0) REVERT: G 254 LYS cc_start: 0.7176 (mmtp) cc_final: 0.6620 (mtpt) REVERT: G 264 LYS cc_start: 0.6601 (ttpp) cc_final: 0.6389 (tttm) REVERT: G 299 GLN cc_start: 0.7177 (mm110) cc_final: 0.6818 (tm-30) REVERT: G 301 GLU cc_start: 0.7728 (pt0) cc_final: 0.6966 (tt0) REVERT: J 4 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6829 (tmt170) outliers start: 67 outliers final: 18 residues processed: 469 average time/residue: 0.7392 time to fit residues: 386.8164 Evaluate side-chains 406 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 380 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP 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 B residue 323 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 363 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 D residue 320 ILE Chi-restraints excluded: chain E residue 96 VAL 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 F residue 344 VAL Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 192 SER 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: 0.4980 chunk 191 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS C 39 HIS C 269 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 HIS E 101 ASN E 126 ASN G 221 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.189120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.156947 restraints weight = 23122.136| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.00 r_work: 0.3791 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21280 Z= 0.149 Angle : 0.571 8.597 29085 Z= 0.284 Chirality : 0.039 0.186 3356 Planarity : 0.004 0.058 3612 Dihedral : 14.472 140.921 3298 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.11 % Allowed : 14.85 % Favored : 81.04 % 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: 1.37 (0.17), residues: 2516 helix: 1.68 (0.15), residues: 1263 sheet: 0.32 (0.24), residues: 422 loop : 0.17 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 168 TYR 0.011 0.001 TYR B 329 PHE 0.020 0.001 PHE G 75 TRP 0.018 0.001 TRP D 10 HIS 0.005 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (21264) covalent geometry : angle 0.55692 / 0.28 (29061) hydrogen bonds : bond 0.03542 / 2.39 ( 1122) hydrogen bonds : angle 4.09326 / 2.93 ( 3166) metal coordination : bond 0.01196 / 0.46 ( 16) metal coordination : angle 4.44754 / 2.90 ( 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 490 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 403 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 66 SER cc_start: 0.6564 (OUTLIER) cc_final: 0.6253 (p) REVERT: A 71 MET cc_start: 0.7546 (ptp) cc_final: 0.7063 (ptp) REVERT: A 78 GLN cc_start: 0.8138 (pt0) cc_final: 0.7380 (tm-30) REVERT: A 126 TRP cc_start: 0.6608 (p-90) cc_final: 0.6013 (p-90) REVERT: A 211 HIS cc_start: 0.7081 (t70) cc_final: 0.6444 (m-70) REVERT: A 234 GLN cc_start: 0.7550 (mt0) cc_final: 0.7273 (pt0) REVERT: A 286 MET cc_start: 0.7297 (mmm) cc_final: 0.6440 (mmt) REVERT: A 325 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: A 338 ASP cc_start: 0.7443 (m-30) cc_final: 0.6806 (t0) REVERT: B 77 ASP cc_start: 0.7081 (m-30) cc_final: 0.6051 (m-30) REVERT: B 80 ARG cc_start: 0.6890 (mtm110) cc_final: 0.6637 (ttm110) REVERT: B 81 GLU cc_start: 0.6706 (mt-10) cc_final: 0.6343 (mp0) REVERT: B 92 GLU cc_start: 0.7715 (tt0) cc_final: 0.7314 (tm-30) REVERT: B 133 ARG cc_start: 0.7546 (tpp80) cc_final: 0.7233 (ttp80) REVERT: B 160 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: B 185 HIS cc_start: 0.7460 (OUTLIER) cc_final: 0.7002 (t70) REVERT: B 231 GLN cc_start: 0.7162 (mt0) cc_final: 0.6911 (mt0) REVERT: B 274 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6658 (ptm160) REVERT: B 310 GLU cc_start: 0.6992 (tp30) cc_final: 0.6749 (tm-30) REVERT: B 314 ARG cc_start: 0.7755 (mmt-90) cc_final: 0.7292 (mmm160) REVERT: B 338 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7325 (pt0) REVERT: C 22 GLU cc_start: 0.7497 (tp30) cc_final: 0.7153 (mp0) REVERT: C 77 ASP cc_start: 0.6756 (t70) cc_final: 0.6272 (t0) REVERT: C 94 ASP cc_start: 0.7574 (p0) cc_final: 0.7370 (p0) REVERT: C 106 ASP cc_start: 0.7603 (m-30) cc_final: 0.7327 (m-30) REVERT: C 127 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7108 (tp30) REVERT: C 133 ARG cc_start: 0.7549 (ttp80) cc_final: 0.7314 (ttp80) REVERT: C 148 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: C 176 LYS cc_start: 0.8238 (mtpp) cc_final: 0.7395 (mmtm) REVERT: C 192 ASN cc_start: 0.7859 (t0) cc_final: 0.7390 (t0) REVERT: C 193 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.5774 (mp0) REVERT: C 211 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7287 (mm-30) REVERT: C 231 GLN cc_start: 0.7718 (pt0) cc_final: 0.7293 (pp30) REVERT: C 258 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6152 (tt0) REVERT: C 318 ARG cc_start: 0.7222 (ptm-80) cc_final: 0.6622 (ttm110) REVERT: C 337 LYS cc_start: 0.8363 (mtmt) cc_final: 0.8048 (mtmm) REVERT: C 363 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7332 (ptt) REVERT: D 17 ASP cc_start: 0.7347 (t0) cc_final: 0.7005 (m-30) REVERT: D 92 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7983 (tp30) REVERT: D 106 ASP cc_start: 0.6589 (m-30) cc_final: 0.6318 (m-30) REVERT: D 126 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8254 (m-30) REVERT: D 127 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7498 (mt-10) REVERT: D 141 LYS cc_start: 0.8272 (tptt) cc_final: 0.7718 (tppt) REVERT: D 176 LYS cc_start: 0.8412 (mttm) cc_final: 0.8088 (mtpp) REVERT: D 211 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7494 (mm-30) REVERT: D 284 GLU cc_start: 0.7479 (tt0) cc_final: 0.6883 (mp0) REVERT: D 291 ARG cc_start: 0.7869 (tpp80) cc_final: 0.7590 (tpp-160) REVERT: E 98 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: E 126 ASN cc_start: 0.8479 (m-40) cc_final: 0.8129 (m-40) REVERT: E 130 LYS cc_start: 0.7780 (tppp) cc_final: 0.7455 (tptp) REVERT: E 170 GLN cc_start: 0.6767 (tp40) cc_final: 0.6252 (mp10) REVERT: E 228 ASP cc_start: 0.7997 (t0) cc_final: 0.7763 (t0) REVERT: E 322 TYR cc_start: 0.7780 (m-10) cc_final: 0.7331 (m-10) REVERT: F 1 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7435 (ptt) REVERT: F 36 GLN cc_start: 0.7740 (mt0) cc_final: 0.7345 (mt0) REVERT: F 87 GLU cc_start: 0.6740 (tt0) cc_final: 0.6437 (pp20) REVERT: F 95 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6369 (pp20) REVERT: F 105 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7481 (ttp-170) REVERT: F 136 LYS cc_start: 0.7472 (ttpt) cc_final: 0.6940 (tppt) REVERT: F 205 ARG cc_start: 0.7170 (mtp-110) cc_final: 0.6965 (mtm-85) REVERT: F 300 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6862 (mp0) REVERT: F 301 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7095 (mm-30) REVERT: F 343 SER cc_start: 0.8474 (p) cc_final: 0.7984 (t) REVERT: F 364 MET cc_start: 0.7795 (ttp) cc_final: 0.6864 (mmp) REVERT: G 27 LEU cc_start: 0.8111 (mm) cc_final: 0.7807 (tm) REVERT: G 36 GLN cc_start: 0.6219 (OUTLIER) cc_final: 0.5896 (pp30) REVERT: G 48 ASP cc_start: 0.8021 (t0) cc_final: 0.7795 (t0) REVERT: G 50 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6294 (mm-30) REVERT: G 91 GLN cc_start: 0.6608 (mt0) cc_final: 0.6249 (pp30) REVERT: G 93 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6179 (mt-10) REVERT: G 153 TYR cc_start: 0.6980 (p90) cc_final: 0.6612 (p90) REVERT: G 161 GLU cc_start: 0.7452 (tt0) cc_final: 0.6565 (tt0) REVERT: G 251 ASN cc_start: 0.7592 (p0) cc_final: 0.7218 (p0) REVERT: G 299 GLN cc_start: 0.7317 (mm110) cc_final: 0.6906 (tm-30) REVERT: G 301 GLU cc_start: 0.7673 (pt0) cc_final: 0.7058 (tt0) outliers start: 87 outliers final: 35 residues processed: 453 average time/residue: 0.6865 time to fit residues: 349.2901 Evaluate side-chains 420 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 372 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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 101 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 185 HIS 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 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 251 SER Chi-restraints excluded: chain C residue 363 MET 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 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 231 SER 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 134 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 338 MET Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 93 GLU 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 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: 1.9990 chunk 220 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 183 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 219 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS 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** E 101 ASN G 148 HIS G 217 GLN G 299 GLN G 348 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.185779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.151465 restraints weight = 23228.640| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.15 r_work: 0.3805 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21280 Z= 0.207 Angle : 0.621 9.014 29085 Z= 0.306 Chirality : 0.041 0.165 3356 Planarity : 0.005 0.069 3612 Dihedral : 14.727 141.090 3298 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.07 % Allowed : 17.12 % Favored : 78.82 % 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: 1.08 (0.17), residues: 2516 helix: 1.41 (0.15), residues: 1259 sheet: 0.14 (0.24), residues: 417 loop : 0.13 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 86 TYR 0.017 0.002 TYR G 310 PHE 0.027 0.002 PHE G 75 TRP 0.011 0.002 TRP D 10 HIS 0.006 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (21264) covalent geometry : angle 0.60947 / 0.30 (29061) hydrogen bonds : bond 0.03764 / 2.55 ( 1122) hydrogen bonds : angle 4.13643 / 2.96 ( 3166) metal coordination : bond 0.00620 / 0.28 ( 16) metal coordination : angle 4.23692 / 2.71 ( 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 458 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 372 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.7584 (ptp) cc_final: 0.7141 (ptp) REVERT: A 108 LEU cc_start: 0.5373 (OUTLIER) cc_final: 0.5037 (tp) REVERT: A 126 TRP cc_start: 0.6481 (p-90) cc_final: 0.5999 (p-90) REVERT: A 211 HIS cc_start: 0.7079 (t70) cc_final: 0.6402 (m-70) REVERT: A 234 GLN cc_start: 0.7529 (mt0) cc_final: 0.7240 (pt0) REVERT: A 325 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: B 77 ASP cc_start: 0.7113 (m-30) cc_final: 0.6243 (m-30) REVERT: B 80 ARG cc_start: 0.7000 (mtm110) cc_final: 0.6748 (ttm110) REVERT: B 81 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6338 (mt-10) REVERT: B 92 GLU cc_start: 0.7768 (tt0) cc_final: 0.7302 (tm-30) REVERT: B 133 ARG cc_start: 0.7545 (tpp80) cc_final: 0.7208 (ttp80) REVERT: B 160 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7341 (mp10) REVERT: B 185 HIS cc_start: 0.7335 (OUTLIER) cc_final: 0.7089 (t-90) REVERT: B 231 GLN cc_start: 0.7289 (mt0) cc_final: 0.7012 (mt0) REVERT: B 314 ARG cc_start: 0.7817 (mmt-90) cc_final: 0.6834 (mtt-85) REVERT: B 338 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7387 (pt0) REVERT: C 22 GLU cc_start: 0.7529 (tp30) cc_final: 0.7268 (mp0) REVERT: C 94 ASP cc_start: 0.7612 (p0) cc_final: 0.7319 (p0) REVERT: C 106 ASP cc_start: 0.7599 (m-30) cc_final: 0.7309 (m-30) REVERT: C 127 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7174 (tp30) REVERT: C 133 ARG cc_start: 0.7626 (ttp80) cc_final: 0.7364 (ttp80) REVERT: C 148 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8385 (mp0) REVERT: C 176 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7380 (mmtm) REVERT: C 192 ASN cc_start: 0.7870 (t0) cc_final: 0.7373 (t0) REVERT: C 193 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6032 (mp0) REVERT: C 211 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7332 (mm-30) REVERT: C 231 GLN cc_start: 0.7796 (pt0) cc_final: 0.7319 (pp30) REVERT: C 258 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6405 (tt0) REVERT: C 318 ARG cc_start: 0.7209 (ptm-80) cc_final: 0.6580 (ttm110) REVERT: C 337 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8027 (mtmm) REVERT: C 363 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7346 (ptt) REVERT: D 17 ASP cc_start: 0.7418 (t0) cc_final: 0.6958 (m-30) REVERT: D 92 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7949 (tp30) REVERT: D 106 ASP cc_start: 0.6652 (m-30) cc_final: 0.6383 (m-30) REVERT: D 126 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8323 (m-30) REVERT: D 127 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7646 (mt-10) REVERT: D 141 LYS cc_start: 0.8403 (tptt) cc_final: 0.7818 (tppt) REVERT: D 176 LYS cc_start: 0.8349 (mttm) cc_final: 0.7962 (mtpp) REVERT: D 262 GLU cc_start: 0.7680 (mp0) cc_final: 0.7365 (mp0) REVERT: D 291 ARG cc_start: 0.7878 (tpp80) cc_final: 0.7518 (tpp-160) REVERT: E 72 THR cc_start: 0.7129 (OUTLIER) cc_final: 0.6793 (t) REVERT: E 78 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8531 (p) REVERT: E 126 ASN cc_start: 0.8615 (m-40) cc_final: 0.8250 (m-40) REVERT: E 130 LYS cc_start: 0.7829 (tppp) cc_final: 0.7483 (tptp) REVERT: E 170 GLN cc_start: 0.6837 (tp40) cc_final: 0.6242 (mp10) REVERT: E 228 ASP cc_start: 0.8106 (t0) cc_final: 0.7836 (t0) REVERT: F 36 GLN cc_start: 0.7779 (mt0) cc_final: 0.7374 (mt0) REVERT: F 87 GLU cc_start: 0.6776 (tt0) cc_final: 0.6451 (pp20) REVERT: F 95 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6257 (pp20) REVERT: F 105 ARG cc_start: 0.7967 (ttt180) cc_final: 0.7495 (ttp-170) REVERT: F 152 ARG cc_start: 0.6702 (mtm180) cc_final: 0.6317 (mtm180) REVERT: F 182 MET cc_start: 0.8046 (mmm) cc_final: 0.7626 (mtm) REVERT: F 205 ARG cc_start: 0.7241 (mtp-110) cc_final: 0.6686 (mtm-85) REVERT: F 300 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6895 (mp0) REVERT: F 301 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7150 (mm-30) REVERT: F 305 ILE cc_start: 0.8533 (mt) cc_final: 0.8248 (mp) REVERT: F 343 SER cc_start: 0.8371 (p) cc_final: 0.7909 (t) REVERT: G 27 LEU cc_start: 0.8173 (mm) cc_final: 0.7831 (tm) REVERT: G 36 GLN cc_start: 0.6230 (OUTLIER) cc_final: 0.5735 (pp30) REVERT: G 50 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6275 (mm-30) REVERT: G 91 GLN cc_start: 0.6693 (mt0) cc_final: 0.6372 (pp30) REVERT: G 97 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7288 (mmm) REVERT: G 127 GLU cc_start: 0.7993 (pt0) cc_final: 0.7375 (pt0) REVERT: G 153 TYR cc_start: 0.7138 (p90) cc_final: 0.6653 (p90) REVERT: G 161 GLU cc_start: 0.7545 (tt0) cc_final: 0.6606 (tt0) REVERT: G 217 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.6940 (mm110) REVERT: G 251 ASN cc_start: 0.7566 (p0) cc_final: 0.7203 (p0) REVERT: G 299 GLN cc_start: 0.7491 (mm-40) cc_final: 0.6963 (tm-30) REVERT: G 301 GLU cc_start: 0.7696 (pt0) cc_final: 0.7060 (tt0) REVERT: G 339 MET cc_start: 0.6583 (mpp) cc_final: 0.6324 (mpp) outliers start: 86 outliers final: 39 residues processed: 421 average time/residue: 0.6716 time to fit residues: 317.5085 Evaluate side-chains 400 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 348 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER 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 325 GLU Chi-restraints excluded: chain B residue 66 THR 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 251 SER Chi-restraints excluded: chain C residue 363 MET 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 320 ILE 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 96 VAL 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 126 VAL 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 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 77 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 97 MET 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 229 ASP 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: 6.9990 chunk 122 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 175 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS C 13 GLN C 269 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN E 211 GLN E 259 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.187788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.154747 restraints weight = 23187.165| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.21 r_work: 0.3847 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21280 Z= 0.139 Angle : 0.568 8.528 29085 Z= 0.281 Chirality : 0.039 0.202 3356 Planarity : 0.004 0.066 3612 Dihedral : 14.618 140.668 3298 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.59 % Allowed : 18.49 % Favored : 77.92 % 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: 1.56 (0.15), residues: 1259 sheet: 0.16 (0.25), residues: 407 loop : 0.15 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 244 TYR 0.027 0.002 TYR B 341 PHE 0.012 0.001 PHE F 3 TRP 0.012 0.001 TRP B 278 HIS 0.003 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (21264) covalent geometry : angle 0.55616 / 0.28 (29061) hydrogen bonds : bond 0.03298 / 2.24 ( 1122) hydrogen bonds : angle 3.96296 / 2.83 ( 3166) metal coordination : bond 0.00367 / 0.16 ( 16) metal coordination : angle 4.09830 / 2.64 ( 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 443 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 367 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.7602 (ptp) cc_final: 0.7166 (ptp) REVERT: A 126 TRP cc_start: 0.6487 (p-90) cc_final: 0.5990 (p-90) REVERT: A 211 HIS cc_start: 0.7055 (t70) cc_final: 0.6396 (m-70) REVERT: A 234 GLN cc_start: 0.7539 (mt0) cc_final: 0.7266 (pt0) REVERT: A 244 VAL cc_start: 0.7514 (OUTLIER) cc_final: 0.7264 (p) REVERT: A 325 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: B 77 ASP cc_start: 0.7027 (m-30) cc_final: 0.6159 (m-30) REVERT: B 80 ARG cc_start: 0.6993 (mtm110) cc_final: 0.6742 (ttm110) REVERT: B 81 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6364 (mt-10) REVERT: B 92 GLU cc_start: 0.7743 (tt0) cc_final: 0.7292 (tm-30) REVERT: B 133 ARG cc_start: 0.7540 (tpp80) cc_final: 0.7215 (ttp80) REVERT: B 160 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7309 (mp10) REVERT: B 185 HIS cc_start: 0.7425 (OUTLIER) cc_final: 0.7108 (t-90) REVERT: B 231 GLN cc_start: 0.7297 (mt0) cc_final: 0.7026 (mt0) REVERT: B 314 ARG cc_start: 0.7608 (mmt-90) cc_final: 0.6854 (mtt-85) REVERT: B 338 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7372 (pt0) REVERT: B 351 MET cc_start: 0.8449 (mmt) cc_final: 0.8089 (mmt) REVERT: C 9 LYS cc_start: 0.8518 (tttp) cc_final: 0.8305 (tttm) REVERT: C 22 GLU cc_start: 0.7496 (tp30) cc_final: 0.7170 (mp0) REVERT: C 94 ASP cc_start: 0.7641 (p0) cc_final: 0.7307 (p0) REVERT: C 106 ASP cc_start: 0.7605 (m-30) cc_final: 0.7360 (m-30) REVERT: C 127 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7571 (tp30) REVERT: C 133 ARG cc_start: 0.7537 (ttp80) cc_final: 0.7285 (ttp80) REVERT: C 148 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7428 (tm-30) REVERT: C 176 LYS cc_start: 0.8283 (mtpp) cc_final: 0.7388 (mmtm) REVERT: C 192 ASN cc_start: 0.7837 (t0) cc_final: 0.7325 (t0) REVERT: C 193 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.5975 (mp0) REVERT: C 211 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7356 (mm-30) REVERT: C 231 GLN cc_start: 0.7801 (pt0) cc_final: 0.7330 (pp30) REVERT: C 258 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6344 (tt0) REVERT: C 318 ARG cc_start: 0.7157 (ptm-80) cc_final: 0.6543 (ttm110) REVERT: C 337 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7996 (mtmm) REVERT: C 363 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7330 (ptt) REVERT: D 17 ASP cc_start: 0.7386 (t0) cc_final: 0.6956 (m-30) REVERT: D 92 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7828 (tp30) REVERT: D 106 ASP cc_start: 0.6648 (m-30) cc_final: 0.6394 (m-30) REVERT: D 126 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8292 (m-30) REVERT: D 127 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7594 (mt-10) REVERT: D 141 LYS cc_start: 0.8370 (tptt) cc_final: 0.7789 (tppt) REVERT: D 154 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8182 (mt) REVERT: D 176 LYS cc_start: 0.8373 (mttm) cc_final: 0.7988 (mtpp) REVERT: D 211 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7240 (mm-30) REVERT: D 262 GLU cc_start: 0.7669 (mp0) cc_final: 0.7392 (mp0) REVERT: D 291 ARG cc_start: 0.7888 (tpp80) cc_final: 0.7556 (tpp-160) REVERT: E 72 THR cc_start: 0.7100 (OUTLIER) cc_final: 0.6816 (t) REVERT: E 126 ASN cc_start: 0.8574 (m-40) cc_final: 0.8210 (m-40) REVERT: E 130 LYS cc_start: 0.7783 (tppp) cc_final: 0.7451 (tptp) REVERT: E 170 GLN cc_start: 0.6849 (tp40) cc_final: 0.6252 (mp10) REVERT: E 277 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7036 (tt) REVERT: F 36 GLN cc_start: 0.7758 (mt0) cc_final: 0.7353 (mt0) REVERT: F 69 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7693 (p) REVERT: F 87 GLU cc_start: 0.6777 (tt0) cc_final: 0.6474 (pp20) REVERT: F 95 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6231 (pp20) REVERT: F 105 ARG cc_start: 0.7955 (ttt180) cc_final: 0.7460 (ttp-110) REVERT: F 150 ASP cc_start: 0.7557 (t0) cc_final: 0.7297 (t0) REVERT: F 152 ARG cc_start: 0.6792 (mtm180) cc_final: 0.6248 (mtm180) REVERT: F 165 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.6052 (tm-30) REVERT: F 182 MET cc_start: 0.8041 (mmm) cc_final: 0.7697 (mtm) REVERT: F 205 ARG cc_start: 0.7219 (mtp-110) cc_final: 0.6742 (mtm-85) REVERT: F 300 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6915 (mp0) REVERT: F 301 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7251 (mm-30) REVERT: F 343 SER cc_start: 0.8362 (p) cc_final: 0.7838 (t) REVERT: G 27 LEU cc_start: 0.8139 (mm) cc_final: 0.7809 (tm) REVERT: G 36 GLN cc_start: 0.6160 (OUTLIER) cc_final: 0.5767 (pp30) REVERT: G 48 ASP cc_start: 0.8177 (t0) cc_final: 0.7898 (t0) REVERT: G 91 GLN cc_start: 0.6550 (mt0) cc_final: 0.6204 (pp30) REVERT: G 93 GLU cc_start: 0.6845 (tp30) cc_final: 0.6583 (tp30) REVERT: G 97 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7378 (tmm) REVERT: G 161 GLU cc_start: 0.7557 (tt0) cc_final: 0.6676 (tt0) REVERT: G 207 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7255 (mm) REVERT: G 251 ASN cc_start: 0.7443 (p0) cc_final: 0.7130 (p0) REVERT: G 299 GLN cc_start: 0.7433 (mm-40) cc_final: 0.6918 (tm-30) REVERT: G 339 MET cc_start: 0.6484 (mpp) cc_final: 0.6062 (mpp) outliers start: 76 outliers final: 36 residues processed: 418 average time/residue: 0.6902 time to fit residues: 323.6783 Evaluate side-chains 398 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 346 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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 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 251 SER Chi-restraints excluded: chain C residue 363 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 E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 134 GLU 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 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 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 97 MET Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 212 ASN 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: 5.9990 chunk 75 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 201 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 225 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 HIS C 269 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS G 348 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.187447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.153445 restraints weight = 23049.026| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.13 r_work: 0.3838 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21280 Z= 0.153 Angle : 0.575 12.640 29085 Z= 0.284 Chirality : 0.039 0.158 3356 Planarity : 0.004 0.065 3612 Dihedral : 14.607 140.673 3298 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.74 % Allowed : 19.76 % Favored : 76.50 % 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: 1.20 (0.17), residues: 2516 helix: 1.52 (0.15), residues: 1265 sheet: 0.25 (0.25), residues: 401 loop : 0.13 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 244 TYR 0.027 0.002 TYR B 328 PHE 0.013 0.001 PHE F 3 TRP 0.013 0.001 TRP E 140 HIS 0.008 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (21264) covalent geometry : angle 0.56357 / 0.28 (29061) hydrogen bonds : bond 0.03323 / 2.26 ( 1122) hydrogen bonds : angle 3.93857 / 2.81 ( 3166) metal coordination : bond 0.00354 / 0.17 ( 16) metal coordination : angle 3.93454 / 2.54 ( 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: 79 poor density : 361 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7608 (ptp) cc_final: 0.7324 (ptp) REVERT: A 78 GLN cc_start: 0.8186 (pt0) cc_final: 0.7985 (tt0) REVERT: A 126 TRP cc_start: 0.6315 (p-90) cc_final: 0.5808 (p-90) REVERT: A 211 HIS cc_start: 0.7069 (t70) cc_final: 0.6431 (m-70) REVERT: A 234 GLN cc_start: 0.7539 (mt0) cc_final: 0.7265 (pt0) REVERT: B 77 ASP cc_start: 0.7003 (m-30) cc_final: 0.6204 (m-30) REVERT: B 80 ARG cc_start: 0.7045 (mtm110) cc_final: 0.6790 (ttm110) REVERT: B 81 GLU cc_start: 0.6694 (mt-10) cc_final: 0.6329 (mt-10) REVERT: B 92 GLU cc_start: 0.7680 (tt0) cc_final: 0.7257 (tm-30) REVERT: B 133 ARG cc_start: 0.7508 (tpp80) cc_final: 0.7191 (ttp80) REVERT: B 160 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7254 (mp10) REVERT: B 231 GLN cc_start: 0.7365 (mt0) cc_final: 0.7097 (mt0) REVERT: B 256 MET cc_start: 0.7633 (ttm) cc_final: 0.7431 (ttp) REVERT: B 314 ARG cc_start: 0.7467 (mmt-90) cc_final: 0.6866 (mtt-85) REVERT: B 338 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7359 (pt0) REVERT: C 9 LYS cc_start: 0.8585 (tttp) cc_final: 0.8384 (tttm) REVERT: C 22 GLU cc_start: 0.7505 (tp30) cc_final: 0.7201 (mp0) REVERT: C 94 ASP cc_start: 0.7601 (p0) cc_final: 0.7324 (p0) REVERT: C 106 ASP cc_start: 0.7619 (m-30) cc_final: 0.7366 (m-30) REVERT: C 133 ARG cc_start: 0.7592 (ttp80) cc_final: 0.7345 (ttp80) REVERT: C 148 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7488 (tm-30) REVERT: C 176 LYS cc_start: 0.8339 (mtpp) cc_final: 0.7436 (mmtm) REVERT: C 192 ASN cc_start: 0.7866 (t0) cc_final: 0.7358 (t0) REVERT: C 193 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6042 (mp0) REVERT: C 211 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7374 (mm-30) REVERT: C 231 GLN cc_start: 0.7814 (pt0) cc_final: 0.7335 (pp30) REVERT: C 258 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6425 (tt0) REVERT: C 274 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7640 (mtm180) REVERT: C 318 ARG cc_start: 0.7193 (ptm-80) cc_final: 0.6573 (ttm110) REVERT: C 337 LYS cc_start: 0.8369 (mtmt) cc_final: 0.7938 (mtmm) REVERT: C 351 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8520 (mmt) REVERT: C 363 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7320 (ptt) REVERT: D 17 ASP cc_start: 0.7447 (t0) cc_final: 0.7005 (m-30) REVERT: D 92 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7931 (tp30) REVERT: D 106 ASP cc_start: 0.6675 (m-30) cc_final: 0.6422 (m-30) REVERT: D 126 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: D 127 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7598 (mt-10) REVERT: D 141 LYS cc_start: 0.8365 (tptt) cc_final: 0.7789 (tppt) REVERT: D 154 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8154 (mt) REVERT: D 176 LYS cc_start: 0.8416 (mttm) cc_final: 0.8035 (mtpp) REVERT: D 211 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7265 (mm-30) REVERT: D 262 GLU cc_start: 0.7680 (mp0) cc_final: 0.7412 (mp0) REVERT: D 291 ARG cc_start: 0.7929 (tpp80) cc_final: 0.7605 (tpp-160) REVERT: E 72 THR cc_start: 0.7160 (OUTLIER) cc_final: 0.6869 (t) REVERT: E 126 ASN cc_start: 0.8608 (m-40) cc_final: 0.8230 (m-40) REVERT: E 130 LYS cc_start: 0.7823 (tppp) cc_final: 0.7473 (tptt) REVERT: E 170 GLN cc_start: 0.6834 (tp40) cc_final: 0.6345 (tp40) REVERT: E 277 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7109 (tt) REVERT: F 36 GLN cc_start: 0.7739 (mt0) cc_final: 0.7366 (mt0) REVERT: F 69 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7760 (p) REVERT: F 73 ARG cc_start: 0.7785 (tpp80) cc_final: 0.7529 (mpp80) REVERT: F 87 GLU cc_start: 0.6743 (tt0) cc_final: 0.6465 (pp20) REVERT: F 95 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6220 (pp20) REVERT: F 105 ARG cc_start: 0.7953 (ttt180) cc_final: 0.7498 (ttp-110) REVERT: F 136 LYS cc_start: 0.7441 (ttpt) cc_final: 0.7058 (tptm) REVERT: F 150 ASP cc_start: 0.7524 (t0) cc_final: 0.7234 (t0) REVERT: F 152 ARG cc_start: 0.6739 (mtm180) cc_final: 0.6210 (mtm180) REVERT: F 165 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.6028 (tm-30) REVERT: F 182 MET cc_start: 0.8056 (mmm) cc_final: 0.7778 (mtm) REVERT: F 205 ARG cc_start: 0.7220 (mtp-110) cc_final: 0.6757 (mtm-85) REVERT: F 300 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6897 (mp0) REVERT: F 301 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7258 (mm-30) REVERT: F 343 SER cc_start: 0.8381 (p) cc_final: 0.7786 (t) REVERT: G 27 LEU cc_start: 0.8199 (mm) cc_final: 0.7872 (tm) REVERT: G 36 GLN cc_start: 0.6252 (OUTLIER) cc_final: 0.5750 (pp30) REVERT: G 48 ASP cc_start: 0.8242 (t0) cc_final: 0.7892 (t0) REVERT: G 50 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6596 (mm-30) REVERT: G 51 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7645 (ptp) REVERT: G 91 GLN cc_start: 0.6663 (mt0) cc_final: 0.6274 (pp30) REVERT: G 93 GLU cc_start: 0.6854 (tp30) cc_final: 0.6643 (tp30) REVERT: G 97 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7331 (tmm) REVERT: G 126 VAL cc_start: 0.7458 (t) cc_final: 0.7194 (p) REVERT: G 153 TYR cc_start: 0.7001 (p90) cc_final: 0.6509 (p90) REVERT: G 161 GLU cc_start: 0.7542 (tt0) cc_final: 0.6869 (tt0) REVERT: G 207 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7218 (mm) REVERT: G 235 LYS cc_start: 0.7295 (mmtm) cc_final: 0.6900 (mtmt) REVERT: G 251 ASN cc_start: 0.7428 (p0) cc_final: 0.7086 (p0) REVERT: G 299 GLN cc_start: 0.7473 (mm-40) cc_final: 0.6982 (tm-30) REVERT: G 339 MET cc_start: 0.6447 (mpp) cc_final: 0.6166 (mpp) outliers start: 79 outliers final: 38 residues processed: 408 average time/residue: 0.6863 time to fit residues: 315.6744 Evaluate side-chains 400 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 347 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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 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 251 SER Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 363 MET 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 E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 96 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 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 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 52 GLU Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 212 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 117 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 223 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS E 211 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.188858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.155370 restraints weight = 23006.591| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.29 r_work: 0.3853 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21280 Z= 0.123 Angle : 0.545 13.058 29085 Z= 0.270 Chirality : 0.038 0.159 3356 Planarity : 0.004 0.059 3612 Dihedral : 14.489 140.315 3298 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.69 % Allowed : 20.28 % 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: 1.37 (0.17), residues: 2516 helix: 1.69 (0.15), residues: 1267 sheet: 0.29 (0.25), residues: 399 loop : 0.17 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 244 TYR 0.019 0.001 TYR B 341 PHE 0.012 0.001 PHE F 3 TRP 0.014 0.001 TRP E 140 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (21264) covalent geometry : angle 0.53397 / 0.27 (29061) hydrogen bonds : bond 0.03055 / 2.07 ( 1122) hydrogen bonds : angle 3.82331 / 2.73 ( 3166) metal coordination : bond 0.00316 / 0.14 ( 16) metal coordination : angle 3.75050 / 2.42 ( 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 446 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 368 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.7602 (ptp) cc_final: 0.7314 (ptp) REVERT: A 78 GLN cc_start: 0.8080 (pt0) cc_final: 0.7714 (tm-30) REVERT: A 126 TRP cc_start: 0.6268 (p-90) cc_final: 0.5787 (p-90) REVERT: A 211 HIS cc_start: 0.7046 (t70) cc_final: 0.6354 (m-70) REVERT: A 234 GLN cc_start: 0.7565 (mt0) cc_final: 0.7273 (pt0) REVERT: A 244 VAL cc_start: 0.7426 (OUTLIER) cc_final: 0.7183 (p) REVERT: A 286 MET cc_start: 0.7425 (mmm) cc_final: 0.6547 (mmt) REVERT: B 77 ASP cc_start: 0.7006 (m-30) cc_final: 0.6101 (m-30) REVERT: B 80 ARG cc_start: 0.7000 (mtm110) cc_final: 0.6730 (ttm110) REVERT: B 81 GLU cc_start: 0.6498 (mt-10) cc_final: 0.6294 (mp0) REVERT: B 92 GLU cc_start: 0.7635 (tt0) cc_final: 0.7165 (tm-30) REVERT: B 133 ARG cc_start: 0.7463 (tpp80) cc_final: 0.7232 (mmm-85) REVERT: B 160 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7226 (mp10) REVERT: B 231 GLN cc_start: 0.7345 (mt0) cc_final: 0.7087 (mt0) REVERT: B 256 MET cc_start: 0.7666 (ttm) cc_final: 0.7454 (ttp) REVERT: B 314 ARG cc_start: 0.7413 (mmt-90) cc_final: 0.6790 (mtt-85) REVERT: B 338 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7236 (pt0) REVERT: C 22 GLU cc_start: 0.7487 (tp30) cc_final: 0.7116 (mp0) REVERT: C 94 ASP cc_start: 0.7611 (p0) cc_final: 0.7360 (p0) REVERT: C 106 ASP cc_start: 0.7652 (m-30) cc_final: 0.7397 (m-30) REVERT: C 127 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7577 (tp30) REVERT: C 133 ARG cc_start: 0.7548 (ttp80) cc_final: 0.7274 (ttp80) REVERT: C 148 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: C 176 LYS cc_start: 0.8313 (mtpp) cc_final: 0.7378 (mmtm) REVERT: C 192 ASN cc_start: 0.7824 (t0) cc_final: 0.7554 (t0) REVERT: C 211 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7272 (mm-30) REVERT: C 231 GLN cc_start: 0.7809 (pt0) cc_final: 0.7284 (pp30) REVERT: C 258 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6369 (tt0) REVERT: C 274 ARG cc_start: 0.7885 (ttm-80) cc_final: 0.7618 (mtm180) REVERT: C 318 ARG cc_start: 0.7105 (ptm-80) cc_final: 0.6498 (ttm110) REVERT: C 337 LYS cc_start: 0.8299 (mtmt) cc_final: 0.7977 (mtmm) REVERT: C 363 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7276 (ptt) REVERT: D 17 ASP cc_start: 0.7397 (t0) cc_final: 0.6954 (m-30) REVERT: D 92 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7864 (tp30) REVERT: D 106 ASP cc_start: 0.6589 (m-30) cc_final: 0.6318 (m-30) REVERT: D 126 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8320 (m-30) REVERT: D 127 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7565 (mt-10) REVERT: D 141 LYS cc_start: 0.8312 (tptt) cc_final: 0.7733 (tppt) REVERT: D 154 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8157 (mt) REVERT: D 176 LYS cc_start: 0.8397 (mttm) cc_final: 0.7974 (mtpp) REVERT: D 211 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7259 (mm-30) REVERT: D 262 GLU cc_start: 0.7647 (mp0) cc_final: 0.7380 (mp0) REVERT: D 291 ARG cc_start: 0.7878 (tpp80) cc_final: 0.7559 (tpp-160) REVERT: D 315 GLU cc_start: 0.6861 (tp30) cc_final: 0.6446 (tp30) REVERT: E 72 THR cc_start: 0.7131 (OUTLIER) cc_final: 0.6829 (t) REVERT: E 126 ASN cc_start: 0.8605 (m-40) cc_final: 0.8258 (m-40) REVERT: E 130 LYS cc_start: 0.7767 (tppp) cc_final: 0.7420 (tptt) REVERT: E 170 GLN cc_start: 0.6787 (tp40) cc_final: 0.6193 (mp10) REVERT: E 277 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7174 (tt) REVERT: F 87 GLU cc_start: 0.6777 (tt0) cc_final: 0.6443 (pp20) REVERT: F 95 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6164 (pp20) REVERT: F 105 ARG cc_start: 0.7985 (ttt180) cc_final: 0.7440 (ttp-170) REVERT: F 136 LYS cc_start: 0.7464 (ttpt) cc_final: 0.7021 (tptm) REVERT: F 150 ASP cc_start: 0.7460 (t0) cc_final: 0.7138 (t0) REVERT: F 152 ARG cc_start: 0.6709 (mtm180) cc_final: 0.6109 (mtm180) REVERT: F 165 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.6046 (tm-30) REVERT: F 182 MET cc_start: 0.8085 (mmm) cc_final: 0.7783 (mtm) REVERT: F 205 ARG cc_start: 0.7162 (mtp-110) cc_final: 0.6593 (mtm-85) REVERT: F 300 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6877 (mp0) REVERT: F 301 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7329 (mm-30) REVERT: F 343 SER cc_start: 0.8305 (p) cc_final: 0.7776 (t) REVERT: G 27 LEU cc_start: 0.8166 (mm) cc_final: 0.7843 (tm) REVERT: G 34 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6915 (mt) REVERT: G 36 GLN cc_start: 0.6286 (OUTLIER) cc_final: 0.5821 (pp30) REVERT: G 48 ASP cc_start: 0.8213 (t0) cc_final: 0.7883 (t0) REVERT: G 50 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6575 (mm-30) REVERT: G 51 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7713 (ptp) REVERT: G 91 GLN cc_start: 0.6394 (mt0) cc_final: 0.6068 (pp30) REVERT: G 97 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7312 (tmm) REVERT: G 154 TYR cc_start: 0.7340 (p90) cc_final: 0.7054 (p90) REVERT: G 161 GLU cc_start: 0.7572 (tt0) cc_final: 0.6681 (tt0) REVERT: G 207 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7224 (mm) REVERT: G 235 LYS cc_start: 0.7272 (mmtm) cc_final: 0.6874 (mtmt) REVERT: G 251 ASN cc_start: 0.7410 (p0) cc_final: 0.7097 (p0) REVERT: G 285 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8037 (p) REVERT: G 299 GLN cc_start: 0.7428 (mm-40) cc_final: 0.6909 (tm-30) REVERT: J 6 ASP cc_start: 0.7222 (m-30) cc_final: 0.7013 (m-30) outliers start: 78 outliers final: 33 residues processed: 418 average time/residue: 0.7025 time to fit residues: 329.5200 Evaluate side-chains 384 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 336 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 148 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 C residue 252 LEU Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 82 ILE 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 96 VAL 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 126 VAL Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 192 SER 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 51 MET Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 212 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 75 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 224 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 103 optimal weight: 0.0170 chunk 151 optimal weight: 0.9980 chunk 219 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS E 259 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.188109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.155356 restraints weight = 22659.898| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.21 r_work: 0.3844 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21280 Z= 0.142 Angle : 0.575 13.730 29085 Z= 0.281 Chirality : 0.038 0.157 3356 Planarity : 0.004 0.056 3612 Dihedral : 14.520 140.266 3298 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.55 % Allowed : 21.37 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.17), residues: 2516 helix: 1.65 (0.15), residues: 1268 sheet: 0.31 (0.25), residues: 420 loop : 0.20 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 244 TYR 0.026 0.002 TYR B 328 PHE 0.017 0.001 PHE G 75 TRP 0.016 0.001 TRP E 140 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (21264) covalent geometry : angle 0.55839 / 0.28 (29061) hydrogen bonds : bond 0.03152 / 2.14 ( 1122) hydrogen bonds : angle 3.86196 / 2.76 ( 3166) metal coordination : bond 0.00957 / 0.33 ( 16) metal coordination : angle 4.78482 / 3.15 ( 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 422 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 347 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.7636 (ptp) cc_final: 0.7370 (ptp) REVERT: A 78 GLN cc_start: 0.8123 (pt0) cc_final: 0.7715 (tm-30) REVERT: A 126 TRP cc_start: 0.6217 (p-90) cc_final: 0.5726 (p-90) REVERT: A 211 HIS cc_start: 0.7073 (t70) cc_final: 0.6387 (m-70) REVERT: A 234 GLN cc_start: 0.7561 (mt0) cc_final: 0.7261 (pt0) REVERT: A 244 VAL cc_start: 0.7456 (OUTLIER) cc_final: 0.7207 (p) REVERT: B 77 ASP cc_start: 0.6975 (m-30) cc_final: 0.6163 (m-30) REVERT: B 80 ARG cc_start: 0.7030 (mtm110) cc_final: 0.6776 (ttm110) REVERT: B 92 GLU cc_start: 0.7575 (tt0) cc_final: 0.7134 (tm-30) REVERT: B 133 ARG cc_start: 0.7501 (tpp80) cc_final: 0.7265 (ttp80) REVERT: B 160 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: B 231 GLN cc_start: 0.7374 (mt0) cc_final: 0.7109 (mt0) REVERT: B 314 ARG cc_start: 0.7426 (mmt-90) cc_final: 0.6811 (mtt-85) REVERT: B 338 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7292 (pt0) REVERT: C 22 GLU cc_start: 0.7471 (tp30) cc_final: 0.7159 (mp0) REVERT: C 44 SER cc_start: 0.9254 (m) cc_final: 0.8973 (t) REVERT: C 94 ASP cc_start: 0.7580 (p0) cc_final: 0.7354 (p0) REVERT: C 106 ASP cc_start: 0.7661 (m-30) cc_final: 0.7401 (m-30) REVERT: C 127 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7591 (tp30) REVERT: C 133 ARG cc_start: 0.7535 (ttp80) cc_final: 0.7304 (ttp80) REVERT: C 148 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: C 176 LYS cc_start: 0.8315 (mtpp) cc_final: 0.7366 (mmtm) REVERT: C 192 ASN cc_start: 0.7850 (t0) cc_final: 0.7357 (t0) REVERT: C 193 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.5839 (mp0) REVERT: C 211 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7309 (mm-30) REVERT: C 231 GLN cc_start: 0.7817 (pt0) cc_final: 0.7289 (pp30) REVERT: C 235 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6670 (tm-30) REVERT: C 258 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6402 (tt0) REVERT: C 318 ARG cc_start: 0.7203 (ptm-80) cc_final: 0.6604 (ttm110) REVERT: C 337 LYS cc_start: 0.8320 (mtmt) cc_final: 0.7995 (mtmm) REVERT: C 363 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7298 (ptt) REVERT: D 17 ASP cc_start: 0.7429 (t0) cc_final: 0.6973 (m-30) REVERT: D 92 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7930 (tp30) REVERT: D 106 ASP cc_start: 0.6644 (m-30) cc_final: 0.6382 (m-30) REVERT: D 126 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8301 (m-30) REVERT: D 127 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7591 (mt-10) REVERT: D 141 LYS cc_start: 0.8294 (tptt) cc_final: 0.7710 (tppt) REVERT: D 154 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8167 (mt) REVERT: D 176 LYS cc_start: 0.8386 (mttm) cc_final: 0.7984 (mtpp) REVERT: D 211 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7296 (mm-30) REVERT: D 262 GLU cc_start: 0.7627 (mp0) cc_final: 0.7360 (mp0) REVERT: D 291 ARG cc_start: 0.7924 (tpp80) cc_final: 0.7640 (tpp-160) REVERT: D 315 GLU cc_start: 0.6898 (tp30) cc_final: 0.6485 (tp30) REVERT: E 72 THR cc_start: 0.7126 (OUTLIER) cc_final: 0.6841 (t) REVERT: E 126 ASN cc_start: 0.8632 (m-40) cc_final: 0.8277 (m-40) REVERT: E 130 LYS cc_start: 0.7782 (tppp) cc_final: 0.7453 (tptp) REVERT: E 170 GLN cc_start: 0.6818 (tp40) cc_final: 0.6235 (mp10) REVERT: E 220 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.6849 (mt) REVERT: E 277 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7159 (tt) REVERT: F 87 GLU cc_start: 0.6784 (tt0) cc_final: 0.6445 (pp20) REVERT: F 95 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6172 (pp20) REVERT: F 105 ARG cc_start: 0.8012 (ttt180) cc_final: 0.7529 (ttp-110) REVERT: F 136 LYS cc_start: 0.7547 (ttpt) cc_final: 0.7065 (tptm) REVERT: F 165 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6185 (tm-30) REVERT: F 182 MET cc_start: 0.8082 (mmm) cc_final: 0.7800 (mtm) REVERT: F 205 ARG cc_start: 0.7165 (mtp-110) cc_final: 0.6591 (mtm-85) REVERT: F 300 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6963 (mp0) REVERT: F 301 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7331 (mm-30) REVERT: F 364 MET cc_start: 0.7874 (ttp) cc_final: 0.7650 (mtp) REVERT: G 27 LEU cc_start: 0.8167 (mm) cc_final: 0.7844 (tm) REVERT: G 34 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6936 (mt) REVERT: G 36 GLN cc_start: 0.6375 (OUTLIER) cc_final: 0.5873 (pp30) REVERT: G 50 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6650 (mm-30) REVERT: G 91 GLN cc_start: 0.6525 (mt0) cc_final: 0.6169 (pp30) REVERT: G 97 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7314 (tmm) REVERT: G 153 TYR cc_start: 0.6955 (p90) cc_final: 0.6518 (p90) REVERT: G 154 TYR cc_start: 0.7386 (p90) cc_final: 0.7130 (p90) REVERT: G 161 GLU cc_start: 0.7572 (tt0) cc_final: 0.6665 (tt0) REVERT: G 207 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7242 (mm) REVERT: G 235 LYS cc_start: 0.7265 (mmtm) cc_final: 0.6888 (mtmt) REVERT: G 251 ASN cc_start: 0.7377 (p0) cc_final: 0.7062 (p0) REVERT: G 285 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.8060 (p) REVERT: G 299 GLN cc_start: 0.7423 (mm-40) cc_final: 0.6913 (tm-30) outliers start: 75 outliers final: 37 residues processed: 397 average time/residue: 0.6785 time to fit residues: 302.5655 Evaluate side-chains 381 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 327 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 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 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 235 GLN Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 82 ILE 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 96 VAL Chi-restraints excluded: chain E residue 220 LEU 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 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 177 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 52 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 212 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 22 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 219 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 198 optimal weight: 6.9990 chunk 182 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS E 211 GLN E 259 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.188692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.154961 restraints weight = 22813.701| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.31 r_work: 0.3856 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21280 Z= 0.120 Angle : 0.569 13.430 29085 Z= 0.279 Chirality : 0.038 0.158 3356 Planarity : 0.004 0.050 3612 Dihedral : 14.458 139.951 3298 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.88 % Allowed : 22.32 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.17), residues: 2516 helix: 1.70 (0.15), residues: 1272 sheet: 0.43 (0.25), residues: 401 loop : 0.20 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 274 TYR 0.019 0.001 TYR B 328 PHE 0.012 0.001 PHE F 3 TRP 0.020 0.001 TRP E 140 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (21264) covalent geometry : angle 0.55336 / 0.28 (29061) hydrogen bonds : bond 0.02962 / 2.01 ( 1122) hydrogen bonds : angle 3.80209 / 2.72 ( 3166) metal coordination : bond 0.00592 / 0.21 ( 16) metal coordination : angle 4.59760 / 3.05 ( 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 412 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 351 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.7593 (ptp) cc_final: 0.7370 (ptp) REVERT: A 78 GLN cc_start: 0.8107 (pt0) cc_final: 0.7689 (tm-30) REVERT: A 126 TRP cc_start: 0.5989 (p-90) cc_final: 0.5580 (p-90) REVERT: A 211 HIS cc_start: 0.7022 (t70) cc_final: 0.6311 (m-70) REVERT: A 234 GLN cc_start: 0.7587 (mt0) cc_final: 0.7271 (pt0) REVERT: A 244 VAL cc_start: 0.7375 (OUTLIER) cc_final: 0.7128 (p) REVERT: A 325 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7330 (mp0) REVERT: B 77 ASP cc_start: 0.6675 (m-30) cc_final: 0.6420 (m-30) REVERT: B 80 ARG cc_start: 0.6983 (mtm110) cc_final: 0.6756 (ttm110) REVERT: B 92 GLU cc_start: 0.7622 (tt0) cc_final: 0.7168 (tm-30) REVERT: B 133 ARG cc_start: 0.7441 (tpp80) cc_final: 0.7194 (ttp80) REVERT: B 160 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: B 231 GLN cc_start: 0.7365 (mt0) cc_final: 0.7061 (mp10) REVERT: B 314 ARG cc_start: 0.7381 (mmt-90) cc_final: 0.6759 (mtt-85) REVERT: B 338 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7264 (pt0) REVERT: C 22 GLU cc_start: 0.7439 (tp30) cc_final: 0.7047 (mp0) REVERT: C 94 ASP cc_start: 0.7569 (p0) cc_final: 0.7346 (p0) REVERT: C 106 ASP cc_start: 0.7677 (m-30) cc_final: 0.7409 (m-30) REVERT: C 119 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.8108 (mtm-85) REVERT: C 127 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7551 (tp30) REVERT: C 133 ARG cc_start: 0.7494 (ttp80) cc_final: 0.7288 (ttp80) REVERT: C 148 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: C 176 LYS cc_start: 0.8279 (mtpp) cc_final: 0.7324 (mmtm) REVERT: C 192 ASN cc_start: 0.7817 (t0) cc_final: 0.7331 (t0) REVERT: C 193 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.5818 (mp0) REVERT: C 211 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7306 (mm-30) REVERT: C 231 GLN cc_start: 0.7824 (pt0) cc_final: 0.7295 (pp30) REVERT: C 235 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6685 (tm-30) REVERT: C 258 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6354 (tt0) REVERT: C 274 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7570 (mtm180) REVERT: C 318 ARG cc_start: 0.7182 (ptm-80) cc_final: 0.6608 (ttm110) REVERT: C 337 LYS cc_start: 0.8305 (mtmt) cc_final: 0.7982 (mtmm) REVERT: C 363 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7222 (ptt) REVERT: D 17 ASP cc_start: 0.7411 (t0) cc_final: 0.6955 (m-30) REVERT: D 92 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7801 (tp30) REVERT: D 106 ASP cc_start: 0.6553 (m-30) cc_final: 0.6289 (m-30) REVERT: D 107 LEU cc_start: 0.8534 (tt) cc_final: 0.8309 (tt) REVERT: D 126 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: D 127 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7596 (mt-10) REVERT: D 141 LYS cc_start: 0.8285 (tptt) cc_final: 0.7711 (tppt) REVERT: D 154 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8126 (mt) REVERT: D 176 LYS cc_start: 0.8411 (mttm) cc_final: 0.7991 (mtpp) REVERT: D 211 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7308 (mm-30) REVERT: D 262 GLU cc_start: 0.7647 (mp0) cc_final: 0.7374 (mp0) REVERT: D 291 ARG cc_start: 0.7890 (tpp80) cc_final: 0.7536 (tpp-160) REVERT: D 315 GLU cc_start: 0.6854 (tp30) cc_final: 0.6531 (tp30) REVERT: D 346 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7805 (ttt180) REVERT: E 72 THR cc_start: 0.7127 (OUTLIER) cc_final: 0.6863 (t) REVERT: E 100 LEU cc_start: 0.7483 (mt) cc_final: 0.7220 (mp) REVERT: E 126 ASN cc_start: 0.8601 (m-40) cc_final: 0.8265 (m-40) REVERT: E 130 LYS cc_start: 0.7752 (tppp) cc_final: 0.7428 (tptp) REVERT: E 170 GLN cc_start: 0.6784 (tp40) cc_final: 0.6191 (mp10) REVERT: E 277 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7200 (tt) REVERT: F 1 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6310 (ptp) REVERT: F 87 GLU cc_start: 0.6761 (tt0) cc_final: 0.6393 (pp20) REVERT: F 95 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6149 (pp20) REVERT: F 105 ARG cc_start: 0.8011 (ttt180) cc_final: 0.7518 (ttp-110) REVERT: F 136 LYS cc_start: 0.7501 (ttpt) cc_final: 0.7046 (tptm) REVERT: F 152 ARG cc_start: 0.6584 (mtm180) cc_final: 0.6276 (mtm180) REVERT: F 182 MET cc_start: 0.8070 (mmm) cc_final: 0.7848 (mtm) REVERT: F 205 ARG cc_start: 0.7075 (mtp-110) cc_final: 0.6537 (mtm-85) REVERT: F 300 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7004 (mp0) REVERT: F 301 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7363 (mm-30) REVERT: G 27 LEU cc_start: 0.8176 (mm) cc_final: 0.7837 (tm) REVERT: G 34 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6914 (mt) REVERT: G 36 GLN cc_start: 0.6325 (OUTLIER) cc_final: 0.5838 (pp30) REVERT: G 91 GLN cc_start: 0.6362 (mt0) cc_final: 0.6053 (pp30) REVERT: G 97 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7284 (tmm) REVERT: G 154 TYR cc_start: 0.7328 (p90) cc_final: 0.6936 (p90) REVERT: G 161 GLU cc_start: 0.7574 (tt0) cc_final: 0.6689 (tt0) REVERT: G 207 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7243 (mm) REVERT: G 235 LYS cc_start: 0.7255 (mmtm) cc_final: 0.6897 (mtmt) REVERT: G 251 ASN cc_start: 0.7382 (p0) cc_final: 0.7103 (p0) REVERT: G 299 GLN cc_start: 0.7367 (mm-40) cc_final: 0.6876 (tm-30) REVERT: G 351 ASP cc_start: 0.7750 (t0) cc_final: 0.7526 (t70) REVERT: J 4 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6583 (tmt170) outliers start: 61 outliers final: 36 residues processed: 388 average time/residue: 0.7120 time to fit residues: 309.1343 Evaluate side-chains 388 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 66 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 15 PHE Chi-restraints excluded: chain C residue 33 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 235 GLN Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 82 ILE 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 346 ARG Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 96 VAL 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 44 LEU Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 177 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 70 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 364 MET Chi-restraints excluded: chain J residue 4 ARG 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: 2.9990 chunk 44 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 222 optimal weight: 0.6980 chunk 177 optimal weight: 0.0970 chunk 120 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 HIS F 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.189610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.156438 restraints weight = 23050.799| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.26 r_work: 0.3866 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21280 Z= 0.120 Angle : 0.571 13.948 29085 Z= 0.283 Chirality : 0.038 0.204 3356 Planarity : 0.004 0.047 3612 Dihedral : 14.458 139.883 3298 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.74 % Allowed : 22.74 % Favored : 74.52 % 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: 1.47 (0.17), residues: 2516 helix: 1.79 (0.15), residues: 1265 sheet: 0.38 (0.25), residues: 398 loop : 0.16 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 274 TYR 0.024 0.001 TYR G 310 PHE 0.018 0.001 PHE G 75 TRP 0.025 0.001 TRP E 140 HIS 0.003 0.000 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (21264) covalent geometry : angle 0.55804 / 0.28 (29061) hydrogen bonds : bond 0.02944 / 1.99 ( 1122) hydrogen bonds : angle 3.80413 / 2.72 ( 3166) metal coordination : bond 0.00507 / 0.18 ( 16) metal coordination : angle 4.29679 / 2.81 ( 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 397 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 339 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.7549 (ptp) cc_final: 0.7329 (ptp) REVERT: A 78 GLN cc_start: 0.8104 (pt0) cc_final: 0.7694 (tm-30) REVERT: A 126 TRP cc_start: 0.5887 (p-90) cc_final: 0.5473 (p-90) REVERT: A 211 HIS cc_start: 0.7023 (t70) cc_final: 0.6293 (m-70) REVERT: A 234 GLN cc_start: 0.7582 (mt0) cc_final: 0.7271 (pt0) REVERT: A 244 VAL cc_start: 0.7379 (OUTLIER) cc_final: 0.7129 (p) REVERT: A 325 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7346 (mp0) REVERT: B 66 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7339 (t) REVERT: B 77 ASP cc_start: 0.6640 (m-30) cc_final: 0.6377 (m-30) REVERT: B 80 ARG cc_start: 0.6978 (mtm110) cc_final: 0.6759 (ttm110) REVERT: B 92 GLU cc_start: 0.7641 (tt0) cc_final: 0.7193 (tm-30) REVERT: B 133 ARG cc_start: 0.7411 (tpp80) cc_final: 0.7181 (ttp80) REVERT: B 160 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7253 (mp10) REVERT: B 231 GLN cc_start: 0.7405 (mt0) cc_final: 0.7106 (mp10) REVERT: B 314 ARG cc_start: 0.7379 (mmt-90) cc_final: 0.6603 (mmt90) REVERT: B 338 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7256 (pt0) REVERT: C 22 GLU cc_start: 0.7439 (tp30) cc_final: 0.7106 (mp0) REVERT: C 94 ASP cc_start: 0.7548 (p0) cc_final: 0.7324 (p0) REVERT: C 106 ASP cc_start: 0.7645 (m-30) cc_final: 0.7403 (m-30) REVERT: C 127 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7549 (tp30) REVERT: C 133 ARG cc_start: 0.7538 (ttp80) cc_final: 0.7309 (ttp80) REVERT: C 148 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: C 176 LYS cc_start: 0.8275 (mtpp) cc_final: 0.7326 (mmtm) REVERT: C 192 ASN cc_start: 0.7808 (t0) cc_final: 0.7549 (t0) REVERT: C 211 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7296 (mm-30) REVERT: C 231 GLN cc_start: 0.7810 (pt0) cc_final: 0.7274 (pp30) REVERT: C 235 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6681 (tm-30) REVERT: C 258 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6339 (tt0) REVERT: C 274 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7535 (mtm180) REVERT: C 318 ARG cc_start: 0.7166 (ptm-80) cc_final: 0.6584 (ttm110) REVERT: C 337 LYS cc_start: 0.8283 (mtmt) cc_final: 0.7958 (mtmm) REVERT: C 363 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7195 (ptt) REVERT: D 17 ASP cc_start: 0.7379 (t0) cc_final: 0.6953 (m-30) REVERT: D 92 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7827 (tp30) REVERT: D 106 ASP cc_start: 0.6579 (m-30) cc_final: 0.6317 (m-30) REVERT: D 107 LEU cc_start: 0.8538 (tt) cc_final: 0.8308 (tt) REVERT: D 126 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8297 (m-30) REVERT: D 127 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7607 (mt-10) REVERT: D 141 LYS cc_start: 0.8277 (tptt) cc_final: 0.7709 (tppt) REVERT: D 154 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8178 (mt) REVERT: D 176 LYS cc_start: 0.8413 (mttm) cc_final: 0.7986 (mtpp) REVERT: D 211 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7322 (mm-30) REVERT: D 262 GLU cc_start: 0.7681 (mp0) cc_final: 0.7420 (mp0) REVERT: D 291 ARG cc_start: 0.7890 (tpp80) cc_final: 0.7531 (tpp-160) REVERT: D 315 GLU cc_start: 0.6855 (tp30) cc_final: 0.6570 (tp30) REVERT: D 346 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7786 (ttt180) REVERT: E 72 THR cc_start: 0.7066 (OUTLIER) cc_final: 0.6801 (t) REVERT: E 126 ASN cc_start: 0.8600 (m-40) cc_final: 0.8248 (m-40) REVERT: E 130 LYS cc_start: 0.7761 (tppp) cc_final: 0.7421 (tptp) REVERT: E 170 GLN cc_start: 0.6786 (tp40) cc_final: 0.6184 (mp10) REVERT: E 211 GLN cc_start: 0.7918 (tp40) cc_final: 0.7635 (tp-100) REVERT: E 220 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.6829 (mt) REVERT: E 277 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7236 (tt) REVERT: F 1 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6282 (ptp) REVERT: F 73 ARG cc_start: 0.7549 (tpp80) cc_final: 0.7048 (mmt-90) REVERT: F 87 GLU cc_start: 0.6766 (tt0) cc_final: 0.6393 (pp20) REVERT: F 105 ARG cc_start: 0.8002 (ttt180) cc_final: 0.7523 (ttp-110) REVERT: F 136 LYS cc_start: 0.7521 (ttpt) cc_final: 0.7052 (tptm) REVERT: F 152 ARG cc_start: 0.6671 (mtm180) cc_final: 0.6362 (mtm180) REVERT: F 182 MET cc_start: 0.8054 (mmm) cc_final: 0.7846 (mtp) REVERT: F 300 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7019 (mp0) REVERT: F 301 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7298 (mm-30) REVERT: G 27 LEU cc_start: 0.8185 (mm) cc_final: 0.7839 (tm) REVERT: G 34 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6928 (mt) REVERT: G 36 GLN cc_start: 0.6315 (OUTLIER) cc_final: 0.5833 (pp30) REVERT: G 50 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6965 (mm-30) REVERT: G 91 GLN cc_start: 0.6321 (mt0) cc_final: 0.6099 (pp30) REVERT: G 97 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7231 (mmm) REVERT: G 154 TYR cc_start: 0.7278 (p90) cc_final: 0.6931 (p90) REVERT: G 161 GLU cc_start: 0.7576 (tt0) cc_final: 0.6714 (tt0) REVERT: G 207 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7246 (mm) REVERT: G 235 LYS cc_start: 0.7257 (mmtm) cc_final: 0.6907 (mtmt) REVERT: G 251 ASN cc_start: 0.7397 (p0) cc_final: 0.7099 (p0) REVERT: G 299 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6863 (tm-30) REVERT: J 4 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6699 (tmt170) REVERT: J 8 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7781 (mt0) outliers start: 58 outliers final: 37 residues processed: 377 average time/residue: 0.7056 time to fit residues: 298.6084 Evaluate side-chains 383 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 327 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 66 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 160 GLN 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 148 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 82 ILE 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 346 ARG Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 220 LEU 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 44 LEU Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 177 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 70 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 212 ASN 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 4 ARG Chi-restraints excluded: chain J residue 8 GLN 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: 0.1980 chunk 73 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 145 optimal weight: 0.3980 chunk 139 optimal weight: 1.9990 chunk 243 optimal weight: 0.0980 chunk 153 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 HIS G 221 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.191319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.157984 restraints weight = 22851.881| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.28 r_work: 0.3898 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21280 Z= 0.107 Angle : 0.552 13.917 29085 Z= 0.274 Chirality : 0.037 0.196 3356 Planarity : 0.004 0.045 3612 Dihedral : 14.370 139.561 3298 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.36 % Allowed : 23.36 % Favored : 74.28 % 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: 1.60 (0.17), residues: 2516 helix: 1.91 (0.15), residues: 1266 sheet: 0.21 (0.25), residues: 409 loop : 0.32 (0.23), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 274 TYR 0.016 0.001 TYR G 153 PHE 0.012 0.001 PHE F 3 TRP 0.021 0.001 TRP E 140 HIS 0.003 0.000 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (21264) covalent geometry : angle 0.53907 / 0.27 (29061) hydrogen bonds : bond 0.02768 / 1.87 ( 1122) hydrogen bonds : angle 3.73978 / 2.68 ( 3166) metal coordination : bond 0.00431 / 0.17 ( 16) metal coordination : angle 4.09272 / 2.71 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9019.63 seconds wall clock time: 153 minutes 44.98 seconds (9224.98 seconds total)