Starting phenix.real_space_refine on Fri Aug 7 12:34:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyf_71017/08_2026/9oyf_71017.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyf_71017/08_2026/9oyf_71017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oyf_71017/08_2026/9oyf_71017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyf_71017/08_2026/9oyf_71017.map" model { file = "/net/cci-nas-00/data/ceres_data/9oyf_71017/08_2026/9oyf_71017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyf_71017/08_2026/9oyf_71017.cif" } resolution = 3.12 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= 0.016 sd= 0.630 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 71 5.49 5 Mg 3 5.21 5 S 112 5.16 5 C 13082 2.51 5 N 3785 2.21 5 O 4070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21127 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2726 Classifications: {'peptide': 343} Modifications used: {'COO': 1} 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: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2873 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 17, 'TRANS': 351} Chain: "D" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2799 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "E" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2602 Classifications: {'peptide': 334} Modifications used: {'COO': 1} 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: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2844 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 345} Chain: "H" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 655 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} 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: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 238 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "M" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 204 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} 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 3209 SG CYS B 64 29.943 79.035 35.047 1.00 56.39 S ATOM 3269 SG CYS B 73 26.361 78.696 35.352 1.00 68.61 S ATOM 3286 SG CYS B 76 28.251 75.423 34.784 1.00 50.98 S ATOM 3308 SG CYS B 79 28.706 77.042 37.998 1.00 61.53 S ATOM 6057 SG CYS C 64 9.583 53.558 68.363 1.00 54.27 S ATOM 6117 SG CYS C 73 7.974 51.230 70.663 1.00 54.43 S ATOM 6134 SG CYS C 76 10.631 49.733 68.481 1.00 58.35 S ATOM 6156 SG CYS C 79 11.834 51.940 71.039 1.00 54.26 S ATOM 8922 SG CYS D 64 35.045 28.622 99.161 1.00 56.68 S ATOM 8982 SG CYS D 73 37.193 26.661 101.416 1.00 63.10 S ATOM 8999 SG CYS D 76 38.016 26.460 97.787 1.00 62.43 S ATOM 9021 SG CYS D 79 38.763 29.622 99.423 1.00 57.02 S ATOM 11645 SG CYS E 50 81.751 33.843 99.664 1.00 60.42 S ATOM 11714 SG CYS E 59 85.004 32.725 98.565 1.00 69.52 S ATOM 11734 SG CYS E 62 82.494 32.851 95.902 1.00 64.30 S ATOM 11755 SG CYS E 65 83.593 36.118 97.128 1.00 56.94 S Time building chain proxies: 4.05, per 1000 atoms: 0.19 Number of scatterers: 21127 At special positions: 0 Unit cell: (110.952, 118.404, 149.868, 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 71 15.00 Mg 3 11.99 O 4070 8.00 N 3785 7.00 C 13082 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: 1.74 Conformation dependent library (CDL) restraints added in 859.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 79 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 64 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 76 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 76 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 64 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 79 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 76 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 73 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 79 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 64 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 62 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 59 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 65 " Number of angles added : 24 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 16 sheets defined 56.6% alpha, 14.7% beta 29 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 8 through 16 removed outlier: 3.829A pdb=" N GLN A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 45 Processing helix chain 'A' and resid 60 through 68 removed outlier: 3.800A pdb=" N ILE A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 4.886A pdb=" N GLN A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 removed outlier: 3.505A pdb=" N ASN A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 131 removed outlier: 3.942A pdb=" N ALA A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 159 Processing helix chain 'A' and resid 163 through 175 Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 198 through 206 removed outlier: 3.625A pdb=" N ALA A 205 " --> pdb=" O ARG A 201 " (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 265 removed outlier: 3.680A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 277 removed outlier: 3.540A pdb=" N LEU A 272 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 293 removed outlier: 4.200A pdb=" N GLY A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N MET A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.599A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.705A pdb=" N VAL B 18 " --> pdb=" O PHE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 50 through 64 Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 100 through 110 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 128 through 131 Processing helix chain 'B' and resid 132 through 145 removed outlier: 3.942A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.555A pdb=" N LYS B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 169 removed outlier: 3.656A pdb=" N LEU B 167 " --> pdb=" O VAL B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 195 Processing helix chain 'B' and resid 199 through 210 Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 247 through 259 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 277 through 298 Processing helix chain 'B' and resid 299 through 302 removed outlier: 3.739A pdb=" N LEU B 302 " --> pdb=" O PRO B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.871A pdb=" N ALA B 307 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ALA B 308 " --> pdb=" O ASP B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 321 through 339 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 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: 3.590A 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 111 Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 132 through 145 removed outlier: 4.528A pdb=" N LYS C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.582A pdb=" N LYS C 161 " --> pdb=" O ASP C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 169 removed outlier: 3.645A pdb=" N ARG C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 195 Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.928A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 229 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.506A pdb=" N ALA C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 274 Processing helix chain 'C' and resid 277 through 298 removed outlier: 3.810A pdb=" N LEU C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 282 " --> pdb=" O TRP C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 302 removed outlier: 4.195A pdb=" N LEU C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 299 through 302' Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 321 through 339 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 14 through 18 removed outlier: 3.505A pdb=" N VAL D 18 " --> pdb=" O PHE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 35 Processing helix chain 'D' and resid 50 through 64 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 100 through 111 removed outlier: 3.512A pdb=" N VAL D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 132 through 145 removed outlier: 3.612A pdb=" N LEU D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N THR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 163 through 170 removed outlier: 3.663A pdb=" N ARG D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 195 Processing helix chain 'D' and resid 199 through 211 removed outlier: 4.143A pdb=" N GLU D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 245 through 259 removed outlier: 3.821A pdb=" N ALA D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) 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: 3.677A 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: 3.794A pdb=" N MET D 306 " --> pdb=" O GLY D 303 " (cutoff:3.500A) removed outlier: 5.706A 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 339 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'E' and resid 6 through 20 removed outlier: 4.770A pdb=" N ASP E 10 " --> pdb=" O TRP E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 49 Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 89 through 100 removed outlier: 3.537A 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: 4.850A pdb=" N LYS E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 4.664A 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 157 Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 197 through 206 Processing helix chain 'E' and resid 208 through 227 removed outlier: 3.515A pdb=" N TYR E 222 " --> pdb=" O GLN E 218 " (cutoff:3.500A) 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 261 Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 282 through 303 Processing helix chain 'E' and resid 307 through 324 removed outlier: 3.556A pdb=" N GLN E 324 " --> pdb=" O GLU E 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 18 removed outlier: 3.991A 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 27 through 30 Processing helix chain 'F' and resid 72 through 82 Processing helix chain 'F' and resid 114 through 116 No H-bonds generated for 'chain 'F' and resid 114 through 116' Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.592A pdb=" N MET F 135 " --> pdb=" O PRO F 131 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 155 Processing helix chain 'F' and resid 197 through 207 Processing helix chain 'F' and resid 244 through 248 removed outlier: 3.531A pdb=" N LEU F 248 " --> pdb=" O ARG F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.793A pdb=" N LEU F 263 " --> pdb=" O GLY F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 332 Processing helix chain 'G' and resid 7 through 18 removed outlier: 3.571A pdb=" N LEU G 11 " --> pdb=" O ARG G 7 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYS G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) Proline residue: G 13 - end of helix removed outlier: 4.120A pdb=" N GLN G 16 " --> pdb=" O LYS G 12 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 71 through 81 Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.526A pdb=" N THR G 142 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N PHE G 144 " --> pdb=" O GLU G 140 " (cutoff:3.500A) 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: 3.571A pdb=" N VAL G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 271 Processing helix chain 'G' and resid 272 through 274 No H-bonds generated for 'chain 'G' and resid 272 through 274' Processing helix chain 'G' and resid 321 through 332 removed outlier: 3.624A 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 2 through 4 removed outlier: 6.316A pdb=" N ILE A 2 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N THR A 138 " --> pdb=" O ILE A 2 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU A 4 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 139 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG A 77 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 49 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.655A 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 90 through 94 removed outlier: 6.119A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR B 41 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ALA B 40 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE B 173 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU B 42 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 197 through 198 removed outlier: 6.611A pdb=" N ALA B 197 " --> pdb=" O VAL B 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 94 removed outlier: 6.225A pdb=" N TYR C 41 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N THR C 156 " --> pdb=" O TYR C 41 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE C 43 " --> pdb=" O THR C 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 197 through 198 removed outlier: 6.677A pdb=" N ALA C 197 " --> pdb=" O VAL C 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 90 through 94 removed outlier: 6.470A pdb=" N ILE D 91 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASP D 126 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE D 93 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR D 41 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N THR D 156 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N PHE D 43 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ALA D 40 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N PHE D 173 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU D 42 " --> pdb=" O PHE D 173 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 76 through 79 Processing sheet with id=AB1, first strand: chain 'F' and resid 63 through 64 removed outlier: 4.733A pdb=" N ASN G 295 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY G 280 " --> pdb=" O ASN G 295 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 111 through 112 removed outlier: 6.772A pdb=" N ASN F 32 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR F 47 " --> pdb=" O ASN F 32 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 309 through 311 removed outlier: 16.091A pdb=" N SER F 181 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 16.038A pdb=" N THR F 172 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 14.462A pdb=" N VAL F 170 " --> pdb=" O PRO F 183 " (cutoff:3.500A) removed outlier: 14.131A pdb=" N GLY F 185 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 14.224A pdb=" N ARG F 168 " --> pdb=" O GLY F 185 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N SER F 187 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N GLU F 166 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLY F 164 " --> pdb=" O PRO F 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 304 through 307 removed outlier: 3.658A pdb=" N GLU F 304 " --> pdb=" O ILE F 292 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 2 through 6 Processing sheet with id=AB6, first strand: chain 'G' and resid 66 through 68 removed outlier: 3.592A pdb=" N VAL G 126 " --> pdb=" O ILE G 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 192 through 196 removed outlier: 6.130A pdb=" N GLY G 157 " --> pdb=" O THR G 172 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N THR G 172 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLU G 165 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ALA G 357 " --> pdb=" O ASP G 351 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASP G 351 " --> pdb=" O ALA G 357 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7208 1.36 - 1.51: 5910 1.51 - 1.65: 8329 1.65 - 1.80: 146 1.80 - 1.95: 40 Bond restraints: 21633 Sorted by residual: bond pdb=" O2G AGS D 702 " pdb=" PG AGS D 702 " ideal model delta sigma weight residual 1.604 1.506 0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O3B AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" O3A AGS C 702 " pdb=" PA AGS C 702 " ideal model delta sigma weight residual 1.664 1.578 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" O3B AGS B 702 " pdb=" PB AGS B 702 " ideal model delta sigma weight residual 1.673 1.589 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" O3A AGS B 702 " pdb=" PA AGS B 702 " ideal model delta sigma weight residual 1.664 1.580 0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 21628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 28641 1.89 - 3.78: 813 3.78 - 5.67: 122 5.67 - 7.56: 44 7.56 - 9.46: 10 Bond angle restraints: 29630 Sorted by residual: angle pdb=" N3 DT I 14 " pdb=" C4 DT I 14 " pdb=" O4 DT I 14 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT M 4 " pdb=" C4 DT M 4 " pdb=" O4 DT M 4 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT M 7 " pdb=" C4 DT M 7 " pdb=" O4 DT M 7 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT H 21 " pdb=" C4 DT H 21 " pdb=" O4 DT H 21 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT H 22 " pdb=" C4 DT H 22 " pdb=" O4 DT H 22 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 ... (remaining 29625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.92: 12423 33.92 - 67.85: 628 67.85 - 101.77: 30 101.77 - 135.70: 3 135.70 - 169.62: 5 Dihedral angle restraints: 13089 sinusoidal: 5757 harmonic: 7332 Sorted by residual: dihedral pdb=" CA GLU F 165 " pdb=" C GLU F 165 " pdb=" N GLU F 166 " pdb=" CA GLU F 166 " ideal model delta harmonic sigma weight residual -180.00 -156.26 -23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA TYR D 3 " pdb=" C TYR D 3 " pdb=" N GLN D 4 " pdb=" CA GLN D 4 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLN G 299 " pdb=" C GLN G 299 " pdb=" N GLU G 300 " pdb=" CA GLU G 300 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 13086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 3330 0.125 - 0.249: 55 0.249 - 0.374: 4 0.374 - 0.499: 0 0.499 - 0.624: 24 Chirality restraints: 3413 Sorted by residual: chirality pdb=" P DC I 7 " pdb=" OP1 DC I 7 " pdb=" OP2 DC I 7 " pdb=" O5' DC I 7 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.72e+00 chirality pdb=" P DG I 19 " pdb=" OP1 DG I 19 " pdb=" OP2 DG I 19 " pdb=" O5' DG I 19 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" P DG I 6 " pdb=" OP1 DG I 6 " pdb=" OP2 DG I 6 " pdb=" O5' DG I 6 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.60 2.00e-01 2.50e+01 9.02e+00 ... (remaining 3410 not shown) Planarity restraints: 3630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS G 12 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO G 13 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO G 13 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 13 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 320 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO D 321 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 298 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO D 299 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 299 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 299 " 0.025 5.00e-02 4.00e+02 ... (remaining 3627 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 14 2.40 - 3.02: 12476 3.02 - 3.65: 31722 3.65 - 4.27: 47880 4.27 - 4.90: 80317 Nonbonded interactions: 172409 Sorted by model distance: nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 703 " model vdw 1.774 2.170 nonbonded pdb=" S1G AGS B 702 " pdb="MG MG B 703 " model vdw 1.917 2.530 nonbonded pdb=" S1G AGS C 702 " pdb="MG MG C 703 " model vdw 1.992 2.530 nonbonded pdb=" OG1 THR B 52 " pdb="MG MG B 703 " model vdw 2.149 2.170 nonbonded pdb=" O ASP F 48 " pdb=" OD1 ASP F 48 " model vdw 2.197 3.040 ... (remaining 172404 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 701 through 703)) selection = (chain 'C' and (resid 2 through 361 or resid 701 through 703)) selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 365) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.890 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 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 : 0.006 0.098 21649 Z= 0.322 Angle : 0.802 9.455 29654 Z= 0.453 Chirality : 0.064 0.624 3413 Planarity : 0.005 0.063 3630 Dihedral : 18.183 169.621 8331 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.90 % Allowed : 12.01 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.17), residues: 2515 helix: 1.35 (0.15), residues: 1257 sheet: 0.15 (0.25), residues: 385 loop : -0.44 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 237 TYR 0.012 0.002 TYR G 153 PHE 0.016 0.002 PHE D 136 TRP 0.028 0.002 TRP F 122 HIS 0.010 0.002 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.32 (21633) covalent geometry : angle 0.78508 / 0.45 (29630) hydrogen bonds : bond 0.14344 / 9.56 ( 1203) hydrogen bonds : angle 5.96680 / 4.31 ( 3363) metal coordination : bond 0.00865 / 0.52 ( 16) metal coordination : angle 5.76372 / 3.79 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 380 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7600 (m-10) cc_final: 0.7056 (m-80) REVERT: B 109 ASP cc_start: 0.8088 (t70) cc_final: 0.7882 (t0) REVERT: C 161 LYS cc_start: 0.8936 (tppp) cc_final: 0.8622 (tppp) REVERT: E 253 MET cc_start: 0.8628 (ttm) cc_final: 0.8351 (ttm) REVERT: F 122 TRP cc_start: 0.8913 (p-90) cc_final: 0.8703 (p-90) REVERT: F 204 MET cc_start: 0.8563 (tpp) cc_final: 0.8332 (tpp) REVERT: F 326 ASP cc_start: 0.8560 (m-30) cc_final: 0.8104 (m-30) REVERT: F 342 ASP cc_start: 0.7988 (t70) cc_final: 0.7447 (p0) REVERT: F 348 GLN cc_start: 0.7223 (tt0) cc_final: 0.6882 (tm-30) REVERT: G 15 GLN cc_start: 0.8391 (pp30) cc_final: 0.7988 (pp30) REVERT: G 48 ASP cc_start: 0.7236 (p0) cc_final: 0.6210 (p0) REVERT: G 50 GLU cc_start: 0.7611 (mp0) cc_final: 0.7018 (mp0) REVERT: G 165 GLU cc_start: 0.7389 (tp30) cc_final: 0.7124 (tp30) outliers start: 19 outliers final: 14 residues processed: 394 average time/residue: 0.1620 time to fit residues: 94.1617 Evaluate side-chains 367 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 353 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 295 ASN Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 361 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 50.0000 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN C 63 ASN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN D 137 ASN D 204 GLN ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS F 32 ASN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS G 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.072656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.051473 restraints weight = 45012.303| |-----------------------------------------------------------------------------| r_work (start): 0.2561 rms_B_bonded: 1.61 r_work: 0.2457 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2349 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21649 Z= 0.152 Angle : 0.659 8.801 29654 Z= 0.336 Chirality : 0.043 0.300 3413 Planarity : 0.004 0.056 3630 Dihedral : 17.244 171.947 3559 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.36 % Allowed : 12.01 % Favored : 85.63 % 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: 1.26 (0.17), residues: 2515 helix: 1.70 (0.15), residues: 1275 sheet: 0.52 (0.24), residues: 406 loop : -0.26 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 86 TYR 0.011 0.001 TYR G 244 PHE 0.020 0.002 PHE F 278 TRP 0.015 0.001 TRP B 10 HIS 0.006 0.001 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (21633) covalent geometry : angle 0.64039 / 0.33 (29630) hydrogen bonds : bond 0.04504 / 3.01 ( 1203) hydrogen bonds : angle 4.49133 / 3.24 ( 3363) metal coordination : bond 0.00452 / 0.27 ( 16) metal coordination : angle 5.54945 / 3.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 377 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7650 (m-10) cc_final: 0.6994 (m-80) REVERT: A 96 GLN cc_start: 0.8265 (mp10) cc_final: 0.7994 (mp10) REVERT: B 127 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: C 161 LYS cc_start: 0.8991 (tppp) cc_final: 0.8746 (tppp) REVERT: C 214 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8707 (mm) REVERT: E 253 MET cc_start: 0.8593 (ttm) cc_final: 0.8365 (ttm) REVERT: F 326 ASP cc_start: 0.8497 (m-30) cc_final: 0.8114 (m-30) REVERT: F 348 GLN cc_start: 0.7375 (tt0) cc_final: 0.6947 (tm-30) REVERT: G 15 GLN cc_start: 0.8524 (pp30) cc_final: 0.8196 (pp30) REVERT: G 48 ASP cc_start: 0.7584 (p0) cc_final: 0.6364 (p0) REVERT: G 50 GLU cc_start: 0.7783 (mp0) cc_final: 0.7215 (mp0) REVERT: G 79 CYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7551 (p) REVERT: G 146 MET cc_start: 0.9053 (ttp) cc_final: 0.8809 (mtp) outliers start: 50 outliers final: 31 residues processed: 410 average time/residue: 0.1406 time to fit residues: 85.5153 Evaluate side-chains 381 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 347 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 79 CYS Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 295 ASN Chi-restraints excluded: chain G residue 300 GLU Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 343 SER Chi-restraints excluded: chain G residue 346 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 94 optimal weight: 1.9990 chunk 112 optimal weight: 0.0470 chunk 31 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 240 optimal weight: 0.5980 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN B 172 GLN C 63 ASN C 129 HIS D 137 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.072532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.051259 restraints weight = 44942.058| |-----------------------------------------------------------------------------| r_work (start): 0.2552 rms_B_bonded: 1.63 r_work: 0.2446 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2335 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21649 Z= 0.152 Angle : 0.629 9.744 29654 Z= 0.319 Chirality : 0.042 0.288 3413 Planarity : 0.004 0.066 3630 Dihedral : 17.161 172.483 3547 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.98 % Allowed : 13.10 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.17), residues: 2515 helix: 1.82 (0.15), residues: 1268 sheet: 0.48 (0.24), residues: 423 loop : -0.14 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 362 TYR 0.018 0.001 TYR G 153 PHE 0.018 0.001 PHE F 278 TRP 0.014 0.001 TRP B 10 HIS 0.005 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (21633) covalent geometry : angle 0.61079 / 0.32 (29630) hydrogen bonds : bond 0.04171 / 2.77 ( 1203) hydrogen bonds : angle 4.24923 / 3.08 ( 3363) metal coordination : bond 0.00480 / 0.28 ( 16) metal coordination : angle 5.37452 / 3.50 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 357 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8063 (mtm) cc_final: 0.7797 (mtm) REVERT: A 65 PHE cc_start: 0.7722 (m-10) cc_final: 0.7405 (m-80) REVERT: A 96 GLN cc_start: 0.8211 (mp10) cc_final: 0.7925 (mp10) REVERT: A 116 LYS cc_start: 0.8857 (ttmm) cc_final: 0.8572 (ttpp) REVERT: A 222 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8758 (mt) REVERT: B 127 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: C 214 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8726 (mm) REVERT: F 243 ASP cc_start: 0.7928 (t0) cc_final: 0.7654 (t0) REVERT: F 326 ASP cc_start: 0.8485 (m-30) cc_final: 0.8093 (m-30) REVERT: F 348 GLN cc_start: 0.7397 (tt0) cc_final: 0.6885 (tm-30) REVERT: G 12 LYS cc_start: 0.8669 (mmmm) cc_final: 0.8360 (mmmt) REVERT: G 15 GLN cc_start: 0.8586 (pp30) cc_final: 0.7952 (pt0) REVERT: G 33 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6957 (tt) REVERT: G 48 ASP cc_start: 0.7639 (p0) cc_final: 0.6314 (p0) REVERT: G 50 GLU cc_start: 0.7811 (mp0) cc_final: 0.7147 (mp0) outliers start: 63 outliers final: 31 residues processed: 400 average time/residue: 0.1603 time to fit residues: 94.7585 Evaluate side-chains 384 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 349 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain G residue 332 LYS Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 343 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 247 optimal weight: 40.0000 chunk 245 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN C 63 ASN D 137 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.071702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.050626 restraints weight = 44975.178| |-----------------------------------------------------------------------------| r_work (start): 0.2527 rms_B_bonded: 1.60 r_work: 0.2423 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2311 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 21649 Z= 0.202 Angle : 0.667 8.989 29654 Z= 0.335 Chirality : 0.043 0.290 3413 Planarity : 0.005 0.059 3630 Dihedral : 17.224 173.195 3543 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.45 % Allowed : 13.29 % 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: 1.34 (0.17), residues: 2515 helix: 1.75 (0.15), residues: 1265 sheet: 0.53 (0.24), residues: 423 loop : -0.17 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 282 TYR 0.018 0.001 TYR G 153 PHE 0.017 0.002 PHE F 278 TRP 0.016 0.002 TRP B 10 HIS 0.006 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (21633) covalent geometry : angle 0.64859 / 0.33 (29630) hydrogen bonds : bond 0.04372 / 2.90 ( 1203) hydrogen bonds : angle 4.24025 / 3.08 ( 3363) metal coordination : bond 0.00666 / 0.40 ( 16) metal coordination : angle 5.54326 / 3.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 355 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8173 (mtm) cc_final: 0.7919 (mtm) REVERT: A 65 PHE cc_start: 0.7729 (m-10) cc_final: 0.7380 (m-80) REVERT: A 96 GLN cc_start: 0.8207 (mp10) cc_final: 0.7980 (mp10) REVERT: A 116 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8585 (ttpp) REVERT: A 222 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8742 (mt) REVERT: B 127 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: C 214 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8742 (mm) REVERT: F 82 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8719 (mp) REVERT: F 243 ASP cc_start: 0.8058 (t0) cc_final: 0.7751 (t0) REVERT: F 326 ASP cc_start: 0.8502 (m-30) cc_final: 0.8137 (m-30) REVERT: F 348 GLN cc_start: 0.7491 (tt0) cc_final: 0.6979 (tm-30) REVERT: G 33 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6931 (tt) REVERT: G 48 ASP cc_start: 0.7649 (p0) cc_final: 0.6284 (p0) REVERT: G 50 GLU cc_start: 0.7889 (mp0) cc_final: 0.7267 (mp0) outliers start: 73 outliers final: 50 residues processed: 399 average time/residue: 0.1709 time to fit residues: 100.9908 Evaluate side-chains 404 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 349 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 295 ASN Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 343 SER Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 361 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 85 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN A 266 HIS A 280 GLN C 63 ASN C 260 ASN D 137 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.072300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.051116 restraints weight = 44423.575| |-----------------------------------------------------------------------------| r_work (start): 0.2549 rms_B_bonded: 1.59 r_work: 0.2445 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2336 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21649 Z= 0.144 Angle : 0.619 8.612 29654 Z= 0.312 Chirality : 0.041 0.295 3413 Planarity : 0.004 0.056 3630 Dihedral : 17.214 173.356 3543 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.31 % Allowed : 14.14 % Favored : 82.55 % 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: 1.51 (0.17), residues: 2515 helix: 1.89 (0.15), residues: 1265 sheet: 0.60 (0.24), residues: 436 loop : -0.10 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 215 TYR 0.017 0.001 TYR G 153 PHE 0.018 0.001 PHE F 278 TRP 0.014 0.001 TRP B 10 HIS 0.006 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (21633) covalent geometry : angle 0.60093 / 0.31 (29630) hydrogen bonds : bond 0.03898 / 2.58 ( 1203) hydrogen bonds : angle 4.13567 / 3.01 ( 3363) metal coordination : bond 0.00401 / 0.24 ( 16) metal coordination : angle 5.24347 / 3.42 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 360 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7732 (m-10) cc_final: 0.7375 (m-80) REVERT: A 116 LYS cc_start: 0.8826 (ttmm) cc_final: 0.8601 (ttpp) REVERT: A 121 GLN cc_start: 0.9171 (mp10) cc_final: 0.8925 (mp10) REVERT: A 222 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8737 (mt) REVERT: A 280 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8249 (tp-100) REVERT: B 127 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: C 214 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8763 (mm) REVERT: F 82 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8640 (mp) REVERT: F 204 MET cc_start: 0.8874 (tpt) cc_final: 0.8589 (tpt) REVERT: F 245 ARG cc_start: 0.8829 (tpp80) cc_final: 0.8562 (mtm-85) REVERT: F 326 ASP cc_start: 0.8477 (m-30) cc_final: 0.8041 (m-30) REVERT: F 348 GLN cc_start: 0.7438 (tt0) cc_final: 0.6950 (tm-30) REVERT: G 33 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6906 (tt) REVERT: G 48 ASP cc_start: 0.7669 (p0) cc_final: 0.6215 (p0) REVERT: G 50 GLU cc_start: 0.7874 (mp0) cc_final: 0.7236 (mp0) REVERT: G 203 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8695 (tt) outliers start: 70 outliers final: 46 residues processed: 405 average time/residue: 0.1705 time to fit residues: 102.2268 Evaluate side-chains 412 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 359 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 343 SER Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 361 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 113 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 76 optimal weight: 0.0030 chunk 64 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 HIS A 280 GLN B 129 HIS C 63 ASN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS D 137 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.072292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.051001 restraints weight = 44490.966| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 1.60 r_work: 0.2444 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2334 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21649 Z= 0.152 Angle : 0.620 8.492 29654 Z= 0.313 Chirality : 0.041 0.297 3413 Planarity : 0.004 0.057 3630 Dihedral : 17.230 173.680 3543 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.88 % Allowed : 14.00 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.17), residues: 2515 helix: 1.91 (0.15), residues: 1265 sheet: 0.68 (0.24), residues: 432 loop : -0.14 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 86 TYR 0.018 0.001 TYR G 153 PHE 0.017 0.001 PHE G 76 TRP 0.014 0.001 TRP B 10 HIS 0.013 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (21633) covalent geometry : angle 0.60250 / 0.31 (29630) hydrogen bonds : bond 0.03878 / 2.57 ( 1203) hydrogen bonds : angle 4.10204 / 2.98 ( 3363) metal coordination : bond 0.00439 / 0.26 ( 16) metal coordination : angle 5.18872 / 3.37 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 363 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7763 (m-10) cc_final: 0.7476 (m-80) REVERT: A 121 GLN cc_start: 0.9180 (mp10) cc_final: 0.8931 (mp10) REVERT: A 222 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8721 (mt) REVERT: B 127 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: C 214 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8749 (mm) REVERT: F 82 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8617 (mp) REVERT: F 204 MET cc_start: 0.8862 (tpt) cc_final: 0.8614 (tpt) REVERT: F 243 ASP cc_start: 0.7912 (t0) cc_final: 0.7657 (t0) REVERT: F 245 ARG cc_start: 0.8862 (tpp80) cc_final: 0.8560 (mtm-85) REVERT: F 326 ASP cc_start: 0.8426 (m-30) cc_final: 0.8034 (m-30) REVERT: F 348 GLN cc_start: 0.7490 (tt0) cc_final: 0.6946 (tm-30) REVERT: G 33 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6894 (tt) REVERT: G 48 ASP cc_start: 0.7665 (p0) cc_final: 0.6250 (p0) REVERT: G 49 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8322 (mt) REVERT: G 50 GLU cc_start: 0.7856 (mp0) cc_final: 0.7228 (mp0) REVERT: G 165 GLU cc_start: 0.7545 (tp30) cc_final: 0.7321 (tp30) REVERT: G 203 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8609 (tt) outliers start: 82 outliers final: 59 residues processed: 415 average time/residue: 0.1549 time to fit residues: 95.5750 Evaluate side-chains 414 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 348 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 295 ASN Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 343 SER Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 361 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 93 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 HIS C 63 ASN C 260 ASN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN F 15 GLN F 132 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.071524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.050348 restraints weight = 44750.341| |-----------------------------------------------------------------------------| r_work (start): 0.2522 rms_B_bonded: 1.59 r_work: 0.2418 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2308 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21649 Z= 0.208 Angle : 0.674 10.844 29654 Z= 0.338 Chirality : 0.043 0.296 3413 Planarity : 0.005 0.067 3630 Dihedral : 17.278 174.133 3543 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.69 % Allowed : 15.13 % Favored : 81.18 % 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: 1.38 (0.17), residues: 2515 helix: 1.77 (0.14), residues: 1267 sheet: 0.59 (0.24), residues: 430 loop : -0.17 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 86 TYR 0.019 0.001 TYR G 153 PHE 0.016 0.002 PHE F 278 TRP 0.015 0.002 TRP B 10 HIS 0.006 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (21633) covalent geometry : angle 0.65633 / 0.34 (29630) hydrogen bonds : bond 0.04285 / 2.83 ( 1203) hydrogen bonds : angle 4.16274 / 3.02 ( 3363) metal coordination : bond 0.00657 / 0.40 ( 16) metal coordination : angle 5.40537 / 3.53 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 354 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7742 (m-10) cc_final: 0.7452 (m-80) REVERT: A 121 GLN cc_start: 0.9166 (mp10) cc_final: 0.8962 (mp10) REVERT: A 222 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8718 (mt) REVERT: B 127 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: C 214 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8771 (mm) REVERT: F 82 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8647 (mp) REVERT: F 204 MET cc_start: 0.8830 (tpt) cc_final: 0.8568 (tpt) REVERT: F 243 ASP cc_start: 0.7991 (t0) cc_final: 0.7743 (t0) REVERT: F 245 ARG cc_start: 0.8810 (tpp80) cc_final: 0.8532 (mtm-85) REVERT: F 326 ASP cc_start: 0.8448 (m-30) cc_final: 0.8106 (m-30) REVERT: F 348 GLN cc_start: 0.7556 (tt0) cc_final: 0.7011 (tm-30) REVERT: G 48 ASP cc_start: 0.7665 (p0) cc_final: 0.6245 (p0) REVERT: G 50 GLU cc_start: 0.7947 (mp0) cc_final: 0.7308 (mp0) REVERT: G 121 ASP cc_start: 0.7722 (p0) cc_final: 0.7501 (p0) REVERT: G 203 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8655 (tt) outliers start: 78 outliers final: 59 residues processed: 402 average time/residue: 0.1688 time to fit residues: 101.1276 Evaluate side-chains 407 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 343 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 314 GLU Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 343 SER Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 361 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 157 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 63 ASN D 137 ASN F 15 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.071236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.050118 restraints weight = 44592.234| |-----------------------------------------------------------------------------| r_work (start): 0.2516 rms_B_bonded: 1.58 r_work: 0.2412 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2304 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21649 Z= 0.208 Angle : 0.693 16.396 29654 Z= 0.345 Chirality : 0.043 0.301 3413 Planarity : 0.005 0.058 3630 Dihedral : 17.305 174.514 3543 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.22 % Allowed : 16.17 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.17), residues: 2515 helix: 1.73 (0.14), residues: 1261 sheet: 0.63 (0.24), residues: 430 loop : -0.13 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 86 TYR 0.020 0.001 TYR G 153 PHE 0.018 0.002 PHE F 319 TRP 0.016 0.002 TRP B 10 HIS 0.006 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (21633) covalent geometry : angle 0.67576 / 0.34 (29630) hydrogen bonds : bond 0.04341 / 2.88 ( 1203) hydrogen bonds : angle 4.19474 / 3.04 ( 3363) metal coordination : bond 0.00663 / 0.39 ( 16) metal coordination : angle 5.44140 / 3.56 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 351 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7747 (m-10) cc_final: 0.7472 (m-80) REVERT: A 222 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8699 (mt) REVERT: B 127 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: F 82 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8647 (mp) REVERT: F 204 MET cc_start: 0.8843 (tpt) cc_final: 0.8586 (tpt) REVERT: F 243 ASP cc_start: 0.8028 (t0) cc_final: 0.7777 (t0) REVERT: F 245 ARG cc_start: 0.8825 (tpp80) cc_final: 0.8588 (mtm-85) REVERT: F 326 ASP cc_start: 0.8443 (m-30) cc_final: 0.8068 (m-30) REVERT: F 348 GLN cc_start: 0.7535 (tt0) cc_final: 0.7025 (tm-30) REVERT: G 15 GLN cc_start: 0.8515 (pp30) cc_final: 0.8094 (pp30) REVERT: G 16 GLN cc_start: 0.7202 (pt0) cc_final: 0.6878 (pt0) REVERT: G 48 ASP cc_start: 0.7675 (p0) cc_final: 0.6374 (p0) REVERT: G 50 GLU cc_start: 0.7966 (mp0) cc_final: 0.7331 (mp0) REVERT: G 97 MET cc_start: 0.6717 (ppp) cc_final: 0.6201 (ppp) REVERT: G 121 ASP cc_start: 0.7776 (p0) cc_final: 0.7563 (p0) REVERT: G 135 MET cc_start: 0.9183 (tpp) cc_final: 0.8964 (tpp) REVERT: G 203 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8692 (tt) outliers start: 68 outliers final: 56 residues processed: 393 average time/residue: 0.1626 time to fit residues: 94.8513 Evaluate side-chains 405 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 345 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 361 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 146 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 132 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 0.0980 chunk 134 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 GLN A 333 HIS C 63 ASN C 260 ASN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.072789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.051493 restraints weight = 44264.110| |-----------------------------------------------------------------------------| r_work (start): 0.2561 rms_B_bonded: 1.60 r_work: 0.2459 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2352 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21649 Z= 0.136 Angle : 0.642 14.872 29654 Z= 0.321 Chirality : 0.041 0.309 3413 Planarity : 0.004 0.058 3630 Dihedral : 17.231 174.542 3543 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.88 % Allowed : 16.93 % Favored : 80.19 % 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: 1.65 (0.17), residues: 2515 helix: 2.00 (0.15), residues: 1261 sheet: 0.62 (0.24), residues: 442 loop : 0.01 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 86 TYR 0.018 0.001 TYR G 153 PHE 0.021 0.001 PHE G 76 TRP 0.016 0.001 TRP B 10 HIS 0.007 0.001 HIS A 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (21633) covalent geometry : angle 0.62626 / 0.32 (29630) hydrogen bonds : bond 0.03652 / 2.42 ( 1203) hydrogen bonds : angle 4.05702 / 2.95 ( 3363) metal coordination : bond 0.00391 / 0.23 ( 16) metal coordination : angle 4.97543 / 3.23 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 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: 61 poor density : 360 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7722 (m-10) cc_final: 0.7404 (m-80) REVERT: A 222 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8672 (mt) REVERT: B 127 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: C 214 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8758 (mm) REVERT: F 82 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8522 (mp) REVERT: F 159 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8604 (tp) REVERT: F 204 MET cc_start: 0.8852 (tpt) cc_final: 0.8618 (tpt) REVERT: F 245 ARG cc_start: 0.8796 (tpp80) cc_final: 0.8540 (mtm-85) REVERT: F 326 ASP cc_start: 0.8413 (m-30) cc_final: 0.8035 (m-30) REVERT: F 348 GLN cc_start: 0.7483 (tt0) cc_final: 0.6977 (tm-30) REVERT: G 48 ASP cc_start: 0.7597 (p0) cc_final: 0.6166 (p0) REVERT: G 49 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8576 (mp) REVERT: G 50 GLU cc_start: 0.7871 (mp0) cc_final: 0.7330 (mp0) REVERT: G 97 MET cc_start: 0.6875 (ppp) cc_final: 0.6372 (ppp) REVERT: G 203 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8577 (tt) outliers start: 61 outliers final: 46 residues processed: 401 average time/residue: 0.1646 time to fit residues: 98.0088 Evaluate side-chains 400 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 347 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 314 GLU Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 361 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 161 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 112 optimal weight: 0.0670 chunk 59 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 chunk 212 optimal weight: 0.1980 chunk 211 optimal weight: 0.7980 chunk 136 optimal weight: 0.0270 chunk 253 optimal weight: 0.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS C 63 ASN C 174 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 248 GLN F 15 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 HIS G 295 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.073793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.053017 restraints weight = 44538.899| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 1.60 r_work: 0.2489 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2379 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21649 Z= 0.126 Angle : 0.632 14.767 29654 Z= 0.316 Chirality : 0.040 0.318 3413 Planarity : 0.004 0.062 3630 Dihedral : 17.132 174.803 3543 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.46 % Allowed : 17.26 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.17), residues: 2515 helix: 2.09 (0.15), residues: 1260 sheet: 0.61 (0.24), residues: 439 loop : 0.13 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 86 TYR 0.018 0.001 TYR G 153 PHE 0.018 0.001 PHE G 230 TRP 0.014 0.001 TRP B 10 HIS 0.008 0.001 HIS A 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (21633) covalent geometry : angle 0.61748 / 0.31 (29630) hydrogen bonds : bond 0.03375 / 2.23 ( 1203) hydrogen bonds : angle 3.96695 / 2.88 ( 3363) metal coordination : bond 0.00313 / 0.18 ( 16) metal coordination : angle 4.74451 / 3.03 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 358 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7776 (m-10) cc_final: 0.7491 (m-80) REVERT: A 222 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8674 (mt) REVERT: A 223 MET cc_start: 0.9340 (mtp) cc_final: 0.8961 (mtm) REVERT: B 127 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: B 188 GLU cc_start: 0.8578 (tt0) cc_final: 0.8327 (tt0) REVERT: C 214 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8746 (mm) REVERT: D 30 ASN cc_start: 0.8641 (m-40) cc_final: 0.8415 (m-40) REVERT: F 82 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8515 (mp) REVERT: F 159 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8518 (tp) REVERT: F 204 MET cc_start: 0.8867 (tpt) cc_final: 0.8647 (tpt) REVERT: F 245 ARG cc_start: 0.8846 (tpp80) cc_final: 0.8530 (mtm-85) REVERT: F 326 ASP cc_start: 0.8390 (m-30) cc_final: 0.8000 (m-30) REVERT: F 348 GLN cc_start: 0.7490 (tt0) cc_final: 0.6910 (tm-30) REVERT: G 48 ASP cc_start: 0.7643 (p0) cc_final: 0.6288 (p0) REVERT: G 49 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8541 (mp) REVERT: G 50 GLU cc_start: 0.7795 (mp0) cc_final: 0.7102 (mp0) REVERT: G 203 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8504 (tt) outliers start: 52 outliers final: 38 residues processed: 394 average time/residue: 0.1602 time to fit residues: 93.8649 Evaluate side-chains 393 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 348 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 361 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 17 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 201 optimal weight: 0.7980 chunk 199 optimal weight: 8.9990 chunk 183 optimal weight: 0.0980 chunk 106 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS C 63 ASN D 137 ASN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.073473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.052113 restraints weight = 44504.260| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 1.61 r_work: 0.2477 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2370 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21649 Z= 0.135 Angle : 0.634 14.479 29654 Z= 0.317 Chirality : 0.041 0.321 3413 Planarity : 0.005 0.061 3630 Dihedral : 17.109 175.008 3543 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.22 % Allowed : 17.87 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.17), residues: 2515 helix: 2.10 (0.15), residues: 1261 sheet: 0.53 (0.24), residues: 447 loop : 0.15 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 86 TYR 0.019 0.001 TYR G 153 PHE 0.017 0.001 PHE G 76 TRP 0.013 0.001 TRP B 10 HIS 0.008 0.001 HIS A 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (21633) covalent geometry : angle 0.61890 / 0.32 (29630) hydrogen bonds : bond 0.03482 / 2.30 ( 1203) hydrogen bonds : angle 3.94699 / 2.87 ( 3363) metal coordination : bond 0.00357 / 0.21 ( 16) metal coordination : angle 4.81063 / 3.09 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5340.58 seconds wall clock time: 91 minutes 59.90 seconds (5519.90 seconds total)