Starting phenix.real_space_refine on Fri Aug 7 11:13:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyk_71024/08_2026/9oyk_71024.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyk_71024/08_2026/9oyk_71024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oyk_71024/08_2026/9oyk_71024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyk_71024/08_2026/9oyk_71024.map" model { file = "/net/cci-nas-00/data/ceres_data/9oyk_71024/08_2026/9oyk_71024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyk_71024/08_2026/9oyk_71024.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 55 5.49 5 Mg 3 5.21 5 S 112 5.16 5 C 12940 2.51 5 N 3722 2.21 5 O 3983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20819 Number of models: 1 Model: "" Number of chains: 14 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: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2849 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 16, 'TRANS': 349} Chain: "C" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2865 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "D" Number of atoms: 2807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2807 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 14, 'TRANS': 346} Chain: "E" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2601 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "F" Number of atoms: 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: "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: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 529 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "I" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 243 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3209 SG CYS B 64 75.313 85.500 113.895 1.00 71.45 S ATOM 3269 SG CYS B 73 78.977 84.927 114.133 1.00 62.89 S ATOM 3286 SG CYS B 76 76.745 81.954 114.816 1.00 66.83 S ATOM 3308 SG CYS B 79 76.780 83.173 111.346 1.00 62.00 S ATOM 6058 SG CYS C 64 97.792 55.298 86.472 1.00 50.97 S ATOM 6118 SG CYS C 73 99.444 52.366 84.826 1.00 53.60 S ATOM 6135 SG CYS C 76 96.458 51.568 86.940 1.00 55.68 S ATOM 6157 SG CYS C 79 95.782 53.464 83.890 1.00 47.88 S ATOM 8931 SG CYS D 64 74.210 27.519 56.459 1.00 58.61 S ATOM 8991 SG CYS D 73 72.193 25.061 54.532 1.00 71.34 S ATOM 9008 SG CYS D 76 71.242 25.593 58.166 1.00 65.34 S ATOM 9030 SG CYS D 79 70.571 28.363 55.823 1.00 47.49 S ATOM 11654 SG CYS E 50 28.487 33.897 50.661 1.00 42.47 S ATOM 11723 SG CYS E 59 24.935 32.987 51.565 1.00 48.22 S ATOM 11743 SG CYS E 62 27.406 33.379 54.399 1.00 46.04 S ATOM 11764 SG CYS E 65 26.479 36.433 52.530 1.00 40.70 S Time building chain proxies: 4.90, per 1000 atoms: 0.24 Number of scatterers: 20819 At special positions: 0 Unit cell: (109.296, 121.716, 151.524, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 112 16.00 P 55 15.00 Mg 3 11.99 O 3983 8.00 N 3722 7.00 C 12940 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: 1.62 Conformation dependent library (CDL) restraints added in 792.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 76 " 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 73 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 79 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 76 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 64 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 76 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 79 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 64 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 73 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 65 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 62 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 59 " Number of angles added : 24 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4764 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 13 sheets defined 55.1% alpha, 14.9% beta 19 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 27 through 44 Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.598A pdb=" N ILE A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 124 through 130 removed outlier: 3.558A pdb=" N LEU A 130 " --> pdb=" O TRP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 198 through 206 removed outlier: 3.744A 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 264 removed outlier: 3.728A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 319 through 332 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 21 through 35 removed outlier: 3.836A pdb=" N ALA B 27 " --> pdb=" O HIS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 132 through 145 removed outlier: 4.301A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.798A pdb=" N GLU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) 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 258 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 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.638A pdb=" N MET B 306 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 307 " --> pdb=" O ASN B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 307' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 321 through 338 Processing helix chain 'B' and resid 339 through 342 Processing helix chain 'B' and resid 344 through 358 Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 21 through 35 removed outlier: 3.552A pdb=" N ALA C 27 " --> pdb=" O HIS C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 100 through 109 Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 163 through 169 removed outlier: 3.702A pdb=" N ARG C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 194 Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.936A 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: 3.575A pdb=" N LEU C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 274 Processing helix chain 'C' and resid 277 through 298 Processing helix chain 'C' and resid 299 through 302 removed outlier: 3.953A 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 removed outlier: 3.860A pdb=" N ALA C 307 " --> pdb=" O ASN C 304 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 21 through 34 Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 100 through 110 removed outlier: 3.646A pdb=" N ASN D 110 " --> pdb=" O ASP D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 163 through 170 removed outlier: 3.699A pdb=" N ARG D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 199 through 210 Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 247 through 258 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: 3.834A 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 307 removed outlier: 3.505A pdb=" N MET D 306 " --> pdb=" O GLY D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 318 Processing helix chain 'D' and resid 321 through 338 Processing helix chain 'D' and resid 339 through 342 Processing helix chain 'D' and resid 344 through 358 removed outlier: 3.546A pdb=" N ALA D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 20 removed outlier: 4.762A pdb=" N ASP E 10 " --> pdb=" O TRP E 6 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER E 17 " --> pdb=" O LYS E 13 " (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: 3.577A 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 128 Processing helix chain 'E' and resid 128 through 134 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 178 removed outlier: 3.557A pdb=" N ARG E 178 " --> pdb=" O THR E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 197 through 206 removed outlier: 3.692A pdb=" N PHE E 205 " --> pdb=" O ALA E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 227 Proline residue: E 225 - end of helix Processing helix chain 'E' and resid 228 through 231 removed outlier: 3.525A pdb=" N SER E 231 " --> pdb=" O ASP E 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 228 through 231' Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 240 through 260 Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 282 through 303 Processing helix chain 'E' and resid 307 through 323 Processing helix chain 'F' and resid 7 through 18 removed outlier: 4.293A 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 112 through 116 Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.737A pdb=" N THR F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 156 Processing helix chain 'F' and resid 196 through 207 Processing helix chain 'F' and resid 243 through 248 removed outlier: 4.149A pdb=" N VAL F 247 " --> pdb=" O ASP F 243 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU F 248 " --> pdb=" O TYR F 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 243 through 248' Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 320 through 332 removed outlier: 3.769A pdb=" N VAL F 327 " --> pdb=" O TYR F 323 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS F 332 " --> pdb=" O LEU F 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 9 No H-bonds generated for 'chain 'G' and resid 7 through 9' Processing helix chain 'G' and resid 10 through 18 removed outlier: 3.670A pdb=" N LEU G 14 " --> pdb=" O LEU G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 81 removed outlier: 4.109A pdb=" N CYS G 79 " --> pdb=" O PHE G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.740A pdb=" N THR G 142 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 4.878A 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: 3.579A 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 321 through 332 Processing helix chain 'J' and resid 4 through 12 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: 6.493A pdb=" N ILE A 2 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR A 138 " --> pdb=" O ILE A 2 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU A 4 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA A 20 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL A 137 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU A 22 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N CYS A 139 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 24 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE A 47 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N THR A 79 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU A 49 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU A 81 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N HIS A 51 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU A 83 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE A 53 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.036A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA B 40 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N PHE B 173 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 42 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AA4, first strand: chain 'C' and resid 90 through 94 removed outlier: 6.148A pdb=" N LYS C 121 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU C 153 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA C 155 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE C 125 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR C 41 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA C 40 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE C 173 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU C 42 " --> pdb=" O PHE C 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 90 through 94 removed outlier: 6.191A pdb=" N LYS D 121 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU D 153 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA D 155 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE D 125 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR D 41 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR D 156 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N PHE D 43 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA D 40 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N PHE D 173 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU D 42 " --> pdb=" O PHE D 173 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU D 175 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER D 44 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 76 through 79 Processing sheet with id=AA7, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.506A pdb=" N ASN G 295 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY G 280 " --> pdb=" O ASN G 295 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.689A pdb=" N ASN F 32 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR F 47 " --> pdb=" O ASN F 32 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 41 " --> pdb=" O ALA F 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 309 through 310 removed outlier: 3.552A pdb=" N VAL F 361 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP F 351 " --> pdb=" O ALA F 357 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ALA F 357 " --> pdb=" O ASP F 351 " (cutoff:3.500A) removed outlier: 15.691A pdb=" N SER F 181 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 15.574A pdb=" N THR F 172 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 14.291A pdb=" N VAL F 170 " --> pdb=" O PRO F 183 " (cutoff:3.500A) removed outlier: 13.304A pdb=" N GLY F 185 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 13.697A pdb=" N ARG F 168 " --> pdb=" O GLY F 185 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N SER F 187 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLU F 166 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLY F 164 " --> pdb=" O PRO F 189 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS F 191 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 302 through 307 removed outlier: 3.748A pdb=" N ALA F 302 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN F 295 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY F 280 " --> pdb=" O ASN F 295 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL F 281 " --> pdb=" O PHE F 319 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.293A pdb=" N ASN G 32 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR G 47 " --> pdb=" O ASN G 32 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 89 through 93 Processing sheet with id=AB4, first strand: chain 'G' and resid 309 through 310 removed outlier: 5.831A pdb=" N GLU G 165 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 9.550A pdb=" N GLN G 186 " --> pdb=" O GLU G 163 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLU G 163 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LEU G 188 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 10.476A pdb=" N GLU G 161 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 13.523A pdb=" N SER G 190 " --> pdb=" O LEU G 159 " (cutoff:3.500A) removed outlier: 14.288A pdb=" N LEU G 159 " --> pdb=" O SER G 190 " (cutoff:3.500A) removed outlier: 13.548A pdb=" N SER G 192 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 13.122A pdb=" N GLY G 157 " --> pdb=" O SER G 192 " (cutoff:3.500A) 1082 hydrogen bonds defined for protein. 3075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 4.16 Time building geometry restraints manager: 2.18 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: 7116 1.36 - 1.50: 5570 1.50 - 1.65: 8412 1.65 - 1.80: 90 1.80 - 1.94: 96 Bond restraints: 21284 Sorted by residual: bond pdb=" O3B AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sigma weight residual 1.673 1.579 0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" O3A AGS D 702 " pdb=" PA AGS D 702 " ideal model delta sigma weight residual 1.664 1.575 0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" O3B AGS D 702 " pdb=" PB AGS D 702 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" O3B AGS B 702 " pdb=" PB AGS B 702 " ideal model delta sigma weight residual 1.673 1.592 0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" O3A AGS B 702 " pdb=" PA AGS B 702 " ideal model delta sigma weight residual 1.664 1.587 0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 21279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 28977 3.60 - 7.20: 100 7.20 - 10.80: 11 10.80 - 14.40: 1 14.40 - 17.99: 1 Bond angle restraints: 29090 Sorted by residual: angle pdb=" O3A AGS C 702 " pdb=" PA AGS C 702 " pdb=" O5' AGS C 702 " ideal model delta sigma weight residual 97.67 115.66 -17.99 3.00e+00 1.11e-01 3.60e+01 angle pdb=" N3 DT I 8 " pdb=" C4 DT I 8 " pdb=" O4 DT I 8 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" O4' DG H 38 " pdb=" C1' DG H 38 " pdb=" N9 DG H 38 " ideal model delta sigma weight residual 108.00 111.09 -3.09 7.00e-01 2.04e+00 1.95e+01 angle pdb=" O3A AGS C 702 " pdb=" PB AGS C 702 " pdb=" O3B AGS C 702 " ideal model delta sigma weight residual 100.38 113.29 -12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" N3 DT H 42 " pdb=" C4 DT H 42 " pdb=" O4 DT H 42 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 29085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.18: 12340 29.18 - 58.37: 537 58.37 - 87.55: 35 87.55 - 116.73: 6 116.73 - 145.91: 4 Dihedral angle restraints: 12922 sinusoidal: 5581 harmonic: 7341 Sorted by residual: dihedral pdb=" CA TYR C 3 " pdb=" C TYR C 3 " pdb=" N GLN C 4 " pdb=" CA GLN C 4 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" O2A AGS C 702 " pdb=" O3A AGS C 702 " pdb=" PA AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sinusoidal sigma weight residual -52.28 93.63 -145.91 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" O5' AGS C 702 " pdb=" O3A AGS C 702 " pdb=" PA AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sinusoidal sigma weight residual -166.80 -26.91 -139.89 1 3.00e+01 1.11e-03 1.88e+01 ... (remaining 12919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 3291 0.111 - 0.223: 53 0.223 - 0.334: 3 0.334 - 0.446: 0 0.446 - 0.557: 6 Chirality restraints: 3353 Sorted by residual: chirality pdb=" P DG H 44 " pdb=" OP1 DG H 44 " pdb=" OP2 DG H 44 " pdb=" O5' DG H 44 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.56 2.00e-01 2.50e+01 7.76e+00 chirality pdb=" P DC H 45 " pdb=" OP1 DC H 45 " pdb=" OP2 DC H 45 " pdb=" O5' DC H 45 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" P DC I 7 " pdb=" OP1 DC I 7 " pdb=" OP2 DC I 7 " pdb=" O5' DC I 7 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.54 2.00e-01 2.50e+01 7.18e+00 ... (remaining 3350 not shown) Planarity restraints: 3618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 56 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO A 57 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 296 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO G 297 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO G 297 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 297 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 96 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" CD GLN A 96 " 0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN A 96 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN A 96 " -0.008 2.00e-02 2.50e+03 ... (remaining 3615 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 10 2.56 - 3.15: 15608 3.15 - 3.73: 33114 3.73 - 4.32: 47481 4.32 - 4.90: 78179 Nonbonded interactions: 174392 Sorted by model distance: nonbonded pdb=" OG1 THR D 52 " pdb="MG MG D 703 " model vdw 1.977 2.170 nonbonded pdb=" OG1 THR B 52 " pdb="MG MG B 703 " model vdw 1.990 2.170 nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 703 " model vdw 2.090 2.170 nonbonded pdb=" O2B AGS D 702 " pdb="MG MG D 703 " model vdw 2.103 2.170 nonbonded pdb=" O3G AGS B 702 " pdb="MG MG B 703 " model vdw 2.107 2.170 ... (remaining 174387 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' and resid 2 through 703) } ncs_group { reference = chain 'F' selection = chain 'G' } 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.940 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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 0.094 21300 Z= 0.289 Angle : 0.676 17.994 29114 Z= 0.365 Chirality : 0.048 0.557 3353 Planarity : 0.004 0.043 3618 Dihedral : 15.582 145.913 8158 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.17), residues: 2518 helix: 1.54 (0.15), residues: 1247 sheet: 1.25 (0.25), residues: 413 loop : 0.22 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 47 TYR 0.013 0.002 TYR E 47 PHE 0.011 0.002 PHE C 15 TRP 0.009 0.002 TRP B 10 HIS 0.006 0.001 HIS D 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.29 (21284) covalent geometry : angle 0.66509 / 0.36 (29090) hydrogen bonds : bond 0.14105 / 9.44 ( 1132) hydrogen bonds : angle 5.08385 / 3.72 ( 3175) metal coordination : bond 0.00215 / 0.13 ( 16) metal coordination : angle 4.28205 / 2.75 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6941 (mt0) cc_final: 0.6412 (mm-40) REVERT: A 45 GLN cc_start: 0.7397 (mt0) cc_final: 0.7136 (mm-40) REVERT: A 77 ARG cc_start: 0.7080 (mtp180) cc_final: 0.6831 (mtp180) REVERT: A 198 THR cc_start: 0.8127 (m) cc_final: 0.7922 (p) REVERT: A 237 ARG cc_start: 0.8182 (ttm170) cc_final: 0.7786 (ttp80) REVERT: A 239 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6705 (pt0) REVERT: A 280 GLN cc_start: 0.8079 (tp40) cc_final: 0.7820 (mm-40) REVERT: A 288 GLU cc_start: 0.7408 (tt0) cc_final: 0.7129 (mm-30) REVERT: B 36 ARG cc_start: 0.7586 (mtp180) cc_final: 0.7382 (mtm-85) REVERT: B 105 ARG cc_start: 0.7489 (ttm110) cc_final: 0.6794 (mtt-85) REVERT: B 127 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7214 (mm-30) REVERT: B 144 GLU cc_start: 0.7153 (tt0) cc_final: 0.6679 (tm-30) REVERT: B 148 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7599 (mm-30) REVERT: B 176 LYS cc_start: 0.8898 (mtmt) cc_final: 0.8002 (mmtm) REVERT: B 208 ARG cc_start: 0.8135 (ttm-80) cc_final: 0.7646 (ttp-110) REVERT: B 258 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7173 (mm-30) REVERT: B 262 GLU cc_start: 0.7899 (pt0) cc_final: 0.7677 (mm-30) REVERT: B 310 GLU cc_start: 0.7862 (tt0) cc_final: 0.7595 (tm-30) REVERT: B 318 ARG cc_start: 0.8461 (ttp80) cc_final: 0.7386 (ttp-110) REVERT: C 77 ASP cc_start: 0.7924 (m-30) cc_final: 0.7601 (m-30) REVERT: C 78 ASN cc_start: 0.8828 (m-40) cc_final: 0.8508 (m110) REVERT: C 80 ARG cc_start: 0.7445 (mtm110) cc_final: 0.7242 (mtm-85) REVERT: C 98 ARG cc_start: 0.7815 (mtp180) cc_final: 0.7564 (mtp180) REVERT: C 112 GLN cc_start: 0.8290 (mp10) cc_final: 0.7885 (mp10) REVERT: C 117 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7594 (ttp80) REVERT: C 141 LYS cc_start: 0.8637 (tttt) cc_final: 0.8374 (tmmt) REVERT: C 161 LYS cc_start: 0.8538 (mmtm) cc_final: 0.8322 (mmtm) REVERT: C 181 GLU cc_start: 0.8156 (tp30) cc_final: 0.7894 (tp30) REVERT: C 193 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8023 (mm-30) REVERT: C 235 GLN cc_start: 0.8261 (tt0) cc_final: 0.7746 (tm130) REVERT: C 284 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7540 (mm-30) REVERT: D 102 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7398 (pm20) REVERT: D 141 LYS cc_start: 0.8730 (tptm) cc_final: 0.8438 (tptp) REVERT: D 176 LYS cc_start: 0.8599 (mtpt) cc_final: 0.7961 (mmtt) REVERT: D 310 GLU cc_start: 0.7041 (tt0) cc_final: 0.6774 (tm-30) REVERT: E 8 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7480 (tpm170) REVERT: E 178 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.7825 (mtm110) REVERT: E 211 GLN cc_start: 0.8327 (tp-100) cc_final: 0.7635 (mp-120) REVERT: E 285 ARG cc_start: 0.8521 (mtt-85) cc_final: 0.8289 (mtt-85) REVERT: F 73 ARG cc_start: 0.7885 (tpt-90) cc_final: 0.7556 (tpp-160) REVERT: F 97 MET cc_start: 0.8831 (ttm) cc_final: 0.8563 (ttp) REVERT: F 105 ARG cc_start: 0.7964 (ttp-110) cc_final: 0.7643 (ttp-110) REVERT: F 136 LYS cc_start: 0.7801 (tttm) cc_final: 0.7461 (tttm) REVERT: F 140 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6679 (mt-10) REVERT: F 154 TYR cc_start: 0.8465 (p90) cc_final: 0.7847 (p90) REVERT: F 227 VAL cc_start: 0.8444 (t) cc_final: 0.8105 (p) REVERT: F 322 SER cc_start: 0.7314 (t) cc_final: 0.7077 (m) REVERT: G 50 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6898 (mm-30) REVERT: G 126 VAL cc_start: 0.8228 (t) cc_final: 0.7972 (m) REVERT: G 129 THR cc_start: 0.8136 (m) cc_final: 0.7919 (t) REVERT: G 166 GLU cc_start: 0.7783 (tt0) cc_final: 0.7400 (tt0) REVERT: G 198 LYS cc_start: 0.8075 (mttp) cc_final: 0.7292 (mptt) REVERT: G 250 LYS cc_start: 0.7164 (mmpt) cc_final: 0.6960 (mtpt) REVERT: G 277 LYS cc_start: 0.8124 (ptpp) cc_final: 0.7468 (ttmm) REVERT: G 282 ARG cc_start: 0.8290 (mtt90) cc_final: 0.7764 (mtp85) REVERT: G 301 GLU cc_start: 0.7684 (tt0) cc_final: 0.7383 (mt-10) outliers start: 0 outliers final: 0 residues processed: 472 average time/residue: 0.8921 time to fit residues: 462.3836 Evaluate side-chains 351 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.2980 chunk 247 optimal weight: 9.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 78 GLN A 259 ASN A 266 HIS A 291 ASN B 78 ASN B 110 ASN B 112 GLN B 204 GLN B 330 GLN C 231 GLN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS G 16 GLN G 186 GLN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.183632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142715 restraints weight = 19670.653| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.50 r_work: 0.3496 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21300 Z= 0.195 Angle : 0.602 9.570 29114 Z= 0.303 Chirality : 0.041 0.233 3353 Planarity : 0.004 0.047 3618 Dihedral : 14.601 142.175 3357 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.50 % Allowed : 8.69 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.17), residues: 2518 helix: 1.68 (0.15), residues: 1257 sheet: 1.23 (0.25), residues: 410 loop : 0.22 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 47 TYR 0.013 0.002 TYR B 341 PHE 0.010 0.002 PHE G 128 TRP 0.013 0.002 TRP B 10 HIS 0.010 0.001 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (21284) covalent geometry : angle 0.58736 / 0.30 (29090) hydrogen bonds : bond 0.04519 / 3.04 ( 1132) hydrogen bonds : angle 4.10946 / 2.99 ( 3175) metal coordination : bond 0.00324 / 0.18 ( 16) metal coordination : angle 4.65238 / 3.00 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 355 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6810 (mt0) cc_final: 0.6338 (mm-40) REVERT: A 77 ARG cc_start: 0.7177 (mtp180) cc_final: 0.6931 (mtp180) REVERT: A 146 GLN cc_start: 0.8167 (mp10) cc_final: 0.7871 (mp10) REVERT: A 237 ARG cc_start: 0.8035 (ttm170) cc_final: 0.7774 (ttp80) REVERT: A 280 GLN cc_start: 0.8168 (tp40) cc_final: 0.7967 (mm-40) REVERT: A 288 GLU cc_start: 0.7477 (tt0) cc_final: 0.7263 (mm-30) REVERT: A 307 ARG cc_start: 0.8457 (mtm110) cc_final: 0.8217 (mtm110) REVERT: B 80 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.6952 (mtm-85) REVERT: B 105 ARG cc_start: 0.7525 (ttm110) cc_final: 0.6911 (mtt-85) REVERT: B 127 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7251 (mm-30) REVERT: B 144 GLU cc_start: 0.7279 (tt0) cc_final: 0.6845 (tm-30) REVERT: B 148 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7664 (mm-30) REVERT: B 169 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7171 (mmp80) REVERT: B 176 LYS cc_start: 0.8916 (mtmt) cc_final: 0.8064 (mmtm) REVERT: B 208 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7689 (ttp-110) REVERT: B 310 GLU cc_start: 0.7895 (tt0) cc_final: 0.7683 (tm-30) REVERT: B 318 ARG cc_start: 0.8476 (ttp80) cc_final: 0.7408 (ttp-110) REVERT: C 77 ASP cc_start: 0.7938 (m-30) cc_final: 0.7671 (m-30) REVERT: C 98 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7615 (mtp180) REVERT: C 112 GLN cc_start: 0.8284 (mp10) cc_final: 0.7912 (mp10) REVERT: C 141 LYS cc_start: 0.8576 (tttt) cc_final: 0.8361 (tmmt) REVERT: C 193 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8065 (mm-30) REVERT: C 235 GLN cc_start: 0.8185 (tt0) cc_final: 0.7710 (tm130) REVERT: D 1 MET cc_start: 0.4699 (ppp) cc_final: 0.4127 (tpp) REVERT: D 102 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7461 (pm20) REVERT: D 141 LYS cc_start: 0.8743 (tptm) cc_final: 0.8478 (tptp) REVERT: D 145 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8343 (mm-30) REVERT: D 176 LYS cc_start: 0.8568 (mtpt) cc_final: 0.8004 (mmtt) REVERT: E 8 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7598 (tpm170) REVERT: E 178 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7827 (mtm110) REVERT: E 211 GLN cc_start: 0.8300 (tp-100) cc_final: 0.7777 (mp10) REVERT: E 285 ARG cc_start: 0.8553 (mtt-85) cc_final: 0.8325 (mtt-85) REVERT: F 73 ARG cc_start: 0.8002 (tpt-90) cc_final: 0.7672 (tpp-160) REVERT: F 97 MET cc_start: 0.8790 (ttm) cc_final: 0.8465 (ttp) REVERT: F 105 ARG cc_start: 0.7983 (ttp-110) cc_final: 0.7770 (ttp-170) REVERT: F 136 LYS cc_start: 0.7920 (tttm) cc_final: 0.7689 (tttm) REVERT: F 137 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6164 (tpt90) REVERT: F 154 TYR cc_start: 0.8460 (p90) cc_final: 0.7880 (p90) REVERT: F 245 ARG cc_start: 0.6212 (mmp-170) cc_final: 0.5858 (mmp80) REVERT: F 322 SER cc_start: 0.7481 (t) cc_final: 0.7222 (m) REVERT: F 339 MET cc_start: 0.5067 (OUTLIER) cc_final: 0.4866 (mmm) REVERT: G 1 MET cc_start: 0.5281 (ttm) cc_final: 0.3600 (tpt) REVERT: G 48 ASP cc_start: 0.7271 (t0) cc_final: 0.6971 (t0) REVERT: G 50 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7050 (mm-30) REVERT: G 149 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7300 (mt0) REVERT: G 166 GLU cc_start: 0.7763 (tt0) cc_final: 0.7433 (tt0) REVERT: G 169 THR cc_start: 0.8824 (m) cc_final: 0.8621 (m) REVERT: G 198 LYS cc_start: 0.8085 (mttp) cc_final: 0.7391 (mptt) REVERT: G 215 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7446 (ttm110) REVERT: G 257 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: G 277 LYS cc_start: 0.8161 (ptpp) cc_final: 0.7575 (ttmm) REVERT: G 282 ARG cc_start: 0.8411 (mtt90) cc_final: 0.7904 (mtp85) REVERT: G 291 LYS cc_start: 0.8575 (ttpt) cc_final: 0.8374 (ttpp) REVERT: G 301 GLU cc_start: 0.7586 (tt0) cc_final: 0.7259 (mt-10) REVERT: J 10 GLN cc_start: 0.8602 (tt0) cc_final: 0.8292 (tt0) outliers start: 53 outliers final: 17 residues processed: 378 average time/residue: 0.8457 time to fit residues: 352.3483 Evaluate side-chains 356 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 333 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 137 ARG Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 215 ARG Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 339 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 28 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 232 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 259 ASN A 291 ASN B 112 GLN C 78 ASN E 52 GLN E 206 GLN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.179553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.137945 restraints weight = 19759.626| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.61 r_work: 0.3441 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21300 Z= 0.165 Angle : 0.559 8.511 29114 Z= 0.281 Chirality : 0.040 0.222 3353 Planarity : 0.004 0.048 3618 Dihedral : 14.538 141.507 3357 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.55 % Allowed : 10.16 % Favored : 87.29 % 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: 2518 helix: 1.81 (0.15), residues: 1256 sheet: 1.00 (0.25), residues: 417 loop : 0.30 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 47 TYR 0.021 0.001 TYR E 47 PHE 0.011 0.001 PHE F 128 TRP 0.013 0.001 TRP B 10 HIS 0.004 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (21284) covalent geometry : angle 0.54601 / 0.28 (29090) hydrogen bonds : bond 0.03996 / 2.69 ( 1132) hydrogen bonds : angle 3.86952 / 2.82 ( 3175) metal coordination : bond 0.00248 / 0.14 ( 16) metal coordination : angle 4.27281 / 2.79 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 346 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7710 (mmt180) cc_final: 0.7471 (mmt-90) REVERT: A 77 ARG cc_start: 0.7084 (mtp180) cc_final: 0.6831 (mtp180) REVERT: A 198 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7732 (p) REVERT: A 237 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7699 (ttp80) REVERT: A 280 GLN cc_start: 0.8049 (tp40) cc_final: 0.7830 (mm-40) REVERT: A 288 GLU cc_start: 0.7357 (tt0) cc_final: 0.7114 (mm-30) REVERT: A 309 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: B 80 ARG cc_start: 0.7541 (mtm-85) cc_final: 0.7026 (mtm-85) REVERT: B 105 ARG cc_start: 0.7404 (ttm110) cc_final: 0.6716 (mtt-85) REVERT: B 127 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7161 (mm-30) REVERT: B 144 GLU cc_start: 0.7234 (tt0) cc_final: 0.6758 (tm-30) REVERT: B 148 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7604 (mm-30) REVERT: B 169 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.6967 (mmp80) REVERT: B 176 LYS cc_start: 0.8880 (mtmt) cc_final: 0.7981 (mmtm) REVERT: B 201 ARG cc_start: 0.8099 (tmt-80) cc_final: 0.7522 (tpm170) REVERT: B 208 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7593 (ttp-110) REVERT: B 277 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6433 (tm-30) REVERT: B 310 GLU cc_start: 0.7853 (tt0) cc_final: 0.7591 (tm-30) REVERT: B 318 ARG cc_start: 0.8459 (ttp80) cc_final: 0.7371 (ttp-110) REVERT: C 98 ARG cc_start: 0.7874 (mtp180) cc_final: 0.7660 (mtp180) REVERT: C 112 GLN cc_start: 0.8268 (mp10) cc_final: 0.7881 (mp10) REVERT: C 141 LYS cc_start: 0.8554 (tttt) cc_final: 0.8275 (tmmt) REVERT: C 193 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8040 (mm-30) REVERT: C 235 GLN cc_start: 0.8150 (tt0) cc_final: 0.7641 (tm130) REVERT: D 102 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7411 (pm20) REVERT: D 141 LYS cc_start: 0.8696 (tptm) cc_final: 0.8394 (tptp) REVERT: D 145 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8267 (mm-30) REVERT: D 176 LYS cc_start: 0.8520 (mtpt) cc_final: 0.7909 (mmtt) REVERT: D 347 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8222 (ttt) REVERT: E 8 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7495 (tpm170) REVERT: E 178 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7821 (mtm110) REVERT: E 206 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7442 (mm110) REVERT: E 285 ARG cc_start: 0.8522 (mtt-85) cc_final: 0.8294 (mtt-85) REVERT: F 73 ARG cc_start: 0.7909 (tpt-90) cc_final: 0.7569 (tpp-160) REVERT: F 97 MET cc_start: 0.8816 (ttm) cc_final: 0.8430 (ttp) REVERT: F 105 ARG cc_start: 0.7930 (ttp-110) cc_final: 0.7647 (ttp-170) REVERT: F 136 LYS cc_start: 0.7723 (tttm) cc_final: 0.7520 (tttm) REVERT: F 154 TYR cc_start: 0.8421 (p90) cc_final: 0.7835 (p90) REVERT: F 198 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7014 (pptt) REVERT: F 322 SER cc_start: 0.7500 (t) cc_final: 0.7174 (m) REVERT: F 339 MET cc_start: 0.5152 (OUTLIER) cc_final: 0.4912 (mmm) REVERT: G 1 MET cc_start: 0.5261 (ttm) cc_final: 0.3580 (tpt) REVERT: G 48 ASP cc_start: 0.7137 (t0) cc_final: 0.6660 (t0) REVERT: G 50 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6875 (mm-30) REVERT: G 149 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7286 (mt0) REVERT: G 166 GLU cc_start: 0.7666 (tt0) cc_final: 0.7422 (tt0) REVERT: G 186 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7897 (pm20) REVERT: G 198 LYS cc_start: 0.8137 (mttp) cc_final: 0.7265 (mptt) REVERT: G 215 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7345 (ttm110) REVERT: G 257 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: G 277 LYS cc_start: 0.8103 (ptpp) cc_final: 0.7449 (ttmm) REVERT: G 282 ARG cc_start: 0.8406 (mtt180) cc_final: 0.7659 (mmt180) REVERT: G 291 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8354 (ttpp) REVERT: G 301 GLU cc_start: 0.7605 (tt0) cc_final: 0.7164 (mt-10) REVERT: J 10 GLN cc_start: 0.8631 (tt0) cc_final: 0.8312 (tt0) outliers start: 54 outliers final: 16 residues processed: 372 average time/residue: 0.8554 time to fit residues: 351.6924 Evaluate side-chains 353 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 327 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain G residue 215 ARG Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 262 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 179 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 238 optimal weight: 0.0070 chunk 1 optimal weight: 0.4980 chunk 218 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 234 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 ASN A 291 ASN B 110 ASN B 112 GLN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** 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 = 0.4052 r_free = 0.4052 target = 0.180685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.138956 restraints weight = 19664.330| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.60 r_work: 0.3430 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21300 Z= 0.128 Angle : 0.521 7.114 29114 Z= 0.263 Chirality : 0.038 0.215 3353 Planarity : 0.004 0.048 3618 Dihedral : 14.450 141.046 3357 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.31 % Allowed : 11.43 % Favored : 86.25 % 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: 1.88 (0.17), residues: 2518 helix: 1.98 (0.15), residues: 1257 sheet: 1.26 (0.26), residues: 395 loop : 0.23 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 47 TYR 0.012 0.001 TYR E 47 PHE 0.009 0.001 PHE F 128 TRP 0.013 0.001 TRP B 10 HIS 0.004 0.001 HIS G 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (21284) covalent geometry : angle 0.50678 / 0.26 (29090) hydrogen bonds : bond 0.03537 / 2.39 ( 1132) hydrogen bonds : angle 3.71918 / 2.72 ( 3175) metal coordination : bond 0.00207 / 0.13 ( 16) metal coordination : angle 4.25971 / 2.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 348 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7090 (mtp180) cc_final: 0.6851 (mtp180) REVERT: A 181 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8748 (tt) REVERT: A 198 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7728 (p) REVERT: A 237 ARG cc_start: 0.8113 (ttm170) cc_final: 0.7713 (ttp80) REVERT: A 280 GLN cc_start: 0.8062 (tp40) cc_final: 0.7861 (mm-40) REVERT: A 288 GLU cc_start: 0.7439 (tt0) cc_final: 0.7180 (mm-30) REVERT: A 309 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: B 80 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.7040 (mtm-85) REVERT: B 105 ARG cc_start: 0.7442 (ttm110) cc_final: 0.6777 (mtt-85) REVERT: B 127 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7115 (mm-30) REVERT: B 144 GLU cc_start: 0.7264 (tt0) cc_final: 0.6800 (tm-30) REVERT: B 148 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7626 (mm-30) REVERT: B 169 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.6852 (mmp80) REVERT: B 176 LYS cc_start: 0.8871 (mtmt) cc_final: 0.7979 (mmtp) REVERT: B 201 ARG cc_start: 0.8120 (tmt-80) cc_final: 0.7520 (tpm170) REVERT: B 208 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7626 (ttp-110) REVERT: B 277 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6297 (tm-30) REVERT: B 298 SER cc_start: 0.7850 (t) cc_final: 0.7634 (p) REVERT: B 310 GLU cc_start: 0.7879 (tt0) cc_final: 0.7633 (tm-30) REVERT: B 318 ARG cc_start: 0.8482 (ttp80) cc_final: 0.7483 (ttm110) REVERT: C 112 GLN cc_start: 0.8275 (mp10) cc_final: 0.7896 (mp10) REVERT: C 141 LYS cc_start: 0.8549 (tttt) cc_final: 0.8305 (tmmt) REVERT: C 193 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8051 (mm-30) REVERT: C 235 GLN cc_start: 0.8217 (tt0) cc_final: 0.7711 (tm130) REVERT: C 338 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7894 (mt-10) REVERT: D 102 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7537 (pm20) REVERT: D 112 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8861 (pm20) REVERT: D 141 LYS cc_start: 0.8678 (tptm) cc_final: 0.8391 (tptm) REVERT: D 145 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8301 (mm-30) REVERT: D 176 LYS cc_start: 0.8518 (mtpt) cc_final: 0.7889 (mmtt) REVERT: E 8 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7615 (ttm170) REVERT: E 178 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7855 (mtm110) REVERT: E 206 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7387 (mm-40) REVERT: E 285 ARG cc_start: 0.8533 (mtt-85) cc_final: 0.8305 (mtt-85) REVERT: F 73 ARG cc_start: 0.7977 (tpt-90) cc_final: 0.7580 (tpp-160) REVERT: F 97 MET cc_start: 0.8819 (ttm) cc_final: 0.8428 (ttp) REVERT: F 105 ARG cc_start: 0.7971 (ttp-110) cc_final: 0.7669 (ttp-170) REVERT: F 149 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8478 (mt0) REVERT: F 154 TYR cc_start: 0.8422 (p90) cc_final: 0.7784 (p90) REVERT: F 198 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7099 (pptt) REVERT: F 245 ARG cc_start: 0.6349 (mmp-170) cc_final: 0.6005 (mmp80) REVERT: F 322 SER cc_start: 0.7478 (t) cc_final: 0.7148 (m) REVERT: G 1 MET cc_start: 0.5231 (ttm) cc_final: 0.3576 (tpt) REVERT: G 48 ASP cc_start: 0.7072 (t0) cc_final: 0.6675 (t0) REVERT: G 50 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6887 (mm-30) REVERT: G 149 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7311 (mt0) REVERT: G 166 GLU cc_start: 0.7654 (tt0) cc_final: 0.7430 (tt0) REVERT: G 186 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7492 (pt0) REVERT: G 198 LYS cc_start: 0.8144 (mttp) cc_final: 0.7292 (mptt) REVERT: G 257 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: G 277 LYS cc_start: 0.8114 (ptpp) cc_final: 0.7465 (ttmm) REVERT: G 282 ARG cc_start: 0.8408 (mtt180) cc_final: 0.7714 (mmt180) REVERT: G 301 GLU cc_start: 0.7714 (tt0) cc_final: 0.7245 (mt-10) REVERT: J 10 GLN cc_start: 0.8647 (tt0) cc_final: 0.8349 (tt0) outliers start: 49 outliers final: 18 residues processed: 370 average time/residue: 0.8160 time to fit residues: 333.6517 Evaluate side-chains 355 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 327 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 339 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 80 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 245 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 158 optimal weight: 0.0370 chunk 42 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 142 optimal weight: 0.4980 chunk 143 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 ASN A 263 GLN A 291 ASN B 112 GLN B 269 ASN C 129 HIS C 137 ASN F 226 HIS G 186 GLN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.181782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.139382 restraints weight = 19626.499| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.56 r_work: 0.3471 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21300 Z= 0.107 Angle : 0.496 6.838 29114 Z= 0.252 Chirality : 0.037 0.204 3353 Planarity : 0.004 0.048 3618 Dihedral : 14.322 140.595 3357 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.46 % Allowed : 11.57 % Favored : 85.97 % 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: 2.05 (0.17), residues: 2518 helix: 2.14 (0.15), residues: 1263 sheet: 1.39 (0.26), residues: 386 loop : 0.25 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 215 TYR 0.011 0.001 TYR E 47 PHE 0.009 0.001 PHE F 128 TRP 0.012 0.001 TRP B 10 HIS 0.003 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (21284) covalent geometry : angle 0.48129 / 0.25 (29090) hydrogen bonds : bond 0.03227 / 2.18 ( 1132) hydrogen bonds : angle 3.60397 / 2.64 ( 3175) metal coordination : bond 0.00174 / 0.12 ( 16) metal coordination : angle 4.15520 / 2.69 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 337 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6804 (mt0) cc_final: 0.6259 (mm-40) REVERT: A 18 ARG cc_start: 0.7484 (mmt-90) cc_final: 0.6872 (mmm160) REVERT: A 77 ARG cc_start: 0.7029 (mtp180) cc_final: 0.6793 (mtp180) REVERT: A 181 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8708 (tt) REVERT: A 198 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7703 (p) REVERT: A 237 ARG cc_start: 0.8054 (ttm170) cc_final: 0.7650 (ttp80) REVERT: A 307 ARG cc_start: 0.8416 (mtm110) cc_final: 0.8212 (mtm110) REVERT: A 309 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: B 80 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.7064 (mtm-85) REVERT: B 105 ARG cc_start: 0.7436 (ttm110) cc_final: 0.6706 (mtt-85) REVERT: B 127 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7096 (mm-30) REVERT: B 144 GLU cc_start: 0.7244 (tt0) cc_final: 0.6783 (tm-30) REVERT: B 148 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 169 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.6680 (mmp80) REVERT: B 176 LYS cc_start: 0.8842 (mtmt) cc_final: 0.7958 (mmtp) REVERT: B 204 GLN cc_start: 0.8245 (mt0) cc_final: 0.7994 (mt0) REVERT: B 208 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7625 (ttp-110) REVERT: B 277 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7137 (tm-30) REVERT: B 310 GLU cc_start: 0.7833 (tt0) cc_final: 0.7611 (tm-30) REVERT: B 318 ARG cc_start: 0.8536 (ttp80) cc_final: 0.7466 (ttm110) REVERT: C 112 GLN cc_start: 0.8276 (mp10) cc_final: 0.7896 (mp10) REVERT: C 141 LYS cc_start: 0.8515 (tttt) cc_final: 0.8297 (tmmt) REVERT: C 193 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8080 (mm-30) REVERT: C 235 GLN cc_start: 0.8210 (tt0) cc_final: 0.7709 (tm130) REVERT: C 338 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7854 (mt-10) REVERT: D 94 ASP cc_start: 0.8381 (t70) cc_final: 0.7913 (t0) REVERT: D 102 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7427 (pm20) REVERT: D 141 LYS cc_start: 0.8645 (tptm) cc_final: 0.8373 (tptm) REVERT: D 145 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8283 (mm-30) REVERT: D 176 LYS cc_start: 0.8484 (mtpt) cc_final: 0.7887 (mmtt) REVERT: D 347 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8141 (ttt) REVERT: E 8 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7648 (ttm170) REVERT: E 178 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7873 (mtm110) REVERT: E 206 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7324 (mm-40) REVERT: E 285 ARG cc_start: 0.8528 (mtt-85) cc_final: 0.8313 (mtt-85) REVERT: F 1 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7862 (ttt) REVERT: F 73 ARG cc_start: 0.7962 (tpt-90) cc_final: 0.7583 (tpp-160) REVERT: F 97 MET cc_start: 0.8822 (ttm) cc_final: 0.8430 (ttp) REVERT: F 105 ARG cc_start: 0.7977 (ttp-110) cc_final: 0.7669 (ttp-170) REVERT: F 149 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8429 (mt0) REVERT: F 154 TYR cc_start: 0.8425 (p90) cc_final: 0.7795 (p90) REVERT: F 198 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7107 (pptt) REVERT: G 1 MET cc_start: 0.5226 (ttm) cc_final: 0.3536 (tpt) REVERT: G 48 ASP cc_start: 0.6910 (t0) cc_final: 0.6579 (t0) REVERT: G 50 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6867 (mm-30) REVERT: G 126 VAL cc_start: 0.8106 (t) cc_final: 0.7822 (m) REVERT: G 149 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7293 (mt0) REVERT: G 166 GLU cc_start: 0.7658 (tt0) cc_final: 0.7443 (tt0) REVERT: G 198 LYS cc_start: 0.8173 (mttp) cc_final: 0.7322 (mptt) REVERT: G 250 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7287 (mmtp) REVERT: G 257 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: G 277 LYS cc_start: 0.8116 (ptpp) cc_final: 0.7458 (ttmm) REVERT: G 282 ARG cc_start: 0.8435 (mtt180) cc_final: 0.7716 (mmt180) REVERT: G 301 GLU cc_start: 0.7688 (tt0) cc_final: 0.7261 (mt-10) REVERT: J 10 GLN cc_start: 0.8637 (tt0) cc_final: 0.8393 (tt0) outliers start: 52 outliers final: 20 residues processed: 359 average time/residue: 0.8343 time to fit residues: 330.8098 Evaluate side-chains 345 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 315 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 262 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 250 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 202 optimal weight: 20.0000 chunk 75 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 210 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 ASN B 110 ASN B 112 GLN B 269 ASN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 ASN F 191 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.179534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.137191 restraints weight = 19630.152| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.62 r_work: 0.3427 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21300 Z= 0.174 Angle : 0.559 8.062 29114 Z= 0.279 Chirality : 0.040 0.212 3353 Planarity : 0.004 0.050 3618 Dihedral : 14.509 141.967 3357 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.79 % Allowed : 12.09 % Favored : 85.12 % 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: 1.85 (0.17), residues: 2518 helix: 1.97 (0.15), residues: 1258 sheet: 1.28 (0.26), residues: 381 loop : 0.19 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 215 TYR 0.014 0.002 TYR E 47 PHE 0.012 0.001 PHE F 128 TRP 0.011 0.001 TRP B 10 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (21284) covalent geometry : angle 0.54616 / 0.28 (29090) hydrogen bonds : bond 0.03734 / 2.52 ( 1132) hydrogen bonds : angle 3.66937 / 2.68 ( 3175) metal coordination : bond 0.00211 / 0.13 ( 16) metal coordination : angle 4.15010 / 2.73 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 324 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6792 (mt0) cc_final: 0.6223 (mm-40) REVERT: A 18 ARG cc_start: 0.7509 (mmt-90) cc_final: 0.6917 (mmm160) REVERT: A 77 ARG cc_start: 0.7077 (mtp180) cc_final: 0.6837 (mtp180) REVERT: A 186 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: A 198 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7694 (p) REVERT: A 225 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8315 (mmtp) REVERT: A 237 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7676 (ttp80) REVERT: A 307 ARG cc_start: 0.8441 (mtm110) cc_final: 0.8222 (mtm110) REVERT: A 309 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: B 80 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.7053 (mtm-85) REVERT: B 105 ARG cc_start: 0.7436 (ttm110) cc_final: 0.6701 (mtt-85) REVERT: B 127 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7196 (mm-30) REVERT: B 144 GLU cc_start: 0.7227 (tt0) cc_final: 0.6766 (tm-30) REVERT: B 148 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 169 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.6818 (mmp80) REVERT: B 176 LYS cc_start: 0.8878 (mtmt) cc_final: 0.7962 (mmtp) REVERT: B 204 GLN cc_start: 0.8309 (mt0) cc_final: 0.7998 (mt0) REVERT: B 208 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7642 (ttp-110) REVERT: B 277 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6251 (tm-30) REVERT: B 310 GLU cc_start: 0.7852 (tt0) cc_final: 0.7613 (tm-30) REVERT: B 318 ARG cc_start: 0.8493 (ttp80) cc_final: 0.7428 (ttp-110) REVERT: C 112 GLN cc_start: 0.8284 (mp10) cc_final: 0.7846 (mp10) REVERT: C 141 LYS cc_start: 0.8567 (tttt) cc_final: 0.8292 (tmmt) REVERT: C 193 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8028 (mm-30) REVERT: C 235 GLN cc_start: 0.8179 (tt0) cc_final: 0.7696 (tm130) REVERT: D 94 ASP cc_start: 0.8407 (t70) cc_final: 0.8001 (t0) REVERT: D 102 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7445 (pm20) REVERT: D 141 LYS cc_start: 0.8680 (tptm) cc_final: 0.8396 (tptm) REVERT: D 145 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8293 (mm-30) REVERT: D 176 LYS cc_start: 0.8542 (mtpt) cc_final: 0.7899 (mmtt) REVERT: D 347 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8211 (ttt) REVERT: E 8 ARG cc_start: 0.7834 (ttp80) cc_final: 0.7548 (ttm170) REVERT: E 178 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7823 (mtm110) REVERT: E 184 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: E 206 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7402 (mm-40) REVERT: E 285 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.8305 (mtt-85) REVERT: F 73 ARG cc_start: 0.7932 (tpt-90) cc_final: 0.7606 (tpp-160) REVERT: F 97 MET cc_start: 0.8815 (ttm) cc_final: 0.8404 (ttp) REVERT: F 105 ARG cc_start: 0.7940 (ttp-110) cc_final: 0.7653 (ttp-170) REVERT: F 149 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8377 (mt0) REVERT: F 154 TYR cc_start: 0.8421 (p90) cc_final: 0.7783 (p90) REVERT: F 198 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7128 (pptt) REVERT: F 245 ARG cc_start: 0.6359 (mmp-170) cc_final: 0.5960 (mmp80) REVERT: F 339 MET cc_start: 0.5277 (mmm) cc_final: 0.4938 (mmp) REVERT: G 1 MET cc_start: 0.5070 (ttm) cc_final: 0.3526 (tpt) REVERT: G 48 ASP cc_start: 0.6972 (t0) cc_final: 0.6659 (t0) REVERT: G 50 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6912 (mm-30) REVERT: G 149 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7303 (mt0) REVERT: G 166 GLU cc_start: 0.7716 (tt0) cc_final: 0.7476 (tt0) REVERT: G 198 LYS cc_start: 0.8159 (mttp) cc_final: 0.7329 (mptt) REVERT: G 257 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: G 277 LYS cc_start: 0.8094 (ptpp) cc_final: 0.7478 (ttmm) REVERT: G 282 ARG cc_start: 0.8403 (mtt180) cc_final: 0.7683 (mmt180) REVERT: G 301 GLU cc_start: 0.7586 (tt0) cc_final: 0.7210 (mt-10) REVERT: J 10 GLN cc_start: 0.8615 (tt0) cc_final: 0.8360 (tt0) outliers start: 59 outliers final: 24 residues processed: 354 average time/residue: 0.7507 time to fit residues: 293.7685 Evaluate side-chains 353 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 318 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 298 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 142 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 120 optimal weight: 0.0470 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 175 optimal weight: 8.9990 chunk 77 optimal weight: 0.0670 chunk 70 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN B 112 GLN B 269 ASN C 78 ASN F 191 HIS G 175 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.186095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145914 restraints weight = 19793.497| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.74 r_work: 0.3525 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21300 Z= 0.108 Angle : 0.496 6.365 29114 Z= 0.251 Chirality : 0.037 0.197 3353 Planarity : 0.004 0.047 3618 Dihedral : 14.328 140.582 3357 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.41 % Allowed : 12.94 % Favored : 84.65 % 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: 2.07 (0.17), residues: 2518 helix: 2.19 (0.15), residues: 1257 sheet: 1.29 (0.27), residues: 381 loop : 0.29 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 215 TYR 0.011 0.001 TYR E 47 PHE 0.008 0.001 PHE F 128 TRP 0.012 0.001 TRP D 10 HIS 0.003 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (21284) covalent geometry : angle 0.48178 / 0.25 (29090) hydrogen bonds : bond 0.03139 / 2.12 ( 1132) hydrogen bonds : angle 3.54334 / 2.59 ( 3175) metal coordination : bond 0.00167 / 0.11 ( 16) metal coordination : angle 4.12654 / 2.68 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 331 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6836 (mt0) cc_final: 0.6318 (mm-40) REVERT: A 18 ARG cc_start: 0.7536 (mmt-90) cc_final: 0.6985 (mmm160) REVERT: A 77 ARG cc_start: 0.7087 (mtp180) cc_final: 0.6862 (mtp180) REVERT: A 181 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8700 (tt) REVERT: A 198 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7654 (p) REVERT: A 307 ARG cc_start: 0.8410 (mtm110) cc_final: 0.8136 (mtm110) REVERT: B 80 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.7099 (mtm-85) REVERT: B 105 ARG cc_start: 0.7492 (ttm110) cc_final: 0.6783 (mtt-85) REVERT: B 127 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7100 (mm-30) REVERT: B 144 GLU cc_start: 0.7286 (tt0) cc_final: 0.6854 (tm-30) REVERT: B 148 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7667 (mm-30) REVERT: B 169 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.6682 (mmp80) REVERT: B 176 LYS cc_start: 0.8827 (mtmt) cc_final: 0.7983 (mmtp) REVERT: B 204 GLN cc_start: 0.8297 (mt0) cc_final: 0.8013 (mt0) REVERT: B 208 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7665 (ttp-110) REVERT: B 256 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8426 (ttp) REVERT: B 277 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: B 310 GLU cc_start: 0.7855 (tt0) cc_final: 0.7651 (tm-30) REVERT: B 318 ARG cc_start: 0.8525 (ttp80) cc_final: 0.7480 (ttp-110) REVERT: C 112 GLN cc_start: 0.8266 (mp10) cc_final: 0.7857 (mp10) REVERT: C 193 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8066 (mm-30) REVERT: C 235 GLN cc_start: 0.8209 (tt0) cc_final: 0.7720 (tm130) REVERT: D 94 ASP cc_start: 0.8389 (t70) cc_final: 0.7935 (t0) REVERT: D 102 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7501 (pm20) REVERT: D 141 LYS cc_start: 0.8674 (tptm) cc_final: 0.8417 (tptm) REVERT: D 145 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8310 (mm-30) REVERT: D 176 LYS cc_start: 0.8503 (mtpt) cc_final: 0.7957 (mmtt) REVERT: E 8 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7687 (ttm170) REVERT: E 102 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: E 178 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7889 (mtm110) REVERT: E 206 GLN cc_start: 0.7546 (mm-40) cc_final: 0.7291 (mm-40) REVERT: E 285 ARG cc_start: 0.8537 (mtt-85) cc_final: 0.8326 (mtt-85) REVERT: F 73 ARG cc_start: 0.7972 (tpt-90) cc_final: 0.7619 (tpp-160) REVERT: F 84 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7348 (mt-10) REVERT: F 97 MET cc_start: 0.8800 (ttm) cc_final: 0.8420 (ttp) REVERT: F 105 ARG cc_start: 0.7974 (ttp-110) cc_final: 0.7702 (ttp-170) REVERT: F 154 TYR cc_start: 0.8434 (p90) cc_final: 0.7810 (p90) REVERT: F 198 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7220 (pptt) REVERT: F 205 ARG cc_start: 0.7537 (mtm-85) cc_final: 0.7306 (mtm110) REVERT: F 339 MET cc_start: 0.5237 (mmm) cc_final: 0.4933 (mmt) REVERT: G 1 MET cc_start: 0.5116 (ttm) cc_final: 0.3478 (tpt) REVERT: G 48 ASP cc_start: 0.6893 (t0) cc_final: 0.6628 (t0) REVERT: G 50 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6925 (mm-30) REVERT: G 149 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7302 (mt0) REVERT: G 166 GLU cc_start: 0.7799 (tt0) cc_final: 0.7557 (tt0) REVERT: G 198 LYS cc_start: 0.8116 (mttp) cc_final: 0.7414 (mptt) REVERT: G 250 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7378 (mmtp) REVERT: G 257 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: G 277 LYS cc_start: 0.8043 (ptpp) cc_final: 0.7523 (ttmm) REVERT: G 282 ARG cc_start: 0.8385 (mtt180) cc_final: 0.7715 (mmt180) REVERT: G 301 GLU cc_start: 0.7572 (tt0) cc_final: 0.7260 (mt-10) REVERT: J 10 GLN cc_start: 0.8631 (tt0) cc_final: 0.8394 (tt0) outliers start: 51 outliers final: 21 residues processed: 356 average time/residue: 0.8308 time to fit residues: 326.0555 Evaluate side-chains 344 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 315 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 298 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 195 optimal weight: 0.4980 chunk 183 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN B 110 ASN B 112 GLN B 269 ASN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN F 191 HIS G 175 HIS G 186 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.184278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.143752 restraints weight = 19497.768| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.47 r_work: 0.3510 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21300 Z= 0.158 Angle : 0.543 7.298 29114 Z= 0.272 Chirality : 0.039 0.204 3353 Planarity : 0.004 0.046 3618 Dihedral : 14.457 141.985 3357 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.13 % Allowed : 13.60 % Favored : 84.27 % 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: 1.96 (0.17), residues: 2518 helix: 2.07 (0.15), residues: 1258 sheet: 1.25 (0.26), residues: 383 loop : 0.27 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 215 TYR 0.014 0.002 TYR E 47 PHE 0.011 0.001 PHE F 128 TRP 0.011 0.001 TRP B 10 HIS 0.005 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (21284) covalent geometry : angle 0.53048 / 0.27 (29090) hydrogen bonds : bond 0.03546 / 2.39 ( 1132) hydrogen bonds : angle 3.60436 / 2.63 ( 3175) metal coordination : bond 0.00204 / 0.14 ( 16) metal coordination : angle 4.06439 / 2.66 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 322 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6844 (mt0) cc_final: 0.6297 (mm-40) REVERT: A 18 ARG cc_start: 0.7534 (mmt-90) cc_final: 0.6752 (mtp-110) REVERT: A 77 ARG cc_start: 0.7123 (mtp180) cc_final: 0.6892 (mtp180) REVERT: A 198 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7745 (p) REVERT: A 307 ARG cc_start: 0.8448 (mtm110) cc_final: 0.8210 (mtm110) REVERT: A 309 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: B 80 ARG cc_start: 0.7604 (mtm-85) cc_final: 0.7192 (mtm-85) REVERT: B 105 ARG cc_start: 0.7528 (ttm110) cc_final: 0.6842 (mtt-85) REVERT: B 144 GLU cc_start: 0.7298 (tt0) cc_final: 0.6879 (tm-30) REVERT: B 148 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7663 (mm-30) REVERT: B 169 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.6829 (mmp80) REVERT: B 176 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8000 (mmtp) REVERT: B 204 GLN cc_start: 0.8274 (mt0) cc_final: 0.8017 (mt0) REVERT: B 208 ARG cc_start: 0.8158 (ttm-80) cc_final: 0.7700 (ttp-110) REVERT: B 277 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6245 (tm-30) REVERT: B 318 ARG cc_start: 0.8503 (ttp80) cc_final: 0.7475 (ttp-110) REVERT: C 112 GLN cc_start: 0.8309 (mp10) cc_final: 0.7953 (mp10) REVERT: C 193 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8057 (mm-30) REVERT: C 235 GLN cc_start: 0.8186 (tt0) cc_final: 0.7746 (tm130) REVERT: D 1 MET cc_start: 0.5198 (pp-130) cc_final: 0.4624 (ptm) REVERT: D 94 ASP cc_start: 0.8497 (t70) cc_final: 0.8043 (t0) REVERT: D 102 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7487 (pm20) REVERT: D 141 LYS cc_start: 0.8673 (tptm) cc_final: 0.8415 (tptm) REVERT: D 145 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8346 (mm-30) REVERT: D 176 LYS cc_start: 0.8559 (mtpt) cc_final: 0.7978 (mmtt) REVERT: E 8 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7655 (ttm170) REVERT: E 178 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7856 (mtm110) REVERT: E 285 ARG cc_start: 0.8546 (mtt-85) cc_final: 0.8329 (mtt-85) REVERT: F 73 ARG cc_start: 0.8000 (tpt-90) cc_final: 0.7704 (tpp-160) REVERT: F 84 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7352 (mt-10) REVERT: F 97 MET cc_start: 0.8800 (ttm) cc_final: 0.8432 (ttp) REVERT: F 105 ARG cc_start: 0.7967 (ttp-110) cc_final: 0.7728 (ttp-170) REVERT: F 154 TYR cc_start: 0.8458 (p90) cc_final: 0.7840 (p90) REVERT: F 198 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7252 (pptt) REVERT: F 205 ARG cc_start: 0.7512 (mtm-85) cc_final: 0.7300 (mtm110) REVERT: F 339 MET cc_start: 0.5223 (mmm) cc_final: 0.4908 (mmp) REVERT: G 1 MET cc_start: 0.5104 (ttm) cc_final: 0.3535 (tpt) REVERT: G 48 ASP cc_start: 0.6965 (t0) cc_final: 0.6732 (t0) REVERT: G 50 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6957 (mm-30) REVERT: G 149 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7333 (mt0) REVERT: G 166 GLU cc_start: 0.7795 (tt0) cc_final: 0.7551 (tt0) REVERT: G 186 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: G 198 LYS cc_start: 0.8117 (mttp) cc_final: 0.7458 (mptt) REVERT: G 250 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7400 (mmtp) REVERT: G 257 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: G 277 LYS cc_start: 0.8065 (ptpp) cc_final: 0.7568 (ttmm) REVERT: G 282 ARG cc_start: 0.8375 (mtt180) cc_final: 0.7740 (mmt180) REVERT: G 301 GLU cc_start: 0.7516 (tt0) cc_final: 0.7258 (mt-10) REVERT: J 10 GLN cc_start: 0.8598 (tt0) cc_final: 0.8371 (tt0) outliers start: 45 outliers final: 23 residues processed: 345 average time/residue: 0.8596 time to fit residues: 327.7277 Evaluate side-chains 346 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 316 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 339 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 88 optimal weight: 0.7980 chunk 158 optimal weight: 0.0770 chunk 221 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN B 112 GLN B 269 ASN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 HIS G 175 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.184413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143932 restraints weight = 19642.893| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.47 r_work: 0.3514 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21300 Z= 0.152 Angle : 0.541 7.137 29114 Z= 0.271 Chirality : 0.039 0.203 3353 Planarity : 0.004 0.046 3618 Dihedral : 14.455 141.593 3357 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.98 % Allowed : 13.89 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.17), residues: 2518 helix: 2.06 (0.15), residues: 1258 sheet: 1.23 (0.26), residues: 383 loop : 0.26 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 215 TYR 0.013 0.001 TYR E 47 PHE 0.010 0.001 PHE F 128 TRP 0.011 0.001 TRP B 10 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (21284) covalent geometry : angle 0.52876 / 0.27 (29090) hydrogen bonds : bond 0.03495 / 2.36 ( 1132) hydrogen bonds : angle 3.59767 / 2.63 ( 3175) metal coordination : bond 0.00189 / 0.12 ( 16) metal coordination : angle 4.05916 / 2.66 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 316 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6813 (mt0) cc_final: 0.6265 (mm-40) REVERT: A 18 ARG cc_start: 0.7538 (mmt-90) cc_final: 0.6753 (mtp-110) REVERT: A 77 ARG cc_start: 0.7090 (mtp180) cc_final: 0.6854 (mtp180) REVERT: A 198 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7703 (p) REVERT: A 307 ARG cc_start: 0.8432 (mtm110) cc_final: 0.8200 (mtm110) REVERT: A 309 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: B 80 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7159 (mtm-85) REVERT: B 105 ARG cc_start: 0.7476 (ttm110) cc_final: 0.6813 (mtt-85) REVERT: B 144 GLU cc_start: 0.7268 (tt0) cc_final: 0.6847 (tm-30) REVERT: B 148 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 169 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6701 (mmp80) REVERT: B 176 LYS cc_start: 0.8855 (mtmt) cc_final: 0.7991 (mmtp) REVERT: B 204 GLN cc_start: 0.8261 (mt0) cc_final: 0.8007 (mt0) REVERT: B 208 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7670 (ttp-110) REVERT: B 277 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6227 (tm-30) REVERT: B 318 ARG cc_start: 0.8471 (ttp80) cc_final: 0.7465 (ttp-110) REVERT: C 112 GLN cc_start: 0.8307 (mp10) cc_final: 0.7951 (mp10) REVERT: C 235 GLN cc_start: 0.8166 (tt0) cc_final: 0.7714 (tm130) REVERT: D 1 MET cc_start: 0.5147 (pp-130) cc_final: 0.4579 (ptm) REVERT: D 94 ASP cc_start: 0.8496 (t70) cc_final: 0.7975 (t0) REVERT: D 102 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7484 (pm20) REVERT: D 141 LYS cc_start: 0.8670 (tptm) cc_final: 0.8413 (tptm) REVERT: D 145 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8339 (mm-30) REVERT: D 176 LYS cc_start: 0.8558 (mtpt) cc_final: 0.7978 (mmtt) REVERT: E 8 ARG cc_start: 0.7888 (ttp80) cc_final: 0.7650 (ttm170) REVERT: E 178 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7849 (mtm110) REVERT: E 285 ARG cc_start: 0.8526 (mtt-85) cc_final: 0.8306 (mtt-85) REVERT: F 73 ARG cc_start: 0.7977 (tpt-90) cc_final: 0.7687 (tpp-160) REVERT: F 84 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7373 (mt-10) REVERT: F 97 MET cc_start: 0.8782 (ttm) cc_final: 0.8421 (ttp) REVERT: F 105 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7718 (ttp-170) REVERT: F 154 TYR cc_start: 0.8449 (p90) cc_final: 0.7824 (p90) REVERT: F 198 LYS cc_start: 0.8243 (mtmt) cc_final: 0.7211 (pptt) REVERT: F 339 MET cc_start: 0.5239 (mmm) cc_final: 0.4928 (mmp) REVERT: G 1 MET cc_start: 0.5100 (ttm) cc_final: 0.3528 (tpt) REVERT: G 48 ASP cc_start: 0.6958 (t0) cc_final: 0.6727 (t0) REVERT: G 50 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6911 (mm-30) REVERT: G 149 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7318 (mt0) REVERT: G 166 GLU cc_start: 0.7756 (tt0) cc_final: 0.7512 (tt0) REVERT: G 198 LYS cc_start: 0.8087 (mttp) cc_final: 0.7429 (mptt) REVERT: G 250 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7381 (mmtp) REVERT: G 257 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: G 277 LYS cc_start: 0.8075 (ptpp) cc_final: 0.7546 (ttmm) REVERT: G 282 ARG cc_start: 0.8356 (mtt180) cc_final: 0.7712 (mmt180) REVERT: G 301 GLU cc_start: 0.7503 (tt0) cc_final: 0.7252 (mt-10) REVERT: J 10 GLN cc_start: 0.8590 (tt0) cc_final: 0.8354 (tt0) outliers start: 42 outliers final: 25 residues processed: 341 average time/residue: 0.8481 time to fit residues: 319.8289 Evaluate side-chains 342 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 311 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 339 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 68 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 194 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN B 110 ASN B 112 GLN B 269 ASN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.186154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145473 restraints weight = 19716.106| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.60 r_work: 0.3528 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21300 Z= 0.111 Angle : 0.507 6.717 29114 Z= 0.256 Chirality : 0.037 0.195 3353 Planarity : 0.004 0.048 3618 Dihedral : 14.311 140.703 3357 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.65 % Allowed : 14.60 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.17), residues: 2518 helix: 2.22 (0.15), residues: 1259 sheet: 1.33 (0.26), residues: 386 loop : 0.32 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 205 TYR 0.013 0.001 TYR E 47 PHE 0.009 0.001 PHE F 128 TRP 0.014 0.001 TRP D 10 HIS 0.003 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (21284) covalent geometry : angle 0.49350 / 0.26 (29090) hydrogen bonds : bond 0.03108 / 2.10 ( 1132) hydrogen bonds : angle 3.51649 / 2.57 ( 3175) metal coordination : bond 0.00198 / 0.15 ( 16) metal coordination : angle 4.05727 / 2.66 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 319 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6847 (mt0) cc_final: 0.6226 (mm-40) REVERT: A 18 ARG cc_start: 0.7546 (mmt-90) cc_final: 0.6772 (mtp-110) REVERT: A 77 ARG cc_start: 0.7098 (mtp180) cc_final: 0.6878 (mtp180) REVERT: A 181 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8716 (tt) REVERT: A 198 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7642 (p) REVERT: A 307 ARG cc_start: 0.8429 (mtm110) cc_final: 0.8181 (mtm110) REVERT: B 80 ARG cc_start: 0.7497 (mtm-85) cc_final: 0.6982 (mtm-85) REVERT: B 84 GLN cc_start: 0.7748 (mt0) cc_final: 0.7290 (mm110) REVERT: B 105 ARG cc_start: 0.7560 (ttm110) cc_final: 0.6861 (mtt-85) REVERT: B 144 GLU cc_start: 0.7285 (tt0) cc_final: 0.6854 (tm-30) REVERT: B 148 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7650 (mm-30) REVERT: B 169 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.6660 (mmp80) REVERT: B 176 LYS cc_start: 0.8815 (mtmt) cc_final: 0.7981 (mmtp) REVERT: B 204 GLN cc_start: 0.8269 (mt0) cc_final: 0.8022 (mt0) REVERT: B 208 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7676 (ttp-110) REVERT: B 277 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: B 318 ARG cc_start: 0.8513 (ttp80) cc_final: 0.7487 (ttp-110) REVERT: C 112 GLN cc_start: 0.8308 (mp10) cc_final: 0.7895 (mp10) REVERT: C 235 GLN cc_start: 0.8198 (tt0) cc_final: 0.7729 (tm130) REVERT: C 258 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7035 (pt0) REVERT: D 1 MET cc_start: 0.4993 (pp-130) cc_final: 0.4354 (ptm) REVERT: D 102 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7521 (pm20) REVERT: D 141 LYS cc_start: 0.8659 (tptm) cc_final: 0.8401 (tptm) REVERT: D 145 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8324 (mm-30) REVERT: D 176 LYS cc_start: 0.8534 (mtpt) cc_final: 0.7976 (mmtt) REVERT: E 8 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7647 (ttm170) REVERT: E 178 ARG cc_start: 0.8105 (mtm-85) cc_final: 0.7894 (mtm110) REVERT: E 285 ARG cc_start: 0.8540 (mtt-85) cc_final: 0.8326 (mtt-85) REVERT: F 73 ARG cc_start: 0.7997 (tpt-90) cc_final: 0.7641 (tpp-160) REVERT: F 84 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7352 (mt-10) REVERT: F 97 MET cc_start: 0.8806 (ttm) cc_final: 0.8464 (ttp) REVERT: F 105 ARG cc_start: 0.7968 (ttp-110) cc_final: 0.7696 (ttp-170) REVERT: F 154 TYR cc_start: 0.8438 (p90) cc_final: 0.7816 (p90) REVERT: F 198 LYS cc_start: 0.8264 (mtmt) cc_final: 0.7204 (pptt) REVERT: F 339 MET cc_start: 0.5270 (mmm) cc_final: 0.4964 (mmp) REVERT: G 1 MET cc_start: 0.5108 (ttm) cc_final: 0.3468 (tpt) REVERT: G 50 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6911 (mm-30) REVERT: G 149 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7312 (mt0) REVERT: G 166 GLU cc_start: 0.7813 (tt0) cc_final: 0.7547 (tt0) REVERT: G 198 LYS cc_start: 0.8121 (mttp) cc_final: 0.7436 (mptt) REVERT: G 250 LYS cc_start: 0.8056 (mtpt) cc_final: 0.7436 (mmtp) REVERT: G 257 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: G 277 LYS cc_start: 0.8022 (ptpp) cc_final: 0.7522 (ttmm) REVERT: G 282 ARG cc_start: 0.8358 (mtt180) cc_final: 0.7710 (mmt180) REVERT: G 301 GLU cc_start: 0.7526 (tt0) cc_final: 0.7206 (mt-10) REVERT: J 10 GLN cc_start: 0.8594 (tt0) cc_final: 0.8330 (tt0) outliers start: 35 outliers final: 20 residues processed: 341 average time/residue: 0.8449 time to fit residues: 318.3802 Evaluate side-chains 337 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 311 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 298 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 224 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN B 112 GLN B 269 ASN C 129 HIS D 110 ASN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.185726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.144952 restraints weight = 19604.547| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.60 r_work: 0.3525 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21300 Z= 0.117 Angle : 0.515 6.817 29114 Z= 0.261 Chirality : 0.037 0.193 3353 Planarity : 0.004 0.046 3618 Dihedral : 14.317 141.113 3357 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.42 % Allowed : 15.21 % Favored : 83.37 % 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: 2.13 (0.17), residues: 2518 helix: 2.23 (0.15), residues: 1260 sheet: 1.34 (0.26), residues: 386 loop : 0.31 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 205 TYR 0.012 0.001 TYR E 47 PHE 0.009 0.001 PHE F 128 TRP 0.011 0.001 TRP D 10 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (21284) covalent geometry : angle 0.50171 / 0.26 (29090) hydrogen bonds : bond 0.03128 / 2.12 ( 1132) hydrogen bonds : angle 3.50014 / 2.56 ( 3175) metal coordination : bond 0.00161 / 0.11 ( 16) metal coordination : angle 4.03030 / 2.60 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9326.23 seconds wall clock time: 159 minutes 4.23 seconds (9544.23 seconds total)