Starting phenix.real_space_refine on Fri Jun 5 14:53:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyf_71017/06_2026/9oyf_71017.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyf_71017/06_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_71017/06_2026/9oyf_71017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyf_71017/06_2026/9oyf_71017.map" model { file = "/net/cci-nas-00/data/ceres_data/9oyf_71017/06_2026/9oyf_71017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyf_71017/06_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.39, per 1000 atoms: 0.26 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: 1.93 Conformation dependent library (CDL) restraints added in 962.3 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: 2.77 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: 4.42 Time building geometry restraints manager: 2.48 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=" O3G AGS D 702 " pdb=" PG AGS D 702 " ideal model delta sigma weight residual 1.558 1.496 0.062 2.00e-02 2.50e+03 9.60e+00 bond pdb=" O2A AGS D 702 " pdb=" PA AGS D 702 " ideal model delta sigma weight residual 1.531 1.489 0.042 1.60e-02 3.91e+03 6.87e+00 bond pdb=" O2B AGS D 702 " pdb=" PB AGS D 702 " ideal model delta sigma weight residual 1.531 1.489 0.042 1.60e-02 3.91e+03 6.84e+00 bond pdb=" O2G AGS D 702 " pdb=" PG AGS D 702 " ideal model delta sigma weight residual 1.557 1.506 0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" N SER C 132 " pdb=" CA SER C 132 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.37e-02 5.33e+03 6.35e+00 ... (remaining 21628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 29196 2.63 - 5.25: 382 5.25 - 7.88: 47 7.88 - 10.50: 3 10.50 - 13.13: 2 Bond angle restraints: 29630 Sorted by residual: angle pdb=" PB AGS D 702 " pdb=" O3B AGS D 702 " pdb=" PG AGS D 702 " ideal model delta sigma weight residual 120.12 133.25 -13.13 3.00e+00 1.11e-01 1.91e+01 angle pdb=" PA AGS D 702 " pdb=" O3A AGS D 702 " pdb=" PB AGS D 702 " ideal model delta sigma weight residual 119.76 132.55 -12.79 3.00e+00 1.11e-01 1.82e+01 angle pdb=" CA ASP F 120 " pdb=" C ASP F 120 " pdb=" O ASP F 120 " ideal model delta sigma weight residual 122.37 118.06 4.31 1.15e+00 7.56e-01 1.40e+01 angle pdb=" CA GLU F 166 " pdb=" CB GLU F 166 " pdb=" CG GLU F 166 " ideal model delta sigma weight residual 114.10 121.20 -7.10 2.00e+00 2.50e-01 1.26e+01 angle pdb=" N MET C 130 " pdb=" CA MET C 130 " pdb=" C MET C 130 " ideal model delta sigma weight residual 113.28 108.96 4.32 1.22e+00 6.72e-01 1.25e+01 ... (remaining 29625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.92: 12373 33.92 - 67.85: 620 67.85 - 101.77: 32 101.77 - 135.70: 5 135.70 - 169.62: 5 Dihedral angle restraints: 13035 sinusoidal: 5703 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 13032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 3368 0.123 - 0.245: 26 0.245 - 0.368: 1 0.368 - 0.491: 0 0.491 - 0.613: 24 Chirality restraints: 3419 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 2.35 -2.96 -0.61 2.00e-01 2.50e+01 9.41e+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 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.90e+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 2.35 -2.94 -0.59 2.00e-01 2.50e+01 8.71e+00 ... (remaining 3416 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: 2.990 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.690 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21649 Z= 0.254 Angle : 0.772 13.126 29654 Z= 0.407 Chirality : 0.061 0.613 3419 Planarity : 0.005 0.063 3630 Dihedral : 18.307 169.621 8277 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 0.00549 / 0.25 (21633) covalent geometry : angle 0.75443 / 0.41 (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 : 0.863 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: 0.1880 time to fit residues: 108.0571 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 : 0.798 ------------------------------------------------------------------------------- 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: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN B 172 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.072485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.051257 restraints weight = 45115.988| |-----------------------------------------------------------------------------| r_work (start): 0.2552 rms_B_bonded: 1.63 r_work: 0.2448 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2336 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21649 Z= 0.156 Angle : 0.636 8.626 29654 Z= 0.323 Chirality : 0.040 0.185 3419 Planarity : 0.004 0.056 3630 Dihedral : 17.598 170.085 3505 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.17 % Allowed : 12.01 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.17), residues: 2515 helix: 1.71 (0.15), residues: 1275 sheet: 0.49 (0.24), residues: 406 loop : -0.27 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 86 TYR 0.010 0.001 TYR G 244 PHE 0.021 0.002 PHE F 278 TRP 0.014 0.001 TRP B 10 HIS 0.004 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (21633) covalent geometry : angle 0.61561 / 0.32 (29630) hydrogen bonds : bond 0.04380 / 2.92 ( 1203) hydrogen bonds : angle 4.45756 / 3.22 ( 3363) metal coordination : bond 0.00494 / 0.29 ( 16) metal coordination : angle 5.60942 / 3.68 ( 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 423 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 377 time to evaluate : 0.811 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: 0.7676 (m-10) cc_final: 0.6984 (m-80) REVERT: A 96 GLN cc_start: 0.8310 (mp10) cc_final: 0.8023 (mp10) REVERT: B 127 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: C 117 ARG cc_start: 0.8876 (ttp-110) cc_final: 0.8667 (ttp-110) REVERT: C 161 LYS cc_start: 0.8997 (tppp) cc_final: 0.8760 (tppp) REVERT: E 253 MET cc_start: 0.8585 (ttm) cc_final: 0.8353 (ttm) REVERT: F 326 ASP cc_start: 0.8477 (m-30) cc_final: 0.8078 (m-30) REVERT: F 348 GLN cc_start: 0.7362 (tt0) cc_final: 0.6903 (tm-30) REVERT: G 15 GLN cc_start: 0.8520 (pp30) cc_final: 0.7907 (pp30) REVERT: G 33 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6965 (tt) REVERT: G 48 ASP cc_start: 0.7582 (p0) cc_final: 0.6353 (p0) REVERT: G 50 GLU cc_start: 0.7775 (mp0) cc_final: 0.7141 (mp0) REVERT: G 79 CYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7594 (p) REVERT: G 146 MET cc_start: 0.9040 (ttp) cc_final: 0.8793 (mtp) outliers start: 46 outliers final: 30 residues processed: 410 average time/residue: 0.1796 time to fit residues: 107.7527 Evaluate side-chains 382 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 349 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 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 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 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 2 LYS Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 LEU 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 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: 0.0020 chunk 31 optimal weight: 2.9990 chunk 136 optimal weight: 0.3980 chunk 250 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 186 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 240 optimal weight: 0.5980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN B 110 ASN C 63 ASN C 129 HIS D 137 ASN F 15 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.073723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.052467 restraints weight = 44997.588| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 1.62 r_work: 0.2482 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2374 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1409 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= 0.127 Angle : 0.586 8.976 29654 Z= 0.296 Chirality : 0.039 0.160 3419 Planarity : 0.004 0.053 3630 Dihedral : 17.527 170.501 3495 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.70 % Allowed : 13.00 % Favored : 84.30 % 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: 1.57 (0.17), residues: 2515 helix: 2.00 (0.15), residues: 1267 sheet: 0.42 (0.24), residues: 430 loop : -0.04 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 105 TYR 0.016 0.001 TYR G 153 PHE 0.018 0.001 PHE F 278 TRP 0.012 0.001 TRP B 10 HIS 0.006 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (21633) covalent geometry : angle 0.56817 / 0.30 (29630) hydrogen bonds : bond 0.03630 / 2.42 ( 1203) hydrogen bonds : angle 4.12694 / 3.00 ( 3363) metal coordination : bond 0.00359 / 0.21 ( 16) metal coordination : angle 5.05816 / 3.28 ( 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 425 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 368 time to evaluate : 0.856 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: 0.7668 (m-10) cc_final: 0.7370 (m-80) REVERT: A 96 GLN cc_start: 0.8180 (mp10) cc_final: 0.7955 (mp10) REVERT: A 116 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8573 (ttpp) REVERT: A 283 ARG cc_start: 0.8869 (mtm-85) cc_final: 0.8367 (ttm170) REVERT: B 127 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: C 117 ARG cc_start: 0.8881 (ttp-110) cc_final: 0.8667 (ttp-110) REVERT: C 214 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8724 (mm) REVERT: E 182 MET cc_start: 0.9135 (mmm) cc_final: 0.8720 (mmt) REVERT: F 243 ASP cc_start: 0.7985 (t0) cc_final: 0.7759 (t0) REVERT: F 326 ASP cc_start: 0.8449 (m-30) cc_final: 0.8051 (m-30) REVERT: F 348 GLN cc_start: 0.7323 (tt0) cc_final: 0.6862 (tm-30) REVERT: G 32 ASN cc_start: 0.7952 (m110) cc_final: 0.7116 (t0) REVERT: G 33 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6843 (tt) REVERT: G 48 ASP cc_start: 0.7627 (p0) cc_final: 0.6258 (p0) REVERT: G 50 GLU cc_start: 0.7745 (mp0) cc_final: 0.7204 (mp0) REVERT: G 121 ASP cc_start: 0.7728 (p0) cc_final: 0.7483 (p0) outliers start: 57 outliers final: 29 residues processed: 406 average time/residue: 0.1837 time to fit residues: 109.0080 Evaluate side-chains 381 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 349 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 234 GLN Chi-restraints excluded: chain A residue 304 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 B residue 302 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 214 LEU Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 177 LEU 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 214 LEU 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 344 VAL Chi-restraints excluded: chain G residue 346 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: 5.9990 chunk 240 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 247 optimal weight: 10.0000 chunk 245 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 266 HIS C 63 ASN F 15 GLN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.071869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.050758 restraints weight = 44953.135| |-----------------------------------------------------------------------------| r_work (start): 0.2531 rms_B_bonded: 1.60 r_work: 0.2428 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2320 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21649 Z= 0.196 Angle : 0.645 9.062 29654 Z= 0.323 Chirality : 0.041 0.239 3419 Planarity : 0.005 0.054 3630 Dihedral : 17.522 170.863 3491 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.98 % Allowed : 14.14 % Favored : 82.88 % 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: 1.45 (0.17), residues: 2515 helix: 1.84 (0.15), residues: 1267 sheet: 0.49 (0.24), residues: 430 loop : -0.09 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 86 TYR 0.018 0.001 TYR G 153 PHE 0.021 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 0.00470 / 0.20 (21633) covalent geometry : angle 0.62638 / 0.32 (29630) hydrogen bonds : bond 0.04202 / 2.78 ( 1203) hydrogen bonds : angle 4.16028 / 3.02 ( 3363) metal coordination : bond 0.00624 / 0.37 ( 16) metal coordination : angle 5.44022 / 3.56 ( 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 424 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 361 time to evaluate : 0.774 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: 0.7705 (m-10) cc_final: 0.7352 (m-80) REVERT: A 116 LYS cc_start: 0.8816 (ttmm) cc_final: 0.8611 (ttpp) REVERT: A 156 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8450 (mtmm) REVERT: A 222 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8726 (mt) REVERT: B 127 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: C 214 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8747 (mm) REVERT: F 82 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8693 (mp) REVERT: F 243 ASP cc_start: 0.8082 (t0) cc_final: 0.7791 (t0) REVERT: F 326 ASP cc_start: 0.8479 (m-30) cc_final: 0.8043 (m-30) REVERT: F 342 ASP cc_start: 0.7934 (t70) cc_final: 0.7302 (p0) REVERT: F 348 GLN cc_start: 0.7440 (tt0) cc_final: 0.6979 (tm-30) REVERT: G 48 ASP cc_start: 0.7666 (p0) cc_final: 0.6288 (p0) REVERT: G 50 GLU cc_start: 0.7860 (mp0) cc_final: 0.7255 (mp0) outliers start: 63 outliers final: 36 residues processed: 401 average time/residue: 0.1799 time to fit residues: 106.3251 Evaluate side-chains 390 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 349 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 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 136 PHE Chi-restraints excluded: chain B residue 288 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 233 SER 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 205 ARG Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain G residue 2 LYS 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 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 361 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 85 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN C 260 ASN D 134 HIS D 137 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN 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 = 0.072442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.051019 restraints weight = 44382.985| |-----------------------------------------------------------------------------| r_work (start): 0.2548 rms_B_bonded: 1.62 r_work: 0.2443 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2334 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21649 Z= 0.151 Angle : 0.608 9.789 29654 Z= 0.305 Chirality : 0.039 0.145 3419 Planarity : 0.004 0.054 3630 Dihedral : 17.506 170.839 3489 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.03 % Allowed : 14.89 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.17), residues: 2515 helix: 1.91 (0.15), residues: 1267 sheet: 0.45 (0.23), residues: 452 loop : -0.02 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 362 TYR 0.017 0.001 TYR G 153 PHE 0.017 0.001 PHE G 76 TRP 0.014 0.001 TRP B 10 HIS 0.004 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (21633) covalent geometry : angle 0.59036 / 0.30 (29630) hydrogen bonds : bond 0.03752 / 2.49 ( 1203) hydrogen bonds : angle 4.07720 / 2.96 ( 3363) metal coordination : bond 0.00451 / 0.26 ( 16) metal coordination : angle 5.17591 / 3.37 ( 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 425 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 361 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8039 (mtm) cc_final: 0.7790 (mtm) REVERT: A 24 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8735 (mt) REVERT: A 65 PHE cc_start: 0.7754 (m-10) cc_final: 0.7455 (m-80) REVERT: A 97 LEU cc_start: 0.8847 (mt) cc_final: 0.8585 (mt) REVERT: A 116 LYS cc_start: 0.8834 (ttmm) cc_final: 0.8626 (ttpp) REVERT: A 121 GLN cc_start: 0.9149 (mp10) cc_final: 0.8911 (mp10) REVERT: A 156 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8453 (mtmm) REVERT: A 222 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8708 (mt) REVERT: B 127 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: C 214 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8744 (mm) REVERT: C 320 ILE cc_start: 0.8948 (mt) cc_final: 0.8731 (mm) REVERT: F 82 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8632 (mp) REVERT: F 132 GLN cc_start: 0.8049 (mt0) cc_final: 0.7843 (mt0) REVERT: F 162 THR cc_start: 0.8623 (p) cc_final: 0.8256 (p) REVERT: F 204 MET cc_start: 0.8865 (tpt) cc_final: 0.8602 (tpt) REVERT: F 243 ASP cc_start: 0.8084 (t0) cc_final: 0.7795 (t0) REVERT: F 326 ASP cc_start: 0.8477 (m-30) cc_final: 0.8039 (m-30) REVERT: F 342 ASP cc_start: 0.7928 (t70) cc_final: 0.7378 (p0) REVERT: F 348 GLN cc_start: 0.7482 (tt0) cc_final: 0.6971 (tm-30) REVERT: G 48 ASP cc_start: 0.7689 (p0) cc_final: 0.6231 (p0) REVERT: G 50 GLU cc_start: 0.7875 (mp0) cc_final: 0.7263 (mp0) REVERT: G 203 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8710 (tt) outliers start: 64 outliers final: 43 residues processed: 399 average time/residue: 0.1823 time to fit residues: 106.4363 Evaluate side-chains 400 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 350 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 24 LEU 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 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 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 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 D residue 309 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 268 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 130 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 19 optimal weight: 0.0060 chunk 188 optimal weight: 4.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN D 137 ASN G 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.072624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.051187 restraints weight = 44906.739| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 1.63 r_work: 0.2451 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2339 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1756 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= 0.146 Angle : 0.601 9.923 29654 Z= 0.300 Chirality : 0.039 0.139 3419 Planarity : 0.004 0.055 3630 Dihedral : 17.483 170.926 3489 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.55 % Allowed : 14.89 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.17), residues: 2515 helix: 2.02 (0.15), residues: 1261 sheet: 0.48 (0.23), residues: 451 loop : 0.04 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 237 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 0.008 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (21633) covalent geometry : angle 0.58397 / 0.30 (29630) hydrogen bonds : bond 0.03653 / 2.42 ( 1203) hydrogen bonds : angle 4.00856 / 2.92 ( 3363) metal coordination : bond 0.00410 / 0.24 ( 16) metal coordination : angle 5.05485 / 3.28 ( 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 438 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 363 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8027 (mtm) cc_final: 0.7770 (mtm) REVERT: A 65 PHE cc_start: 0.7760 (m-10) cc_final: 0.7427 (m-80) REVERT: A 121 GLN cc_start: 0.9156 (mp10) cc_final: 0.8921 (mp10) REVERT: A 156 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8457 (mtmm) REVERT: A 222 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8687 (mt) REVERT: B 127 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: B 133 ARG cc_start: 0.7635 (mmm160) cc_final: 0.7390 (mmm-85) REVERT: C 214 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8758 (mm) REVERT: C 320 ILE cc_start: 0.8943 (mt) cc_final: 0.8735 (mm) REVERT: F 82 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8585 (mp) REVERT: F 204 MET cc_start: 0.8851 (tpt) cc_final: 0.8595 (tpt) REVERT: F 243 ASP cc_start: 0.8085 (t0) cc_final: 0.7803 (t0) REVERT: F 326 ASP cc_start: 0.8426 (m-30) cc_final: 0.8026 (m-30) REVERT: F 342 ASP cc_start: 0.7925 (t70) cc_final: 0.7349 (p0) REVERT: F 348 GLN cc_start: 0.7520 (tt0) cc_final: 0.6959 (tm-30) REVERT: G 48 ASP cc_start: 0.7763 (p0) cc_final: 0.6281 (p0) REVERT: G 50 GLU cc_start: 0.7890 (mp0) cc_final: 0.7266 (mp0) REVERT: G 121 ASP cc_start: 0.7676 (p0) cc_final: 0.7455 (p0) REVERT: G 203 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8706 (tt) outliers start: 75 outliers final: 47 residues processed: 409 average time/residue: 0.1845 time to fit residues: 110.3010 Evaluate side-chains 401 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 348 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 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 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 281 LEU Chi-restraints excluded: chain C residue 304 ASN 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 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 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 2 LYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 93 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN D 137 ASN ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.071114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.049838 restraints weight = 45119.432| |-----------------------------------------------------------------------------| r_work (start): 0.2518 rms_B_bonded: 1.62 r_work: 0.2413 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2304 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21649 Z= 0.207 Angle : 0.655 10.247 29654 Z= 0.326 Chirality : 0.041 0.176 3419 Planarity : 0.005 0.054 3630 Dihedral : 17.513 171.252 3489 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.45 % Allowed : 15.70 % Favored : 80.85 % 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: 1.46 (0.17), residues: 2515 helix: 1.82 (0.14), residues: 1260 sheet: 0.49 (0.23), residues: 452 loop : 0.01 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 86 TYR 0.019 0.002 TYR G 153 PHE 0.015 0.002 PHE G 76 TRP 0.015 0.002 TRP B 10 HIS 0.007 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (21633) covalent geometry : angle 0.63772 / 0.33 (29630) hydrogen bonds : bond 0.04200 / 2.79 ( 1203) hydrogen bonds : angle 4.12988 / 2.99 ( 3363) metal coordination : bond 0.00631 / 0.38 ( 16) metal coordination : angle 5.35359 / 3.51 ( 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 428 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 355 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8160 (mtm) cc_final: 0.7929 (mtm) REVERT: A 65 PHE cc_start: 0.7768 (m-10) cc_final: 0.7442 (m-80) REVERT: A 156 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8453 (mtmm) REVERT: A 222 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8714 (mt) REVERT: B 127 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: C 320 ILE cc_start: 0.8955 (mt) cc_final: 0.8728 (mm) REVERT: F 82 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8605 (mp) REVERT: F 204 MET cc_start: 0.8851 (tpt) cc_final: 0.8601 (tpt) REVERT: F 243 ASP cc_start: 0.8193 (t0) cc_final: 0.7944 (t0) REVERT: F 326 ASP cc_start: 0.8428 (m-30) cc_final: 0.8046 (m-30) REVERT: F 342 ASP cc_start: 0.8001 (t70) cc_final: 0.7428 (p0) REVERT: F 348 GLN cc_start: 0.7458 (tt0) cc_final: 0.6967 (tm-30) REVERT: G 48 ASP cc_start: 0.7702 (p0) cc_final: 0.6362 (p0) REVERT: G 50 GLU cc_start: 0.7933 (mp0) cc_final: 0.7278 (mp0) REVERT: G 203 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8731 (tt) outliers start: 73 outliers final: 52 residues processed: 400 average time/residue: 0.1831 time to fit residues: 107.0131 Evaluate side-chains 404 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 347 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 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 D residue 171 LEU 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 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 49 LEU Chi-restraints excluded: chain G residue 68 THR 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 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: 1.9990 chunk 66 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 333 HIS B 129 HIS C 63 ASN D 137 ASN D 149 HIS G 16 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.072952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.051646 restraints weight = 44552.559| |-----------------------------------------------------------------------------| r_work (start): 0.2566 rms_B_bonded: 1.61 r_work: 0.2465 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2353 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1947 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= 0.133 Angle : 0.600 9.436 29654 Z= 0.300 Chirality : 0.039 0.183 3419 Planarity : 0.004 0.054 3630 Dihedral : 17.487 171.088 3489 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.60 % Allowed : 16.69 % Favored : 80.71 % 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: 1.67 (0.17), residues: 2515 helix: 2.02 (0.15), residues: 1262 sheet: 0.54 (0.23), residues: 452 loop : 0.07 (0.23), residues: 801 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 0.017 0.001 PHE G 76 TRP 0.015 0.001 TRP B 10 HIS 0.007 0.001 HIS A 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (21633) covalent geometry : angle 0.58411 / 0.30 (29630) hydrogen bonds : bond 0.03500 / 2.32 ( 1203) hydrogen bonds : angle 3.97698 / 2.89 ( 3363) metal coordination : bond 0.00374 / 0.22 ( 16) metal coordination : angle 4.92428 / 3.19 ( 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 412 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 357 time to evaluate : 0.814 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: 0.8100 (mtm) cc_final: 0.7877 (mtm) REVERT: A 65 PHE cc_start: 0.7742 (m-10) cc_final: 0.7429 (m-80) REVERT: A 156 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8431 (mtmm) REVERT: A 222 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8675 (mt) REVERT: B 109 ASP cc_start: 0.8121 (t70) cc_final: 0.7919 (t0) REVERT: B 127 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: C 214 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8748 (mm) REVERT: C 320 ILE cc_start: 0.8926 (mt) cc_final: 0.8666 (mm) REVERT: E 182 MET cc_start: 0.9130 (mmm) cc_final: 0.8679 (mmt) REVERT: F 82 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8520 (mp) REVERT: F 243 ASP cc_start: 0.8185 (t0) cc_final: 0.7870 (t0) REVERT: F 326 ASP cc_start: 0.8391 (m-30) cc_final: 0.7997 (m-30) REVERT: F 348 GLN cc_start: 0.7559 (tt0) cc_final: 0.6997 (tm-30) REVERT: G 48 ASP cc_start: 0.7686 (p0) cc_final: 0.6261 (p0) REVERT: G 50 GLU cc_start: 0.7887 (mp0) cc_final: 0.7273 (mp0) REVERT: G 203 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8619 (tt) REVERT: G 230 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6943 (t80) outliers start: 55 outliers final: 42 residues processed: 393 average time/residue: 0.1840 time to fit residues: 105.2276 Evaluate side-chains 393 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 344 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 156 LYS 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 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 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 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 177 LEU Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 98 LEU 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 230 PHE 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=1.50 ------------------------------------------------------------------------------- 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: 0.9980 chunk 71 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 333 HIS C 63 ASN D 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.072149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.050699 restraints weight = 44420.006| |-----------------------------------------------------------------------------| r_work (start): 0.2542 rms_B_bonded: 1.63 r_work: 0.2437 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2327 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21649 Z= 0.165 Angle : 0.637 10.674 29654 Z= 0.316 Chirality : 0.039 0.142 3419 Planarity : 0.005 0.056 3630 Dihedral : 17.417 171.268 3487 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.74 % Allowed : 16.69 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.17), residues: 2515 helix: 1.96 (0.15), residues: 1261 sheet: 0.84 (0.24), residues: 420 loop : -0.05 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 86 TYR 0.019 0.001 TYR G 153 PHE 0.015 0.001 PHE G 76 TRP 0.014 0.001 TRP B 10 HIS 0.007 0.001 HIS A 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (21633) covalent geometry : angle 0.62059 / 0.32 (29630) hydrogen bonds : bond 0.03812 / 2.52 ( 1203) hydrogen bonds : angle 4.01277 / 2.91 ( 3363) metal coordination : bond 0.00461 / 0.27 ( 16) metal coordination : angle 5.01556 / 3.25 ( 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 413 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 355 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8169 (mtm) cc_final: 0.7939 (mtm) REVERT: A 65 PHE cc_start: 0.7758 (m-10) cc_final: 0.7426 (m-80) REVERT: A 156 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8464 (mtmm) REVERT: A 222 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8680 (mt) REVERT: B 127 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: C 214 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8761 (mm) REVERT: C 320 ILE cc_start: 0.8947 (mt) cc_final: 0.8688 (mm) REVERT: F 82 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8558 (mp) REVERT: F 243 ASP cc_start: 0.8226 (t0) cc_final: 0.7955 (t0) REVERT: F 326 ASP cc_start: 0.8424 (m-30) cc_final: 0.8029 (m-30) REVERT: F 348 GLN cc_start: 0.7540 (tt0) cc_final: 0.6972 (tm-30) REVERT: G 48 ASP cc_start: 0.7794 (p0) cc_final: 0.6420 (p0) REVERT: G 50 GLU cc_start: 0.7914 (mp0) cc_final: 0.7313 (mp0) REVERT: G 135 MET cc_start: 0.9121 (tpp) cc_final: 0.8664 (tpt) REVERT: G 203 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8597 (tt) outliers start: 58 outliers final: 45 residues processed: 394 average time/residue: 0.1785 time to fit residues: 103.2028 Evaluate side-chains 400 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 349 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 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 D residue 171 LEU Chi-restraints excluded: chain D residue 262 GLU 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 177 LEU Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 98 LEU 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 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: 0.9980 chunk 216 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 192 optimal weight: 7.9990 chunk 212 optimal weight: 0.4980 chunk 211 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 253 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 333 HIS C 63 ASN D 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.072743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.051481 restraints weight = 44818.362| |-----------------------------------------------------------------------------| r_work (start): 0.2563 rms_B_bonded: 1.63 r_work: 0.2458 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2348 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2051 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= 0.142 Angle : 0.624 8.978 29654 Z= 0.312 Chirality : 0.039 0.158 3419 Planarity : 0.004 0.057 3630 Dihedral : 17.389 171.217 3487 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.46 % Allowed : 17.49 % Favored : 80.05 % 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: 1.71 (0.17), residues: 2515 helix: 2.04 (0.15), residues: 1261 sheet: 0.85 (0.24), residues: 420 loop : -0.05 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 86 TYR 0.019 0.001 TYR G 153 PHE 0.016 0.001 PHE G 76 TRP 0.014 0.001 TRP B 10 HIS 0.007 0.001 HIS A 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (21633) covalent geometry : angle 0.60795 / 0.31 (29630) hydrogen bonds : bond 0.03552 / 2.34 ( 1203) hydrogen bonds : angle 3.95038 / 2.87 ( 3363) metal coordination : bond 0.00369 / 0.22 ( 16) metal coordination : angle 4.91101 / 3.16 ( 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 399 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 347 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8173 (mtm) cc_final: 0.7942 (mtm) REVERT: A 65 PHE cc_start: 0.7750 (m-10) cc_final: 0.7408 (m-80) REVERT: A 156 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8452 (mtmm) REVERT: A 222 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8664 (mt) REVERT: A 223 MET cc_start: 0.9357 (mtp) cc_final: 0.8993 (mtm) REVERT: B 80 ARG cc_start: 0.8603 (ttm-80) cc_final: 0.8396 (ttm-80) REVERT: B 109 ASP cc_start: 0.8107 (t70) cc_final: 0.7903 (t0) REVERT: B 127 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: B 320 ILE cc_start: 0.8297 (mt) cc_final: 0.8094 (tp) REVERT: C 86 ARG cc_start: 0.8778 (mtm110) cc_final: 0.8476 (mtm110) REVERT: C 214 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8756 (mm) REVERT: C 320 ILE cc_start: 0.8927 (mt) cc_final: 0.8680 (mm) REVERT: E 182 MET cc_start: 0.9130 (mmm) cc_final: 0.8693 (mmt) REVERT: F 82 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8526 (mp) REVERT: F 243 ASP cc_start: 0.8256 (t0) cc_final: 0.7964 (t0) REVERT: F 326 ASP cc_start: 0.8401 (m-30) cc_final: 0.7996 (m-30) REVERT: F 348 GLN cc_start: 0.7515 (tt0) cc_final: 0.6947 (tm-30) REVERT: G 48 ASP cc_start: 0.7782 (p0) cc_final: 0.6363 (p0) REVERT: G 50 GLU cc_start: 0.7876 (mp0) cc_final: 0.7242 (mp0) REVERT: G 135 MET cc_start: 0.9169 (tpp) cc_final: 0.8711 (tpt) outliers start: 52 outliers final: 41 residues processed: 381 average time/residue: 0.1796 time to fit residues: 99.9213 Evaluate side-chains 390 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 344 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 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 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 95 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 259 HIS 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 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 322 SER Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 98 LEU 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 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 17 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 116 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 201 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 238 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 333 HIS C 63 ASN D 137 ASN G 212 ASN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.071353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.050113 restraints weight = 44620.727| |-----------------------------------------------------------------------------| r_work (start): 0.2522 rms_B_bonded: 1.61 r_work: 0.2418 rms_B_bonded: 2.31 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: 0.8705 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21649 Z= 0.193 Angle : 0.671 10.988 29654 Z= 0.334 Chirality : 0.040 0.143 3419 Planarity : 0.005 0.056 3630 Dihedral : 17.402 171.489 3487 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.74 % Allowed : 17.49 % Favored : 79.76 % 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: 1.54 (0.17), residues: 2515 helix: 1.88 (0.15), residues: 1258 sheet: 0.65 (0.23), residues: 443 loop : -0.04 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 86 TYR 0.020 0.001 TYR G 153 PHE 0.014 0.001 PHE G 76 TRP 0.013 0.002 TRP B 10 HIS 0.007 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (21633) covalent geometry : angle 0.65439 / 0.33 (29630) hydrogen bonds : bond 0.04093 / 2.70 ( 1203) hydrogen bonds : angle 4.06483 / 2.95 ( 3363) metal coordination : bond 0.00573 / 0.35 ( 16) metal coordination : angle 5.20248 / 3.39 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6066.50 seconds wall clock time: 104 minutes 18.89 seconds (6258.89 seconds total)