Starting phenix.real_space_refine on Fri Aug 7 11:14:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyl_71025/08_2026/9oyl_71025.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyl_71025/08_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_71025/08_2026/9oyl_71025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyl_71025/08_2026/9oyl_71025.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oyl_71025/08_2026/9oyl_71025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyl_71025/08_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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20799 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2725 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "B" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2840 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 16, 'TRANS': 348} Chain: "C" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2865 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "D" Number of atoms: 2807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2807 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 14, 'TRANS': 346} Chain: "E" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2601 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "F" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2835 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 20, 'TRANS': 344} Chain: "G" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2843 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 20, 'TRANS': 345} Chain: "H" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 529 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "I" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 243 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3208 SG CYS B 64 75.086 86.065 113.386 1.00105.37 S ATOM 3268 SG CYS B 73 78.754 85.160 113.612 1.00115.97 S ATOM 3285 SG CYS B 76 76.272 82.438 114.308 1.00121.32 S ATOM 3307 SG CYS B 79 76.512 83.730 110.816 1.00112.59 S ATOM 6048 SG CYS C 64 99.364 55.880 85.670 1.00104.05 S ATOM 6108 SG CYS C 73 100.639 52.991 83.584 1.00116.50 S ATOM 6125 SG CYS C 76 97.883 52.307 85.960 1.00108.95 S ATOM 6147 SG CYS C 79 97.022 54.356 83.021 1.00 96.62 S ATOM 8921 SG CYS D 64 76.603 28.148 55.188 1.00116.64 S ATOM 8981 SG CYS D 73 74.662 25.584 53.237 1.00134.13 S ATOM 8998 SG CYS D 76 73.458 26.368 56.715 1.00125.58 S ATOM 9020 SG CYS D 79 73.080 29.012 54.170 1.00120.88 S ATOM 11644 SG CYS E 50 28.370 35.856 48.852 1.00126.59 S ATOM 11713 SG CYS E 59 24.780 35.350 50.030 1.00141.95 S ATOM 11733 SG CYS E 62 27.453 35.300 52.598 1.00136.87 S ATOM 11754 SG CYS E 65 26.690 38.580 50.779 1.00121.05 S Time building chain proxies: 4.83, per 1000 atoms: 0.23 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: 1.58 Conformation dependent library (CDL) restraints added in 771.9 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: 2.56 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: 3.96 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7117 1.36 - 1.51: 5531 1.51 - 1.66: 8430 1.66 - 1.80: 142 1.80 - 1.95: 44 Bond restraints: 21264 Sorted by residual: bond pdb=" N ASP A 56 " pdb=" CA ASP A 56 " ideal model delta sigma weight residual 1.455 1.489 -0.034 7.00e-03 2.04e+04 2.33e+01 bond pdb=" O3B AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.05e+01 bond pdb=" O3B AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sigma weight residual 1.673 1.586 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" O3B AGS B 402 " pdb=" PB AGS B 402 " ideal model delta sigma weight residual 1.673 1.588 0.085 2.00e-02 2.50e+03 1.83e+01 bond pdb=" O3A AGS C 402 " pdb=" PA AGS C 402 " ideal model delta sigma weight residual 1.664 1.582 0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 21259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 28609 2.04 - 4.09: 391 4.09 - 6.13: 40 6.13 - 8.18: 10 8.18 - 10.22: 11 Bond angle restraints: 29061 Sorted by residual: angle pdb=" N TYR C 3 " pdb=" CA TYR C 3 " pdb=" C TYR C 3 " ideal model delta sigma weight residual 111.11 105.22 5.89 1.20e+00 6.94e-01 2.41e+01 angle pdb=" N3 DT I 14 " pdb=" C4 DT I 14 " pdb=" O4 DT I 14 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT I 8 " pdb=" C4 DT I 8 " pdb=" O4 DT I 8 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT H 28 " pdb=" C4 DT H 28 " pdb=" O4 DT H 28 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT I 16 " pdb=" C4 DT I 16 " pdb=" O4 DT I 16 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 ... (remaining 29056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.60: 12319 30.60 - 61.20: 543 61.20 - 91.80: 40 91.80 - 122.40: 1 122.40 - 152.99: 5 Dihedral angle restraints: 12908 sinusoidal: 5573 harmonic: 7335 Sorted by residual: dihedral pdb=" O1B AGS C 402 " pdb=" O3B AGS C 402 " pdb=" PB AGS C 402 " pdb=" PG AGS C 402 " ideal model delta sinusoidal sigma weight residual 138.55 -14.44 152.99 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" O2B AGS C 402 " pdb=" O3B AGS C 402 " pdb=" PB AGS C 402 " pdb=" PG AGS C 402 " ideal model delta sinusoidal sigma weight residual 7.37 -137.81 145.18 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" O3A AGS C 402 " pdb=" O3B AGS C 402 " pdb=" PB AGS C 402 " pdb=" PG AGS C 402 " ideal model delta sinusoidal sigma weight residual 252.61 108.22 144.39 1 3.00e+01 1.11e-03 1.93e+01 ... (remaining 12905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2958 0.058 - 0.116: 363 0.116 - 0.174: 25 0.174 - 0.232: 1 0.232 - 0.290: 3 Chirality restraints: 3350 Sorted by residual: chirality pdb=" C3' AGS B 402 " pdb=" C2' AGS B 402 " pdb=" C4' AGS B 402 " pdb=" O3' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' AGS C 402 " pdb=" C2' AGS C 402 " pdb=" C4' AGS C 402 " pdb=" O3' AGS C 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C3' AGS D 402 " pdb=" C2' AGS D 402 " pdb=" C4' AGS D 402 " pdb=" O3' AGS D 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3347 not shown) Planarity restraints: 3612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 27 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO A 28 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 28 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 28 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 296 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO G 297 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO G 297 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 297 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 282 " -0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO E 283 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO E 283 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 283 " -0.017 5.00e-02 4.00e+02 ... (remaining 3609 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 118 2.51 - 3.11: 14814 3.11 - 3.71: 33083 3.71 - 4.30: 45846 4.30 - 4.90: 77790 Nonbonded interactions: 171651 Sorted by model distance: nonbonded pdb=" O2G AGS B 402 " pdb="MG MG B 403 " model vdw 1.918 2.170 nonbonded pdb=" O2G AGS D 402 " pdb="MG MG D 403 " model vdw 1.926 2.170 nonbonded pdb=" OG1 THR B 52 " pdb="MG MG B 403 " model vdw 1.938 2.170 nonbonded pdb=" OG1 THR D 52 " pdb="MG MG D 403 " model vdw 1.969 2.170 nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 403 " model vdw 2.009 2.170 ... (remaining 171646 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 361 or resid 401 through 403)) selection = (chain 'C' and (resid 2 through 361 or resid 401 through 403)) selection = (chain 'D' and resid 2 through 403) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 365) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 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: 0.040 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.130 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 21280 Z= 0.243 Angle : 0.598 10.225 29085 Z= 0.336 Chirality : 0.040 0.290 3350 Planarity : 0.003 0.038 3612 Dihedral : 16.243 152.994 8148 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.38 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.17), residues: 2516 helix: 1.50 (0.15), residues: 1246 sheet: 0.46 (0.26), residues: 437 loop : 0.24 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 246 TYR 0.007 0.001 TYR E 47 PHE 0.018 0.001 PHE B 136 TRP 0.012 0.001 TRP B 278 HIS 0.008 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.24 (21264) covalent geometry : angle 0.59151 / 0.34 (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 : 0.771 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: 0.6563 (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: 0.6631 (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: 0.7677 (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: 0.7127 (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: 0.6522 (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: 0.6702 (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: 0.6983 time to fit residues: 481.3703 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 : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain E residue 138 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN A 157 GLN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS B 38 HIS B 182 GLN B 185 HIS C 4 GLN C 38 HIS C 39 HIS C 269 ASN D 4 GLN D 110 ASN E 101 ASN F 148 HIS F 288 ASN F 320 ASN F 355 GLN G 143 GLN G 221 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.190823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.158858 restraints weight = 23271.202| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.02 r_work: 0.3819 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21280 Z= 0.133 Angle : 0.598 9.432 29085 Z= 0.303 Chirality : 0.039 0.181 3350 Planarity : 0.004 0.047 3612 Dihedral : 15.039 141.915 3357 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.88 % Allowed : 13.85 % 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: 1.39 (0.17), residues: 2516 helix: 1.69 (0.15), residues: 1262 sheet: 0.19 (0.24), residues: 446 loop : 0.28 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 208 TYR 0.021 0.001 TYR G 310 PHE 0.022 0.001 PHE G 75 TRP 0.013 0.001 TRP D 10 HIS 0.008 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (21264) covalent geometry : angle 0.58254 / 0.30 (29061) hydrogen bonds : bond 0.04081 / 2.73 ( 1122) hydrogen bonds : angle 4.43992 / 3.20 ( 3166) metal coordination : bond 0.00332 / 0.17 ( 16) metal coordination : angle 4.75267 / 3.02 ( 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 482 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 421 time to evaluate : 0.767 Fit side-chains REVERT: A 66 SER cc_start: 0.6456 (OUTLIER) cc_final: 0.6203 (p) REVERT: A 71 MET cc_start: 0.7440 (mtp) cc_final: 0.7143 (ptp) REVERT: A 126 TRP cc_start: 0.6553 (p-90) cc_final: 0.6162 (p-90) REVERT: A 211 HIS cc_start: 0.7092 (t70) cc_final: 0.6492 (m170) REVERT: A 234 GLN cc_start: 0.7568 (mt0) cc_final: 0.7303 (pt0) REVERT: A 286 MET cc_start: 0.7267 (mmm) cc_final: 0.6465 (mmt) REVERT: A 325 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: A 338 ASP cc_start: 0.7427 (m-30) cc_final: 0.6821 (t0) REVERT: B 80 ARG cc_start: 0.6737 (mtm110) cc_final: 0.6526 (ttm110) REVERT: B 81 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6375 (mp0) REVERT: B 92 GLU cc_start: 0.7732 (tt0) cc_final: 0.7312 (tm-30) REVERT: B 133 ARG cc_start: 0.7468 (tpp80) cc_final: 0.7179 (ttp80) REVERT: B 185 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6770 (t-90) REVERT: B 231 GLN cc_start: 0.6946 (mt0) cc_final: 0.6719 (mt0) REVERT: B 274 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6515 (ptm160) REVERT: B 311 LEU cc_start: 0.6726 (tp) cc_final: 0.6485 (mm) REVERT: B 338 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7378 (pt0) REVERT: C 44 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8519 (t) REVERT: C 77 ASP cc_start: 0.6783 (t70) cc_final: 0.6238 (t0) REVERT: C 94 ASP cc_start: 0.7534 (p0) cc_final: 0.7317 (p0) REVERT: C 106 ASP cc_start: 0.7593 (m-30) cc_final: 0.7321 (m-30) REVERT: C 130 MET cc_start: 0.8560 (mmp) cc_final: 0.8245 (mmp) REVERT: C 176 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7355 (mmtm) REVERT: C 192 ASN cc_start: 0.7745 (t0) cc_final: 0.7526 (t0) REVERT: C 231 GLN cc_start: 0.7649 (pt0) cc_final: 0.7140 (pp30) REVERT: C 254 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7502 (mt-10) REVERT: C 258 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6060 (tt0) REVERT: C 318 ARG cc_start: 0.7176 (ptm-80) cc_final: 0.6571 (ttm110) REVERT: C 337 LYS cc_start: 0.8281 (mtmt) cc_final: 0.7967 (mtmm) REVERT: D 17 ASP cc_start: 0.7227 (t0) cc_final: 0.6907 (m-30) REVERT: D 106 ASP cc_start: 0.6587 (m-30) cc_final: 0.6302 (m-30) REVERT: D 110 ASN cc_start: 0.7939 (m-40) cc_final: 0.7629 (m110) REVERT: D 126 ASP cc_start: 0.8506 (t0) cc_final: 0.8190 (m-30) REVERT: D 127 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7384 (mt-10) REVERT: D 141 LYS cc_start: 0.8164 (tptt) cc_final: 0.7647 (tppp) REVERT: D 176 LYS cc_start: 0.8415 (mttm) cc_final: 0.8198 (mtpp) REVERT: D 211 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7428 (mm-30) REVERT: D 284 GLU cc_start: 0.7398 (tt0) cc_final: 0.6840 (mp0) REVERT: D 291 ARG cc_start: 0.7846 (tpp80) cc_final: 0.6953 (mmp80) REVERT: E 134 GLU cc_start: 0.7743 (tt0) cc_final: 0.7221 (pt0) REVERT: E 147 GLU cc_start: 0.7806 (tp30) cc_final: 0.7416 (tp30) REVERT: E 156 ARG cc_start: 0.8061 (ttm110) cc_final: 0.7861 (mtm110) REVERT: E 170 GLN cc_start: 0.6640 (tp40) cc_final: 0.6116 (tp-100) REVERT: E 228 ASP cc_start: 0.7917 (t0) cc_final: 0.7533 (t0) REVERT: E 258 ARG cc_start: 0.6944 (tpm170) cc_final: 0.6421 (tmt170) REVERT: F 1 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7219 (ptt) REVERT: F 36 GLN cc_start: 0.7762 (mt0) cc_final: 0.7375 (mt0) REVERT: F 87 GLU cc_start: 0.6712 (tt0) cc_final: 0.6450 (pp20) REVERT: F 95 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6434 (pp20) REVERT: F 105 ARG cc_start: 0.7841 (ttt180) cc_final: 0.7479 (ttp-170) REVERT: F 300 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6867 (mp0) REVERT: F 301 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7173 (mt-10) REVERT: F 343 SER cc_start: 0.8513 (p) cc_final: 0.8105 (t) REVERT: F 364 MET cc_start: 0.7809 (ttp) cc_final: 0.6752 (mmt) REVERT: G 4 THR cc_start: 0.8039 (m) cc_final: 0.7830 (m) REVERT: G 14 LEU cc_start: 0.7348 (mt) cc_final: 0.7065 (mt) REVERT: G 36 GLN cc_start: 0.6168 (OUTLIER) cc_final: 0.5895 (pp30) REVERT: G 48 ASP cc_start: 0.8139 (t0) cc_final: 0.7867 (t0) REVERT: G 50 GLU cc_start: 0.6694 (mm-30) cc_final: 0.6294 (mm-30) REVERT: G 52 GLU cc_start: 0.8068 (pt0) cc_final: 0.7575 (pt0) REVERT: G 91 GLN cc_start: 0.6565 (mt0) cc_final: 0.6146 (pp30) REVERT: G 152 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6448 (mmt90) REVERT: G 153 TYR cc_start: 0.6955 (p90) cc_final: 0.6660 (p90) REVERT: G 161 GLU cc_start: 0.7210 (tt0) cc_final: 0.6477 (tt0) REVERT: G 217 GLN cc_start: 0.6127 (tt0) cc_final: 0.5769 (mm-40) REVERT: G 233 THR cc_start: 0.7057 (m) cc_final: 0.6736 (p) REVERT: G 299 GLN cc_start: 0.7240 (mm110) cc_final: 0.6863 (tm-30) REVERT: G 301 GLU cc_start: 0.7723 (pt0) cc_final: 0.7106 (tt0) REVERT: J 4 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6686 (tmt170) outliers start: 61 outliers final: 18 residues processed: 453 average time/residue: 0.6642 time to fit residues: 337.6288 Evaluate side-chains 396 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 369 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 152 ARG Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 138 optimal weight: 0.5980 chunk 191 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 139 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 chunk 195 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 HIS ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS B 185 HIS C 269 ASN E 101 ASN E 126 ASN G 348 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.190325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.156963 restraints weight = 23130.324| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.14 r_work: 0.3790 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21280 Z= 0.129 Angle : 0.569 8.761 29085 Z= 0.288 Chirality : 0.039 0.228 3350 Planarity : 0.004 0.057 3612 Dihedral : 14.760 140.763 3352 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.74 % Allowed : 14.80 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.17), residues: 2516 helix: 1.76 (0.15), residues: 1258 sheet: 0.16 (0.24), residues: 441 loop : 0.23 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 282 TYR 0.014 0.001 TYR G 310 PHE 0.019 0.001 PHE G 75 TRP 0.010 0.001 TRP D 10 HIS 0.020 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (21264) covalent geometry : angle 0.55331 / 0.29 (29061) hydrogen bonds : bond 0.03611 / 2.43 ( 1122) hydrogen bonds : angle 4.19633 / 3.02 ( 3166) metal coordination : bond 0.01381 / 0.69 ( 16) metal coordination : angle 4.72535 / 3.10 ( 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 477 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 398 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7207 (mtp) cc_final: 0.6896 (ptp) REVERT: A 126 TRP cc_start: 0.6673 (p-90) cc_final: 0.6064 (p-90) REVERT: A 211 HIS cc_start: 0.7030 (t70) cc_final: 0.6444 (m170) REVERT: A 226 SER cc_start: 0.8594 (t) cc_final: 0.7871 (m) REVERT: A 234 GLN cc_start: 0.7559 (mt0) cc_final: 0.7266 (pt0) REVERT: A 286 MET cc_start: 0.7271 (mmm) cc_final: 0.6415 (mmt) REVERT: A 325 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: A 338 ASP cc_start: 0.7436 (m-30) cc_final: 0.6737 (t0) REVERT: B 77 ASP cc_start: 0.7050 (m-30) cc_final: 0.5981 (m-30) REVERT: B 80 ARG cc_start: 0.6782 (mtm110) cc_final: 0.6524 (ttm110) REVERT: B 81 GLU cc_start: 0.6616 (mt-10) cc_final: 0.6265 (mp0) REVERT: B 92 GLU cc_start: 0.7769 (tt0) cc_final: 0.7337 (tm-30) REVERT: B 109 ASP cc_start: 0.7357 (t0) cc_final: 0.6976 (t0) REVERT: B 133 ARG cc_start: 0.7481 (tpp80) cc_final: 0.7150 (ttp80) REVERT: B 160 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7275 (mp10) REVERT: B 181 GLU cc_start: 0.7126 (tp30) cc_final: 0.6682 (tp30) REVERT: B 231 GLN cc_start: 0.6951 (mt0) cc_final: 0.6655 (mp10) REVERT: B 274 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6525 (ptm160) REVERT: B 338 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7307 (pt0) REVERT: C 44 SER cc_start: 0.8782 (OUTLIER) cc_final: 0.8519 (t) REVERT: C 94 ASP cc_start: 0.7547 (p0) cc_final: 0.7194 (p0) REVERT: C 106 ASP cc_start: 0.7589 (m-30) cc_final: 0.7322 (m-30) REVERT: C 148 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8394 (mp0) REVERT: C 176 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7332 (mmtm) REVERT: C 192 ASN cc_start: 0.7764 (t0) cc_final: 0.7313 (t0) REVERT: C 193 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.5617 (mp0) REVERT: C 231 GLN cc_start: 0.7641 (pt0) cc_final: 0.7180 (pp30) REVERT: C 318 ARG cc_start: 0.7141 (ptm-80) cc_final: 0.6520 (ttm110) REVERT: C 337 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7956 (mtmm) REVERT: D 17 ASP cc_start: 0.7251 (t0) cc_final: 0.6879 (m-30) REVERT: D 92 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7919 (tp30) REVERT: D 106 ASP cc_start: 0.6555 (m-30) cc_final: 0.6245 (m-30) REVERT: D 110 ASN cc_start: 0.8004 (m-40) cc_final: 0.7690 (m110) REVERT: D 126 ASP cc_start: 0.8529 (t0) cc_final: 0.8204 (m-30) REVERT: D 127 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7468 (mt-10) REVERT: D 141 LYS cc_start: 0.8167 (tptt) cc_final: 0.7619 (tppp) REVERT: D 176 LYS cc_start: 0.8390 (mttm) cc_final: 0.8115 (mtpp) REVERT: D 211 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7440 (mm-30) REVERT: D 235 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7337 (tp40) REVERT: D 284 GLU cc_start: 0.7395 (tt0) cc_final: 0.6795 (mp0) REVERT: D 291 ARG cc_start: 0.7778 (tpp80) cc_final: 0.7343 (tpp-160) REVERT: D 310 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6871 (pt0) REVERT: E 45 SER cc_start: 0.8125 (p) cc_final: 0.7925 (p) REVERT: E 98 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: E 130 LYS cc_start: 0.7812 (tppp) cc_final: 0.7428 (tptp) REVERT: E 147 GLU cc_start: 0.7732 (tp30) cc_final: 0.7415 (tp30) REVERT: E 170 GLN cc_start: 0.6682 (tp40) cc_final: 0.6108 (mp10) REVERT: E 228 ASP cc_start: 0.7876 (t0) cc_final: 0.7660 (t0) REVERT: F 1 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7131 (ptp) REVERT: F 36 GLN cc_start: 0.7760 (mt0) cc_final: 0.7330 (mt0) REVERT: F 87 GLU cc_start: 0.6709 (tt0) cc_final: 0.6363 (pp20) REVERT: F 95 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6381 (pp20) REVERT: F 105 ARG cc_start: 0.7867 (ttt180) cc_final: 0.7373 (ttp-170) REVERT: F 136 LYS cc_start: 0.7373 (ttpt) cc_final: 0.6850 (tppt) REVERT: F 152 ARG cc_start: 0.6740 (mtm180) cc_final: 0.6187 (mtm180) REVERT: F 260 CYS cc_start: 0.6319 (t) cc_final: 0.6066 (p) REVERT: F 300 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6840 (mp0) REVERT: F 301 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7204 (mt-10) REVERT: F 343 SER cc_start: 0.8445 (p) cc_final: 0.7921 (t) REVERT: F 364 MET cc_start: 0.7799 (ttp) cc_final: 0.6879 (mmp) REVERT: G 4 THR cc_start: 0.7943 (m) cc_final: 0.7722 (m) REVERT: G 36 GLN cc_start: 0.6228 (OUTLIER) cc_final: 0.5884 (pp30) REVERT: G 48 ASP cc_start: 0.8088 (t0) cc_final: 0.7755 (t0) REVERT: G 50 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6272 (mm-30) REVERT: G 51 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7301 (ptp) REVERT: G 52 GLU cc_start: 0.8017 (pt0) cc_final: 0.7689 (pt0) REVERT: G 91 GLN cc_start: 0.6416 (mt0) cc_final: 0.6086 (pp30) REVERT: G 153 TYR cc_start: 0.6987 (p90) cc_final: 0.6699 (p90) REVERT: G 161 GLU cc_start: 0.7269 (tt0) cc_final: 0.6513 (tt0) REVERT: G 251 ASN cc_start: 0.7663 (p0) cc_final: 0.7312 (p0) REVERT: G 299 GLN cc_start: 0.7133 (mm110) cc_final: 0.6753 (tm-30) REVERT: G 301 GLU cc_start: 0.7709 (pt0) cc_final: 0.6964 (tt0) REVERT: G 339 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7210 (mpp) REVERT: J 4 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6820 (tmt170) outliers start: 79 outliers final: 27 residues processed: 441 average time/residue: 0.6422 time to fit residues: 318.9164 Evaluate side-chains 409 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 370 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 364 MET Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 160 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 chunk 183 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 overall best weight: 2.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN A 281 ASN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS C 269 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 HIS ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 ASN G 212 ASN G 217 GLN G 299 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.186505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.153475 restraints weight = 23232.692| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.18 r_work: 0.3728 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 21280 Z= 0.206 Angle : 0.625 8.130 29085 Z= 0.311 Chirality : 0.041 0.185 3350 Planarity : 0.005 0.070 3612 Dihedral : 14.960 141.615 3352 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.54 % Allowed : 16.03 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.17), residues: 2516 helix: 1.39 (0.15), residues: 1270 sheet: 0.13 (0.25), residues: 394 loop : 0.03 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 11 TYR 0.018 0.002 TYR G 310 PHE 0.017 0.002 PHE B 136 TRP 0.011 0.001 TRP B 10 HIS 0.004 0.001 HIS E 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (21264) covalent geometry : angle 0.61254 / 0.31 (29061) hydrogen bonds : bond 0.03855 / 2.61 ( 1122) hydrogen bonds : angle 4.18021 / 3.00 ( 3166) metal coordination : bond 0.00646 / 0.31 ( 16) metal coordination : angle 4.29111 / 2.73 ( 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 481 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 385 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 108 LEU cc_start: 0.5316 (OUTLIER) cc_final: 0.5034 (tp) REVERT: A 126 TRP cc_start: 0.6470 (p-90) cc_final: 0.6046 (p-90) REVERT: A 211 HIS cc_start: 0.7137 (t70) cc_final: 0.6423 (m170) REVERT: A 234 GLN cc_start: 0.7566 (mt0) cc_final: 0.7275 (pt0) REVERT: A 286 MET cc_start: 0.7337 (mmm) cc_final: 0.6460 (mmt) REVERT: B 77 ASP cc_start: 0.7107 (m-30) cc_final: 0.6225 (m-30) REVERT: B 80 ARG cc_start: 0.6977 (mtm110) cc_final: 0.6714 (ttm110) REVERT: B 81 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6387 (mt-10) REVERT: B 92 GLU cc_start: 0.7788 (tt0) cc_final: 0.7318 (tm-30) REVERT: B 102 GLU cc_start: 0.6584 (tt0) cc_final: 0.6219 (tp30) REVERT: B 133 ARG cc_start: 0.7538 (tpp80) cc_final: 0.7182 (ttp80) REVERT: B 160 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7411 (mp10) REVERT: B 185 HIS cc_start: 0.7318 (OUTLIER) cc_final: 0.6841 (t70) REVERT: B 231 GLN cc_start: 0.7259 (mt0) cc_final: 0.6979 (mt0) REVERT: B 314 ARG cc_start: 0.7594 (mmt-90) cc_final: 0.7293 (mtp85) REVERT: B 320 ILE cc_start: 0.8288 (mt) cc_final: 0.8034 (mm) REVERT: B 338 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7394 (pt0) REVERT: C 34 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6935 (mp) REVERT: C 94 ASP cc_start: 0.7570 (p0) cc_final: 0.7296 (p0) REVERT: C 106 ASP cc_start: 0.7614 (m-30) cc_final: 0.7336 (m-30) REVERT: C 127 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7383 (tp30) REVERT: C 148 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: C 176 LYS cc_start: 0.8265 (mtpp) cc_final: 0.7370 (mmtm) REVERT: C 192 ASN cc_start: 0.7860 (t0) cc_final: 0.7325 (t0) REVERT: C 193 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.5953 (mp0) REVERT: C 231 GLN cc_start: 0.7737 (pt0) cc_final: 0.7260 (pp30) REVERT: C 258 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6230 (tt0) REVERT: C 318 ARG cc_start: 0.7162 (ptm-80) cc_final: 0.6533 (ttm110) REVERT: C 337 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8178 (ttmm) REVERT: D 17 ASP cc_start: 0.7331 (t0) cc_final: 0.6922 (m-30) REVERT: D 92 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7929 (tp30) REVERT: D 106 ASP cc_start: 0.6677 (m-30) cc_final: 0.6405 (m-30) REVERT: D 126 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8324 (m-30) REVERT: D 127 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7566 (mt-10) REVERT: D 141 LYS cc_start: 0.8324 (tptt) cc_final: 0.7738 (tppt) REVERT: D 154 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8128 (mt) REVERT: D 176 LYS cc_start: 0.8409 (mttm) cc_final: 0.8056 (mtpp) REVERT: D 211 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7495 (mm-30) REVERT: D 262 GLU cc_start: 0.7718 (mp0) cc_final: 0.7389 (mp0) REVERT: D 284 GLU cc_start: 0.7528 (tt0) cc_final: 0.6831 (mp0) REVERT: D 291 ARG cc_start: 0.7904 (tpp80) cc_final: 0.7596 (tpp80) REVERT: D 310 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6226 (mt-10) REVERT: D 311 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7449 (mm) REVERT: E 45 SER cc_start: 0.8179 (p) cc_final: 0.7973 (p) REVERT: E 72 THR cc_start: 0.7126 (OUTLIER) cc_final: 0.6776 (t) REVERT: E 78 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8500 (p) REVERT: E 98 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: E 130 LYS cc_start: 0.7816 (tppp) cc_final: 0.7434 (tptp) REVERT: E 147 GLU cc_start: 0.7844 (tp30) cc_final: 0.7587 (tp30) REVERT: E 170 GLN cc_start: 0.6832 (tp40) cc_final: 0.6214 (mp10) REVERT: E 258 ARG cc_start: 0.7721 (mmm160) cc_final: 0.7483 (mmm-85) REVERT: E 322 TYR cc_start: 0.7916 (m-10) cc_final: 0.7453 (m-10) REVERT: F 36 GLN cc_start: 0.7802 (mt0) cc_final: 0.7392 (mt0) REVERT: F 50 GLU cc_start: 0.7227 (mt-10) cc_final: 0.7009 (tt0) REVERT: F 73 ARG cc_start: 0.7733 (tpp80) cc_final: 0.7018 (pmt170) REVERT: F 87 GLU cc_start: 0.6760 (tt0) cc_final: 0.6439 (pp20) REVERT: F 95 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6310 (pp20) REVERT: F 105 ARG cc_start: 0.7950 (ttt180) cc_final: 0.7499 (ttp-170) REVERT: F 136 LYS cc_start: 0.7510 (ttpt) cc_final: 0.6945 (tppt) REVERT: F 152 ARG cc_start: 0.6721 (mtm180) cc_final: 0.6158 (mtm180) REVERT: F 300 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6848 (mp0) REVERT: F 301 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7356 (mt-10) REVERT: F 305 ILE cc_start: 0.8506 (mt) cc_final: 0.8213 (mp) REVERT: F 343 SER cc_start: 0.8435 (p) cc_final: 0.7999 (t) REVERT: F 364 MET cc_start: 0.7845 (ttp) cc_final: 0.6934 (mmp) REVERT: G 14 LEU cc_start: 0.7235 (mt) cc_final: 0.6915 (mt) REVERT: G 34 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6889 (mt) REVERT: G 36 GLN cc_start: 0.6257 (OUTLIER) cc_final: 0.5918 (pp30) REVERT: G 48 ASP cc_start: 0.8140 (t0) cc_final: 0.7901 (t0) REVERT: G 50 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6277 (mm-30) REVERT: G 91 GLN cc_start: 0.6707 (mt0) cc_final: 0.6367 (pp30) REVERT: G 127 GLU cc_start: 0.7983 (pt0) cc_final: 0.7162 (pt0) REVERT: G 153 TYR cc_start: 0.7128 (p90) cc_final: 0.6722 (p90) REVERT: G 161 GLU cc_start: 0.7539 (tt0) cc_final: 0.6638 (tt0) REVERT: G 217 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.6887 (mm110) REVERT: G 251 ASN cc_start: 0.7659 (p0) cc_final: 0.7330 (p0) REVERT: G 299 GLN cc_start: 0.7307 (mm-40) cc_final: 0.6915 (tm-30) REVERT: G 301 GLU cc_start: 0.7725 (pt0) cc_final: 0.7075 (tt0) REVERT: G 338 MET cc_start: 0.7619 (mtp) cc_final: 0.7286 (mtm) REVERT: G 339 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7218 (mpp) REVERT: G 365 ARG cc_start: 0.5953 (mmm-85) cc_final: 0.5668 (mmm160) outliers start: 96 outliers final: 41 residues processed: 444 average time/residue: 0.6822 time to fit residues: 342.1055 Evaluate side-chains 422 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 363 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 127 GLU 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 D residue 1 MET Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 311 LEU 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 98 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 217 GLN Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 364 MET Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 246 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 175 optimal weight: 5.9990 chunk 216 optimal weight: 9.9990 chunk 237 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN C 13 GLN C 269 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN E 211 GLN G 148 HIS G 212 ASN G 217 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.188720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.155861 restraints weight = 23133.808| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.17 r_work: 0.3858 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21280 Z= 0.134 Angle : 0.572 8.370 29085 Z= 0.285 Chirality : 0.039 0.169 3350 Planarity : 0.004 0.067 3612 Dihedral : 14.740 148.624 3352 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.64 % Allowed : 18.49 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.17), residues: 2516 helix: 1.61 (0.15), residues: 1260 sheet: 0.13 (0.25), residues: 401 loop : 0.06 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 274 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 0.007 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (21264) covalent geometry : angle 0.55961 / 0.28 (29061) hydrogen bonds : bond 0.03372 / 2.28 ( 1122) hydrogen bonds : angle 3.99569 / 2.87 ( 3166) metal coordination : bond 0.00314 / 0.16 ( 16) metal coordination : angle 4.24131 / 2.71 ( 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 453 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 376 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7445 (ptp) cc_final: 0.6975 (ptp) REVERT: A 78 GLN cc_start: 0.8161 (pt0) cc_final: 0.7943 (tt0) REVERT: A 126 TRP cc_start: 0.6469 (p-90) cc_final: 0.5983 (p-90) REVERT: A 211 HIS cc_start: 0.7216 (t70) cc_final: 0.6491 (m170) REVERT: A 234 GLN cc_start: 0.7559 (mt0) cc_final: 0.7270 (pt0) REVERT: B 77 ASP cc_start: 0.7088 (m-30) cc_final: 0.6239 (m-30) REVERT: B 80 ARG cc_start: 0.6988 (mtm110) cc_final: 0.6719 (ttm110) REVERT: B 81 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6373 (mt-10) REVERT: B 92 GLU cc_start: 0.7730 (tt0) cc_final: 0.7280 (tm-30) REVERT: B 133 ARG cc_start: 0.7474 (tpp80) cc_final: 0.7169 (ttp80) REVERT: B 160 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7385 (mp10) REVERT: B 185 HIS cc_start: 0.7358 (OUTLIER) cc_final: 0.6907 (t-90) REVERT: B 231 GLN cc_start: 0.7268 (mt0) cc_final: 0.7015 (mt0) REVERT: B 320 ILE cc_start: 0.8260 (mt) cc_final: 0.7964 (mm) REVERT: B 338 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7371 (pt0) REVERT: C 34 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6963 (mt) REVERT: C 94 ASP cc_start: 0.7611 (p0) cc_final: 0.7284 (p0) REVERT: C 106 ASP cc_start: 0.7628 (m-30) cc_final: 0.7358 (m-30) REVERT: C 127 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7366 (tp30) REVERT: C 148 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8369 (mp0) REVERT: C 176 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7374 (mmtm) REVERT: C 192 ASN cc_start: 0.7840 (t0) cc_final: 0.7318 (t0) REVERT: C 193 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.5909 (mp0) REVERT: C 231 GLN cc_start: 0.7739 (pt0) cc_final: 0.7267 (pp30) REVERT: C 274 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7641 (mtp-110) REVERT: C 318 ARG cc_start: 0.7157 (ptm-80) cc_final: 0.6558 (ttm110) REVERT: C 337 LYS cc_start: 0.8308 (mtmt) cc_final: 0.7950 (mtmm) REVERT: D 17 ASP cc_start: 0.7319 (t0) cc_final: 0.6942 (m-30) REVERT: D 92 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7915 (tp30) REVERT: D 106 ASP cc_start: 0.6584 (m-30) cc_final: 0.6324 (m-30) REVERT: D 126 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8258 (m-30) REVERT: D 127 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7521 (mt-10) REVERT: D 141 LYS cc_start: 0.8366 (tptt) cc_final: 0.7789 (tppt) REVERT: D 176 LYS cc_start: 0.8347 (mttm) cc_final: 0.7975 (mtpp) REVERT: D 211 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7466 (mm-30) REVERT: D 262 GLU cc_start: 0.7667 (mp0) cc_final: 0.7356 (mp0) REVERT: D 284 GLU cc_start: 0.7475 (tt0) cc_final: 0.6859 (mp0) REVERT: D 291 ARG cc_start: 0.7838 (tpp80) cc_final: 0.6891 (mmp80) REVERT: D 310 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6109 (mt-10) REVERT: E 45 SER cc_start: 0.8170 (p) cc_final: 0.7964 (p) REVERT: E 72 THR cc_start: 0.7139 (OUTLIER) cc_final: 0.6813 (t) REVERT: E 126 ASN cc_start: 0.8430 (m-40) cc_final: 0.8119 (m-40) REVERT: E 130 LYS cc_start: 0.7815 (tppp) cc_final: 0.7447 (tptp) REVERT: E 170 GLN cc_start: 0.6825 (tp40) cc_final: 0.6246 (mp10) REVERT: E 258 ARG cc_start: 0.7767 (mmm160) cc_final: 0.7564 (mmm-85) REVERT: E 277 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7102 (tt) REVERT: F 36 GLN cc_start: 0.7766 (mt0) cc_final: 0.7373 (mt0) REVERT: F 69 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7654 (p) REVERT: F 87 GLU cc_start: 0.6768 (tt0) cc_final: 0.6473 (pp20) REVERT: F 95 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6312 (pp20) REVERT: F 105 ARG cc_start: 0.7914 (ttt180) cc_final: 0.7466 (ttp-170) REVERT: F 136 LYS cc_start: 0.7525 (ttpt) cc_final: 0.6970 (tppt) REVERT: F 152 ARG cc_start: 0.6725 (mtm180) cc_final: 0.6439 (mtm180) REVERT: F 205 ARG cc_start: 0.7285 (mtm-85) cc_final: 0.6926 (mtm-85) REVERT: F 300 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6815 (mp0) REVERT: F 301 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7174 (mm-30) REVERT: F 343 SER cc_start: 0.8357 (p) cc_final: 0.7895 (t) REVERT: G 14 LEU cc_start: 0.7260 (mt) cc_final: 0.7050 (mt) REVERT: G 27 LEU cc_start: 0.8109 (mm) cc_final: 0.7820 (tm) REVERT: G 34 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6928 (mt) REVERT: G 36 GLN cc_start: 0.6198 (OUTLIER) cc_final: 0.5761 (pp30) REVERT: G 50 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6301 (mm-30) REVERT: G 91 GLN cc_start: 0.6473 (mt0) cc_final: 0.6175 (pp30) REVERT: G 127 GLU cc_start: 0.8054 (pt0) cc_final: 0.6997 (pt0) REVERT: G 153 TYR cc_start: 0.7123 (p90) cc_final: 0.6696 (p90) REVERT: G 161 GLU cc_start: 0.7552 (tt0) cc_final: 0.6839 (tt0) REVERT: G 217 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6527 (mm-40) REVERT: G 251 ASN cc_start: 0.7616 (p0) cc_final: 0.7254 (p0) REVERT: G 299 GLN cc_start: 0.7369 (mm-40) cc_final: 0.6937 (tm-30) REVERT: G 301 GLU cc_start: 0.7717 (pt0) cc_final: 0.7060 (tt0) REVERT: G 339 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7067 (mpp) outliers start: 77 outliers final: 36 residues processed: 424 average time/residue: 0.6595 time to fit residues: 315.3682 Evaluate side-chains 403 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 352 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 127 GLU 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 D residue 1 MET Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 310 GLU 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 268 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 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 90 VAL Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 217 GLN Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 364 MET Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 247 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN G 148 HIS G 217 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.188032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.154890 restraints weight = 23087.301| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.09 r_work: 0.3848 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21280 Z= 0.153 Angle : 0.587 8.007 29085 Z= 0.293 Chirality : 0.039 0.168 3350 Planarity : 0.005 0.093 3612 Dihedral : 14.592 151.360 3352 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.64 % Allowed : 19.91 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.17), residues: 2516 helix: 1.57 (0.15), residues: 1263 sheet: 0.12 (0.25), residues: 403 loop : 0.07 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 86 TYR 0.030 0.002 TYR B 328 PHE 0.013 0.001 PHE F 3 TRP 0.011 0.001 TRP B 10 HIS 0.006 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (21264) covalent geometry : angle 0.57528 / 0.29 (29061) hydrogen bonds : bond 0.03409 / 2.31 ( 1122) hydrogen bonds : angle 3.96619 / 2.84 ( 3166) metal coordination : bond 0.00343 / 0.17 ( 16) metal coordination : angle 4.02163 / 2.58 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 361 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7491 (ptp) cc_final: 0.7092 (ptp) REVERT: A 78 GLN cc_start: 0.8120 (pt0) cc_final: 0.7883 (tt0) REVERT: A 126 TRP cc_start: 0.6386 (p-90) cc_final: 0.5896 (p-90) REVERT: A 211 HIS cc_start: 0.7243 (t70) cc_final: 0.6488 (m170) REVERT: A 234 GLN cc_start: 0.7522 (mt0) cc_final: 0.7253 (pt0) REVERT: A 244 VAL cc_start: 0.7521 (OUTLIER) cc_final: 0.7251 (p) REVERT: A 325 GLU cc_start: 0.7672 (mp0) cc_final: 0.7201 (mm-30) REVERT: B 77 ASP cc_start: 0.7094 (m-30) cc_final: 0.6251 (m-30) REVERT: B 80 ARG cc_start: 0.7000 (mtm110) cc_final: 0.6753 (ttm110) REVERT: B 81 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6377 (mt-10) REVERT: B 92 GLU cc_start: 0.7687 (tt0) cc_final: 0.7249 (tm-30) REVERT: B 133 ARG cc_start: 0.7478 (tpp80) cc_final: 0.7166 (ttp80) REVERT: B 160 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7292 (mp10) REVERT: B 185 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.6948 (t70) REVERT: B 231 GLN cc_start: 0.7331 (mt0) cc_final: 0.7088 (mt0) REVERT: B 320 ILE cc_start: 0.8273 (mt) cc_final: 0.7990 (mm) REVERT: B 338 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7353 (pt0) REVERT: C 9 LYS cc_start: 0.8603 (tttp) cc_final: 0.8358 (tttm) REVERT: C 34 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.7004 (mt) REVERT: C 86 ARG cc_start: 0.7410 (mtm110) cc_final: 0.7076 (mtm110) REVERT: C 94 ASP cc_start: 0.7605 (p0) cc_final: 0.7331 (p0) REVERT: C 106 ASP cc_start: 0.7616 (m-30) cc_final: 0.7358 (m-30) REVERT: C 130 MET cc_start: 0.8469 (mmp) cc_final: 0.8143 (mmp) REVERT: C 176 LYS cc_start: 0.8304 (mtpp) cc_final: 0.7409 (mmtm) REVERT: C 192 ASN cc_start: 0.7860 (t0) cc_final: 0.7376 (t0) REVERT: C 193 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6011 (mp0) REVERT: C 231 GLN cc_start: 0.7800 (pt0) cc_final: 0.7331 (pp30) REVERT: C 318 ARG cc_start: 0.7186 (ptm-80) cc_final: 0.6583 (ttm110) REVERT: C 337 LYS cc_start: 0.8323 (mtmt) cc_final: 0.7988 (mtmm) REVERT: D 17 ASP cc_start: 0.7362 (t0) cc_final: 0.6960 (m-30) REVERT: D 92 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7895 (tp30) REVERT: D 106 ASP cc_start: 0.6586 (m-30) cc_final: 0.6333 (m-30) REVERT: D 126 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8263 (m-30) REVERT: D 127 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7531 (mt-10) REVERT: D 141 LYS cc_start: 0.8364 (tptt) cc_final: 0.7787 (tppt) REVERT: D 154 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8190 (mt) REVERT: D 176 LYS cc_start: 0.8330 (mttm) cc_final: 0.7963 (mtpp) REVERT: D 211 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7496 (mm-30) REVERT: D 262 GLU cc_start: 0.7683 (mp0) cc_final: 0.7408 (mp0) REVERT: D 284 GLU cc_start: 0.7505 (tt0) cc_final: 0.6854 (mp0) REVERT: D 291 ARG cc_start: 0.7866 (tpp80) cc_final: 0.6912 (mmp80) REVERT: D 310 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6072 (mt-10) REVERT: E 72 THR cc_start: 0.7151 (OUTLIER) cc_final: 0.6836 (t) REVERT: E 98 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: E 126 ASN cc_start: 0.8490 (m-40) cc_final: 0.8184 (m-40) REVERT: E 130 LYS cc_start: 0.7867 (tppp) cc_final: 0.7512 (tptp) REVERT: E 170 GLN cc_start: 0.6810 (tp40) cc_final: 0.6242 (mp10) REVERT: E 258 ARG cc_start: 0.7659 (mmm160) cc_final: 0.7448 (mmm-85) REVERT: F 36 GLN cc_start: 0.7749 (mt0) cc_final: 0.7372 (mt0) REVERT: F 69 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7776 (p) REVERT: F 87 GLU cc_start: 0.6764 (tt0) cc_final: 0.6484 (pp20) REVERT: F 95 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6268 (pp20) REVERT: F 105 ARG cc_start: 0.7933 (ttt180) cc_final: 0.7498 (ttp-110) REVERT: F 152 ARG cc_start: 0.6777 (mtm180) cc_final: 0.6287 (mtm180) REVERT: F 165 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.5956 (tm-30) REVERT: F 205 ARG cc_start: 0.7274 (mtm-85) cc_final: 0.6846 (mtm-85) REVERT: F 300 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6871 (mp0) REVERT: F 301 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7192 (mm-30) REVERT: F 343 SER cc_start: 0.8391 (p) cc_final: 0.7834 (t) REVERT: G 14 LEU cc_start: 0.7251 (mt) cc_final: 0.7003 (mt) REVERT: G 27 LEU cc_start: 0.8114 (mm) cc_final: 0.7825 (tm) REVERT: G 34 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6953 (mt) REVERT: G 36 GLN cc_start: 0.6163 (OUTLIER) cc_final: 0.5753 (pp30) REVERT: G 48 ASP cc_start: 0.8256 (t0) cc_final: 0.7966 (t0) REVERT: G 50 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6352 (mm-30) REVERT: G 91 GLN cc_start: 0.6539 (mt0) cc_final: 0.6316 (pp30) REVERT: G 126 VAL cc_start: 0.7268 (t) cc_final: 0.7064 (p) REVERT: G 153 TYR cc_start: 0.7153 (p90) cc_final: 0.6718 (p90) REVERT: G 161 GLU cc_start: 0.7507 (tt0) cc_final: 0.6563 (tt0) REVERT: G 207 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7194 (mm) REVERT: G 217 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7331 (mm-40) REVERT: G 251 ASN cc_start: 0.7583 (p0) cc_final: 0.7237 (p0) REVERT: G 299 GLN cc_start: 0.7407 (mm-40) cc_final: 0.6951 (tm-30) REVERT: G 301 GLU cc_start: 0.7682 (pt0) cc_final: 0.7060 (tt0) REVERT: G 339 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7053 (mpp) outliers start: 77 outliers final: 38 residues processed: 411 average time/residue: 0.6607 time to fit residues: 306.4989 Evaluate side-chains 405 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 350 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 310 GLU 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 98 GLU Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 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 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 90 VAL 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 217 GLN Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 364 MET Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 117 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 206 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.186845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.154231 restraints weight = 23244.703| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.99 r_work: 0.3854 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21280 Z= 0.161 Angle : 0.594 12.675 29085 Z= 0.295 Chirality : 0.040 0.226 3350 Planarity : 0.004 0.065 3612 Dihedral : 14.569 148.130 3352 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.97 % Allowed : 20.00 % 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: 1.16 (0.17), residues: 2516 helix: 1.52 (0.15), residues: 1264 sheet: 0.15 (0.24), residues: 413 loop : 0.09 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 86 TYR 0.029 0.002 TYR B 328 PHE 0.013 0.001 PHE G 75 TRP 0.013 0.001 TRP E 140 HIS 0.006 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (21264) covalent geometry : angle 0.58348 / 0.29 (29061) hydrogen bonds : bond 0.03438 / 2.34 ( 1122) hydrogen bonds : angle 3.95980 / 2.83 ( 3166) metal coordination : bond 0.00370 / 0.19 ( 16) metal coordination : angle 3.90620 / 2.49 ( 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 447 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 363 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7563 (ptp) cc_final: 0.7143 (ptp) REVERT: A 78 GLN cc_start: 0.8094 (pt0) cc_final: 0.7670 (tm-30) REVERT: A 126 TRP cc_start: 0.6264 (p-90) cc_final: 0.5780 (p-90) REVERT: A 211 HIS cc_start: 0.7230 (t70) cc_final: 0.6479 (m170) REVERT: A 234 GLN cc_start: 0.7533 (mt0) cc_final: 0.7252 (pt0) REVERT: A 244 VAL cc_start: 0.7512 (OUTLIER) cc_final: 0.7261 (p) REVERT: A 325 GLU cc_start: 0.7619 (mp0) cc_final: 0.7361 (mp0) REVERT: B 77 ASP cc_start: 0.7058 (m-30) cc_final: 0.6213 (m-30) REVERT: B 80 ARG cc_start: 0.6995 (mtm110) cc_final: 0.6752 (ttm110) REVERT: B 81 GLU cc_start: 0.6667 (mt-10) cc_final: 0.6359 (mt-10) REVERT: B 92 GLU cc_start: 0.7654 (tt0) cc_final: 0.7231 (tm-30) REVERT: B 133 ARG cc_start: 0.7470 (tpp80) cc_final: 0.7262 (mmm-85) REVERT: B 160 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: B 185 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.6937 (t70) REVERT: B 231 GLN cc_start: 0.7313 (mt0) cc_final: 0.7062 (mt0) REVERT: B 320 ILE cc_start: 0.8279 (mt) cc_final: 0.7981 (mm) REVERT: B 338 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7277 (pt0) REVERT: C 9 LYS cc_start: 0.8581 (tttp) cc_final: 0.8361 (tttm) REVERT: C 94 ASP cc_start: 0.7528 (p0) cc_final: 0.7279 (p0) REVERT: C 106 ASP cc_start: 0.7604 (m-30) cc_final: 0.7321 (m-30) REVERT: C 127 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7265 (tp30) REVERT: C 176 LYS cc_start: 0.8310 (mtpp) cc_final: 0.7394 (mmtm) REVERT: C 192 ASN cc_start: 0.7847 (t0) cc_final: 0.7332 (t0) REVERT: C 193 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6059 (mp0) REVERT: C 231 GLN cc_start: 0.7783 (pt0) cc_final: 0.7304 (pp30) REVERT: C 318 ARG cc_start: 0.7220 (ptm-80) cc_final: 0.6606 (ttm110) REVERT: C 337 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8000 (mtmm) REVERT: D 17 ASP cc_start: 0.7376 (t0) cc_final: 0.6945 (m-30) REVERT: D 92 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7862 (tp30) REVERT: D 106 ASP cc_start: 0.6575 (m-30) cc_final: 0.6319 (m-30) REVERT: D 126 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8232 (m-30) REVERT: D 127 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7572 (mt-10) REVERT: D 141 LYS cc_start: 0.8358 (tptt) cc_final: 0.7775 (tppt) REVERT: D 154 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8198 (mt) REVERT: D 176 LYS cc_start: 0.8370 (mttm) cc_final: 0.7988 (mtpp) REVERT: D 211 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7471 (mm-30) REVERT: D 262 GLU cc_start: 0.7656 (mp0) cc_final: 0.7395 (mp0) REVERT: D 284 GLU cc_start: 0.7471 (tt0) cc_final: 0.6837 (mp0) REVERT: D 291 ARG cc_start: 0.7853 (tpp80) cc_final: 0.6904 (mmp80) REVERT: D 310 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6085 (mt-10) REVERT: E 72 THR cc_start: 0.7134 (OUTLIER) cc_final: 0.6829 (t) REVERT: E 126 ASN cc_start: 0.8485 (m-40) cc_final: 0.8178 (m-40) REVERT: E 130 LYS cc_start: 0.7838 (tppp) cc_final: 0.7478 (tptp) REVERT: E 170 GLN cc_start: 0.6768 (tp40) cc_final: 0.6289 (tp40) REVERT: E 258 ARG cc_start: 0.7685 (mmm160) cc_final: 0.7468 (mmm-85) REVERT: E 277 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6971 (tt) REVERT: F 36 GLN cc_start: 0.7714 (mt0) cc_final: 0.7318 (mt0) REVERT: F 69 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7763 (p) REVERT: F 87 GLU cc_start: 0.6717 (tt0) cc_final: 0.6451 (pp20) REVERT: F 95 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6218 (pp20) REVERT: F 105 ARG cc_start: 0.7915 (ttt180) cc_final: 0.7466 (ttp-110) REVERT: F 152 ARG cc_start: 0.6748 (mtm180) cc_final: 0.6408 (mtm180) REVERT: F 165 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5994 (tm-30) REVERT: F 205 ARG cc_start: 0.7259 (mtm-85) cc_final: 0.6826 (mtm-85) REVERT: F 300 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6864 (mp0) REVERT: F 301 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7170 (mm-30) REVERT: F 343 SER cc_start: 0.8360 (p) cc_final: 0.7802 (t) REVERT: G 14 LEU cc_start: 0.7212 (mt) cc_final: 0.6965 (mt) REVERT: G 27 LEU cc_start: 0.8144 (mm) cc_final: 0.7836 (tm) REVERT: G 34 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6921 (mt) REVERT: G 36 GLN cc_start: 0.6132 (OUTLIER) cc_final: 0.5709 (pp30) REVERT: G 48 ASP cc_start: 0.8229 (t0) cc_final: 0.7939 (t0) REVERT: G 50 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6534 (mm-30) REVERT: G 51 MET cc_start: 0.7887 (ptp) cc_final: 0.7568 (ptp) REVERT: G 91 GLN cc_start: 0.6508 (mt0) cc_final: 0.6270 (pp30) REVERT: G 153 TYR cc_start: 0.7152 (p90) cc_final: 0.6709 (p90) REVERT: G 161 GLU cc_start: 0.7544 (tt0) cc_final: 0.6665 (tt0) REVERT: G 163 GLU cc_start: 0.6239 (mm-30) cc_final: 0.6009 (mm-30) REVERT: G 207 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7140 (mm) REVERT: G 235 LYS cc_start: 0.7274 (mmtm) cc_final: 0.6881 (mtmt) REVERT: G 251 ASN cc_start: 0.7584 (p0) cc_final: 0.7244 (p0) REVERT: G 299 GLN cc_start: 0.7432 (mm-40) cc_final: 0.6954 (tm-30) REVERT: G 301 GLU cc_start: 0.7642 (pt0) cc_final: 0.7048 (tt0) outliers start: 84 outliers final: 43 residues processed: 417 average time/residue: 0.6536 time to fit residues: 308.7394 Evaluate side-chains 406 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 348 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 310 GLU 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 134 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 364 MET Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 75 optimal weight: 2.9990 chunk 245 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 151 optimal weight: 0.0000 chunk 219 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 269 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.187459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.154498 restraints weight = 22915.263| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.15 r_work: 0.3841 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21280 Z= 0.161 Angle : 0.601 13.057 29085 Z= 0.298 Chirality : 0.040 0.201 3350 Planarity : 0.004 0.065 3612 Dihedral : 14.573 144.990 3352 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.50 % Allowed : 20.90 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.17), residues: 2516 helix: 1.49 (0.15), residues: 1265 sheet: 0.13 (0.25), residues: 401 loop : 0.09 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 274 TYR 0.025 0.002 TYR B 328 PHE 0.013 0.001 PHE F 3 TRP 0.016 0.001 TRP E 140 HIS 0.004 0.001 HIS G 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (21264) covalent geometry : angle 0.59168 / 0.30 (29061) hydrogen bonds : bond 0.03403 / 2.31 ( 1122) hydrogen bonds : angle 3.96760 / 2.83 ( 3166) metal coordination : bond 0.00350 / 0.18 ( 16) metal coordination : angle 3.78616 / 2.42 ( 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 424 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 350 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7643 (ptp) cc_final: 0.7251 (ptp) REVERT: A 78 GLN cc_start: 0.8171 (pt0) cc_final: 0.7703 (tm-30) REVERT: A 126 TRP cc_start: 0.6294 (p-90) cc_final: 0.5813 (p-90) REVERT: A 211 HIS cc_start: 0.7226 (t70) cc_final: 0.6455 (m170) REVERT: A 234 GLN cc_start: 0.7551 (mt0) cc_final: 0.7280 (pt0) REVERT: A 244 VAL cc_start: 0.7533 (OUTLIER) cc_final: 0.7287 (p) REVERT: A 325 GLU cc_start: 0.7644 (mp0) cc_final: 0.7313 (mp0) REVERT: B 77 ASP cc_start: 0.7000 (m-30) cc_final: 0.6182 (m-30) REVERT: B 80 ARG cc_start: 0.7030 (mtm110) cc_final: 0.6774 (ttm110) REVERT: B 81 GLU cc_start: 0.6684 (mt-10) cc_final: 0.6309 (mt-10) REVERT: B 92 GLU cc_start: 0.7669 (tt0) cc_final: 0.7252 (tm-30) REVERT: B 133 ARG cc_start: 0.7486 (tpp80) cc_final: 0.7251 (mmm-85) REVERT: B 160 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7283 (mp10) REVERT: B 181 GLU cc_start: 0.7473 (tp30) cc_final: 0.7233 (mm-30) REVERT: B 185 HIS cc_start: 0.7298 (OUTLIER) cc_final: 0.6914 (t70) REVERT: B 231 GLN cc_start: 0.7327 (mt0) cc_final: 0.7053 (mt0) REVERT: B 320 ILE cc_start: 0.8266 (mt) cc_final: 0.7972 (mm) REVERT: B 338 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7332 (pt0) REVERT: C 9 LYS cc_start: 0.8591 (tttp) cc_final: 0.8374 (tttm) REVERT: C 94 ASP cc_start: 0.7559 (p0) cc_final: 0.7333 (p0) REVERT: C 106 ASP cc_start: 0.7643 (m-30) cc_final: 0.7357 (m-30) REVERT: C 127 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7277 (tp30) REVERT: C 176 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7395 (mmtm) REVERT: C 192 ASN cc_start: 0.7852 (t0) cc_final: 0.7330 (t0) REVERT: C 193 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6009 (mp0) REVERT: C 231 GLN cc_start: 0.7774 (pt0) cc_final: 0.7274 (pp30) REVERT: C 258 GLU cc_start: 0.6717 (mt-10) cc_final: 0.6355 (tt0) REVERT: C 318 ARG cc_start: 0.7223 (ptm-80) cc_final: 0.6603 (ttm110) REVERT: C 337 LYS cc_start: 0.8362 (mtmt) cc_final: 0.8025 (mtmm) REVERT: D 17 ASP cc_start: 0.7405 (t0) cc_final: 0.6953 (m-30) REVERT: D 92 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7863 (tp30) REVERT: D 106 ASP cc_start: 0.6625 (m-30) cc_final: 0.6367 (m-30) REVERT: D 126 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8261 (m-30) REVERT: D 127 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7624 (mt-10) REVERT: D 141 LYS cc_start: 0.8362 (tptt) cc_final: 0.7783 (tppt) REVERT: D 154 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8165 (mt) REVERT: D 176 LYS cc_start: 0.8387 (mttm) cc_final: 0.7992 (mtpp) REVERT: D 211 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7505 (mm-30) REVERT: D 262 GLU cc_start: 0.7680 (mp0) cc_final: 0.7415 (mp0) REVERT: D 284 GLU cc_start: 0.7520 (tt0) cc_final: 0.6857 (mp0) REVERT: D 291 ARG cc_start: 0.7864 (tpp80) cc_final: 0.7418 (tpp-160) REVERT: D 310 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6092 (mt-10) REVERT: E 72 THR cc_start: 0.7141 (OUTLIER) cc_final: 0.6834 (t) REVERT: E 98 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: E 126 ASN cc_start: 0.8506 (m-40) cc_final: 0.8154 (m-40) REVERT: E 130 LYS cc_start: 0.7838 (tppp) cc_final: 0.7477 (tptp) REVERT: E 170 GLN cc_start: 0.6836 (tp40) cc_final: 0.6214 (mp10) REVERT: E 258 ARG cc_start: 0.7728 (mmm160) cc_final: 0.7519 (mmm-85) REVERT: E 277 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7015 (tt) REVERT: F 1 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6543 (ptt) REVERT: F 69 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7782 (p) REVERT: F 87 GLU cc_start: 0.6726 (tt0) cc_final: 0.6443 (pp20) REVERT: F 95 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6197 (pp20) REVERT: F 105 ARG cc_start: 0.7960 (ttt180) cc_final: 0.7492 (ttp-110) REVERT: F 152 ARG cc_start: 0.6769 (mtm180) cc_final: 0.6412 (mtm180) REVERT: F 165 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.6055 (tm-30) REVERT: F 279 ARG cc_start: 0.7989 (mtp85) cc_final: 0.7593 (mtp85) REVERT: F 300 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6860 (mp0) REVERT: F 301 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7196 (mm-30) REVERT: F 343 SER cc_start: 0.8339 (p) cc_final: 0.7770 (t) REVERT: G 14 LEU cc_start: 0.7246 (mt) cc_final: 0.7001 (mt) REVERT: G 27 LEU cc_start: 0.8193 (mm) cc_final: 0.7842 (tm) REVERT: G 34 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6948 (mt) REVERT: G 36 GLN cc_start: 0.6161 (OUTLIER) cc_final: 0.5735 (pp30) REVERT: G 48 ASP cc_start: 0.8221 (t0) cc_final: 0.7845 (t0) REVERT: G 50 GLU cc_start: 0.6832 (mm-30) cc_final: 0.6600 (mm-30) REVERT: G 51 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7640 (ptp) REVERT: G 161 GLU cc_start: 0.7568 (tt0) cc_final: 0.6923 (tt0) REVERT: G 163 GLU cc_start: 0.6292 (mm-30) cc_final: 0.6086 (mm-30) REVERT: G 207 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7160 (mm) REVERT: G 235 LYS cc_start: 0.7298 (mmtm) cc_final: 0.6918 (mtmt) REVERT: G 251 ASN cc_start: 0.7490 (p0) cc_final: 0.7160 (p0) REVERT: G 299 GLN cc_start: 0.7418 (mm-40) cc_final: 0.6935 (tm-30) REVERT: G 301 GLU cc_start: 0.7681 (pt0) cc_final: 0.7061 (tt0) REVERT: G 339 MET cc_start: 0.7166 (mpp) cc_final: 0.6921 (mpp) outliers start: 74 outliers final: 41 residues processed: 402 average time/residue: 0.6511 time to fit residues: 296.4428 Evaluate side-chains 398 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 339 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 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 127 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 D residue 2 SER Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 310 GLU 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 98 GLU Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 90 VAL 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 285 VAL Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 364 MET Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 22 optimal weight: 0.0040 chunk 170 optimal weight: 2.9990 chunk 210 optimal weight: 0.0470 chunk 219 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 95 optimal weight: 0.0970 chunk 198 optimal weight: 4.9990 chunk 182 optimal weight: 0.4980 overall best weight: 0.3288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN C 269 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.190779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.158098 restraints weight = 22970.123| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.17 r_work: 0.3874 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21280 Z= 0.110 Angle : 0.562 13.336 29085 Z= 0.280 Chirality : 0.039 0.507 3350 Planarity : 0.004 0.050 3612 Dihedral : 14.420 142.322 3352 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.51 % Allowed : 21.99 % Favored : 75.51 % 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: 1.40 (0.17), residues: 2516 helix: 1.73 (0.15), residues: 1270 sheet: 0.23 (0.25), residues: 398 loop : 0.17 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 274 TYR 0.024 0.001 TYR B 328 PHE 0.017 0.001 PHE G 75 TRP 0.022 0.001 TRP E 140 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (21264) covalent geometry : angle 0.55178 / 0.28 (29061) hydrogen bonds : bond 0.02985 / 2.03 ( 1122) hydrogen bonds : angle 3.83863 / 2.75 ( 3166) metal coordination : bond 0.00261 / 0.13 ( 16) metal coordination : angle 3.78261 / 2.41 ( 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 421 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 368 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.8023 (pt0) cc_final: 0.7483 (tm-30) REVERT: A 126 TRP cc_start: 0.6157 (p-90) cc_final: 0.5673 (p-90) REVERT: A 211 HIS cc_start: 0.7195 (t70) cc_final: 0.6475 (m170) REVERT: A 234 GLN cc_start: 0.7534 (mt0) cc_final: 0.7249 (pt0) REVERT: A 244 VAL cc_start: 0.7393 (OUTLIER) cc_final: 0.7134 (p) REVERT: A 325 GLU cc_start: 0.7641 (mp0) cc_final: 0.7407 (mp0) REVERT: B 77 ASP cc_start: 0.6933 (m-30) cc_final: 0.6012 (m-30) REVERT: B 80 ARG cc_start: 0.6968 (mtm110) cc_final: 0.6701 (ttm110) REVERT: B 81 GLU cc_start: 0.6489 (mt-10) cc_final: 0.6265 (mp0) REVERT: B 92 GLU cc_start: 0.7621 (tt0) cc_final: 0.7203 (tm-30) REVERT: B 133 ARG cc_start: 0.7406 (tpp80) cc_final: 0.7194 (mmm-85) REVERT: B 160 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: B 181 GLU cc_start: 0.7372 (tp30) cc_final: 0.7151 (mm-30) REVERT: B 185 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.7018 (t70) REVERT: B 231 GLN cc_start: 0.7317 (mt0) cc_final: 0.7051 (mp10) REVERT: B 320 ILE cc_start: 0.8366 (mt) cc_final: 0.8067 (mm) REVERT: B 338 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7204 (pt0) REVERT: C 94 ASP cc_start: 0.7544 (p0) cc_final: 0.7323 (p0) REVERT: C 106 ASP cc_start: 0.7630 (m-30) cc_final: 0.7379 (m-30) REVERT: C 127 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7254 (tp30) REVERT: C 176 LYS cc_start: 0.8281 (mtpp) cc_final: 0.7366 (mmtm) REVERT: C 192 ASN cc_start: 0.7808 (t0) cc_final: 0.7333 (m110) REVERT: C 231 GLN cc_start: 0.7801 (pt0) cc_final: 0.7294 (pp30) REVERT: C 318 ARG cc_start: 0.7170 (ptm-80) cc_final: 0.6581 (ttm110) REVERT: C 337 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7839 (mtmm) REVERT: D 17 ASP cc_start: 0.7378 (t0) cc_final: 0.6990 (m-30) REVERT: D 92 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7759 (tp30) REVERT: D 106 ASP cc_start: 0.6613 (m-30) cc_final: 0.6328 (m-30) REVERT: D 126 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8261 (m-30) REVERT: D 127 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7588 (mt-10) REVERT: D 141 LYS cc_start: 0.8268 (tptt) cc_final: 0.7693 (tppt) REVERT: D 154 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8120 (mt) REVERT: D 176 LYS cc_start: 0.8391 (mttm) cc_final: 0.7983 (mtpp) REVERT: D 211 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7514 (mm-30) REVERT: D 262 GLU cc_start: 0.7636 (mp0) cc_final: 0.7384 (mp0) REVERT: D 284 GLU cc_start: 0.7459 (tt0) cc_final: 0.6853 (mp0) REVERT: D 291 ARG cc_start: 0.7767 (tpp80) cc_final: 0.6799 (mmp80) REVERT: E 72 THR cc_start: 0.7100 (OUTLIER) cc_final: 0.6823 (t) REVERT: E 98 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: E 126 ASN cc_start: 0.8406 (m-40) cc_final: 0.8131 (m-40) REVERT: E 130 LYS cc_start: 0.7819 (tppp) cc_final: 0.7469 (tptp) REVERT: E 170 GLN cc_start: 0.6755 (tp40) cc_final: 0.6144 (mp10) REVERT: E 211 GLN cc_start: 0.7956 (tp40) cc_final: 0.7685 (tp-100) REVERT: E 258 ARG cc_start: 0.7755 (mmm160) cc_final: 0.7540 (mmm-85) REVERT: E 277 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7153 (tt) REVERT: F 73 ARG cc_start: 0.7519 (tpp80) cc_final: 0.7294 (mmt-90) REVERT: F 87 GLU cc_start: 0.6773 (tt0) cc_final: 0.6467 (pp20) REVERT: F 95 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6151 (pp20) REVERT: F 105 ARG cc_start: 0.7954 (ttt180) cc_final: 0.7496 (ttp-110) REVERT: F 152 ARG cc_start: 0.6747 (mtm180) cc_final: 0.6392 (mtm180) REVERT: F 165 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5993 (tm-30) REVERT: F 300 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6846 (mp0) REVERT: F 301 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7227 (mm-30) REVERT: F 343 SER cc_start: 0.8280 (p) cc_final: 0.7792 (t) REVERT: G 14 LEU cc_start: 0.7228 (mt) cc_final: 0.6961 (mt) REVERT: G 27 LEU cc_start: 0.8191 (mm) cc_final: 0.7856 (tm) REVERT: G 34 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6937 (mt) REVERT: G 36 GLN cc_start: 0.6346 (OUTLIER) cc_final: 0.5807 (pp30) REVERT: G 48 ASP cc_start: 0.8236 (t0) cc_final: 0.7898 (t0) REVERT: G 50 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6582 (mm-30) REVERT: G 51 MET cc_start: 0.7938 (ptp) cc_final: 0.7700 (ptp) REVERT: G 91 GLN cc_start: 0.6198 (mt0) cc_final: 0.5958 (pp30) REVERT: G 161 GLU cc_start: 0.7570 (tt0) cc_final: 0.6855 (tt0) REVERT: G 207 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7141 (mm) REVERT: G 235 LYS cc_start: 0.7253 (mmtm) cc_final: 0.6861 (mtmt) REVERT: G 251 ASN cc_start: 0.7438 (p0) cc_final: 0.7141 (p0) REVERT: G 285 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.8062 (p) REVERT: G 299 GLN cc_start: 0.7309 (mm-40) cc_final: 0.6863 (tm-30) REVERT: G 339 MET cc_start: 0.7093 (mpp) cc_final: 0.6875 (mpp) outliers start: 53 outliers final: 24 residues processed: 405 average time/residue: 0.5878 time to fit residues: 268.9175 Evaluate side-chains 378 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 340 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 244 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 188 LEU 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 90 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 196 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 177 optimal weight: 0.0870 chunk 120 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS F 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.190390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.157748 restraints weight = 23018.469| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.17 r_work: 0.3872 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21280 Z= 0.121 Angle : 0.596 16.950 29085 Z= 0.293 Chirality : 0.039 0.321 3350 Planarity : 0.004 0.047 3612 Dihedral : 14.426 141.766 3352 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.32 % Allowed : 22.93 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.17), residues: 2516 helix: 1.73 (0.15), residues: 1270 sheet: 0.23 (0.25), residues: 409 loop : 0.22 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 279 TYR 0.027 0.002 TYR G 153 PHE 0.012 0.001 PHE F 3 TRP 0.024 0.001 TRP E 140 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (21264) covalent geometry : angle 0.57549 / 0.29 (29061) hydrogen bonds : bond 0.03039 / 2.07 ( 1122) hydrogen bonds : angle 3.84951 / 2.76 ( 3166) metal coordination : bond 0.00523 / 0.19 ( 16) metal coordination : angle 5.40884 / 3.53 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 345 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7536 (ptp) cc_final: 0.7278 (ptp) REVERT: A 78 GLN cc_start: 0.8063 (pt0) cc_final: 0.7512 (tm-30) REVERT: A 126 TRP cc_start: 0.6123 (p-90) cc_final: 0.5663 (p-90) REVERT: A 211 HIS cc_start: 0.7196 (t70) cc_final: 0.6487 (m170) REVERT: A 234 GLN cc_start: 0.7549 (mt0) cc_final: 0.7250 (pt0) REVERT: A 244 VAL cc_start: 0.7383 (OUTLIER) cc_final: 0.7118 (p) REVERT: A 286 MET cc_start: 0.7368 (mmm) cc_final: 0.6492 (mmt) REVERT: A 325 GLU cc_start: 0.7626 (mp0) cc_final: 0.7299 (OUTLIER) REVERT: B 39 HIS cc_start: 0.7159 (p-80) cc_final: 0.6858 (p-80) REVERT: B 77 ASP cc_start: 0.6988 (m-30) cc_final: 0.6063 (m-30) REVERT: B 80 ARG cc_start: 0.6961 (mtm110) cc_final: 0.6702 (ttm110) REVERT: B 92 GLU cc_start: 0.7635 (tt0) cc_final: 0.7213 (tm-30) REVERT: B 133 ARG cc_start: 0.7439 (tpp80) cc_final: 0.7222 (mmm-85) REVERT: B 160 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7238 (mp10) REVERT: B 167 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7212 (mt) REVERT: B 181 GLU cc_start: 0.7440 (tp30) cc_final: 0.7211 (mm-30) REVERT: B 185 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.7003 (t70) REVERT: B 231 GLN cc_start: 0.7318 (mt0) cc_final: 0.7061 (mp10) REVERT: B 320 ILE cc_start: 0.8362 (mt) cc_final: 0.8064 (mm) REVERT: B 338 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7241 (pt0) REVERT: C 44 SER cc_start: 0.9259 (m) cc_final: 0.8976 (t) REVERT: C 94 ASP cc_start: 0.7530 (p0) cc_final: 0.7313 (p0) REVERT: C 106 ASP cc_start: 0.7611 (m-30) cc_final: 0.7363 (m-30) REVERT: C 127 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7295 (tp30) REVERT: C 176 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7372 (mmtm) REVERT: C 192 ASN cc_start: 0.7792 (t0) cc_final: 0.7237 (m110) REVERT: C 193 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.5789 (mp0) REVERT: C 231 GLN cc_start: 0.7815 (pt0) cc_final: 0.7305 (pp30) REVERT: C 318 ARG cc_start: 0.7163 (ptm-80) cc_final: 0.6583 (ttm110) REVERT: C 337 LYS cc_start: 0.8272 (mtmt) cc_final: 0.7916 (mtmm) REVERT: D 17 ASP cc_start: 0.7375 (t0) cc_final: 0.6952 (m-30) REVERT: D 92 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7967 (tp30) REVERT: D 106 ASP cc_start: 0.6434 (m-30) cc_final: 0.6172 (m-30) REVERT: D 126 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: D 127 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7584 (mt-10) REVERT: D 141 LYS cc_start: 0.8297 (tptt) cc_final: 0.7730 (tppt) REVERT: D 154 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8138 (mt) REVERT: D 176 LYS cc_start: 0.8402 (mttm) cc_final: 0.7991 (mtpp) REVERT: D 211 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7495 (mm-30) REVERT: D 262 GLU cc_start: 0.7662 (mp0) cc_final: 0.7419 (mp0) REVERT: D 284 GLU cc_start: 0.7448 (tt0) cc_final: 0.6828 (mp0) REVERT: D 291 ARG cc_start: 0.7821 (tpp80) cc_final: 0.6890 (mmp80) REVERT: D 310 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6024 (mt-10) REVERT: E 72 THR cc_start: 0.7108 (OUTLIER) cc_final: 0.6834 (t) REVERT: E 126 ASN cc_start: 0.8411 (m-40) cc_final: 0.8098 (m-40) REVERT: E 134 GLU cc_start: 0.7676 (tt0) cc_final: 0.7129 (pt0) REVERT: E 156 ARG cc_start: 0.8152 (ttp-110) cc_final: 0.7856 (mtm110) REVERT: E 170 GLN cc_start: 0.6778 (tp40) cc_final: 0.6163 (mp10) REVERT: E 211 GLN cc_start: 0.7952 (tp40) cc_final: 0.7682 (tp-100) REVERT: E 258 ARG cc_start: 0.7760 (mmm160) cc_final: 0.7555 (mmm-85) REVERT: E 277 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7220 (tt) REVERT: F 73 ARG cc_start: 0.7553 (tpp80) cc_final: 0.7334 (mmt-90) REVERT: F 87 GLU cc_start: 0.6785 (tt0) cc_final: 0.6459 (pp20) REVERT: F 95 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6187 (pp20) REVERT: F 105 ARG cc_start: 0.7976 (ttt180) cc_final: 0.7505 (ttp-110) REVERT: F 152 ARG cc_start: 0.6732 (mtm180) cc_final: 0.6368 (mtm180) REVERT: F 165 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5968 (tm-30) REVERT: F 182 MET cc_start: 0.8076 (mmm) cc_final: 0.7620 (mtm) REVERT: F 300 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6839 (mp0) REVERT: F 301 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7276 (mm-30) REVERT: F 343 SER cc_start: 0.8266 (p) cc_final: 0.7690 (t) REVERT: G 14 LEU cc_start: 0.7239 (mt) cc_final: 0.7000 (mt) REVERT: G 27 LEU cc_start: 0.8194 (mm) cc_final: 0.7859 (tm) REVERT: G 34 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6938 (mt) REVERT: G 36 GLN cc_start: 0.6418 (OUTLIER) cc_final: 0.5826 (pp30) REVERT: G 48 ASP cc_start: 0.8225 (t0) cc_final: 0.7958 (t0) REVERT: G 51 MET cc_start: 0.7923 (ptp) cc_final: 0.7687 (ptp) REVERT: G 91 GLN cc_start: 0.6234 (mt0) cc_final: 0.6016 (pp30) REVERT: G 152 ARG cc_start: 0.7230 (mmt90) cc_final: 0.6225 (mmm160) REVERT: G 161 GLU cc_start: 0.7589 (tt0) cc_final: 0.6657 (tt0) REVERT: G 207 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7158 (mm) REVERT: G 235 LYS cc_start: 0.7261 (mmtm) cc_final: 0.6903 (mtmt) REVERT: G 251 ASN cc_start: 0.7452 (p0) cc_final: 0.7119 (p0) REVERT: G 299 GLN cc_start: 0.7309 (mm-40) cc_final: 0.6886 (tm-30) REVERT: G 339 MET cc_start: 0.7145 (mpp) cc_final: 0.6850 (mpp) REVERT: G 344 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7728 (p) outliers start: 49 outliers final: 26 residues processed: 378 average time/residue: 0.6624 time to fit residues: 282.0040 Evaluate side-chains 377 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 336 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 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 15 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 96 VAL 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 188 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 364 MET Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 243 optimal weight: 0.2980 chunk 153 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.189385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.156347 restraints weight = 22856.903| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.23 r_work: 0.3869 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21280 Z= 0.123 Angle : 0.590 13.201 29085 Z= 0.292 Chirality : 0.039 0.307 3350 Planarity : 0.004 0.045 3612 Dihedral : 14.411 140.492 3352 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.46 % Allowed : 23.03 % 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: 1.40 (0.17), residues: 2516 helix: 1.72 (0.15), residues: 1263 sheet: 0.17 (0.25), residues: 425 loop : 0.26 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 274 TYR 0.023 0.002 TYR G 310 PHE 0.021 0.001 PHE G 75 TRP 0.031 0.002 TRP E 140 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (21264) covalent geometry : angle 0.57559 / 0.29 (29061) hydrogen bonds : bond 0.03043 / 2.07 ( 1122) hydrogen bonds : angle 3.85174 / 2.77 ( 3166) metal coordination : bond 0.00690 / 0.23 ( 16) metal coordination : angle 4.59358 / 3.08 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8316.23 seconds wall clock time: 141 minutes 57.76 seconds (8517.76 seconds total)