Starting phenix.real_space_refine on Fri Jun 5 13:50:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyk_71024/06_2026/9oyk_71024.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyk_71024/06_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_71024/06_2026/9oyk_71024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyk_71024/06_2026/9oyk_71024.map" model { file = "/net/cci-nas-00/data/ceres_data/9oyk_71024/06_2026/9oyk_71024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyk_71024/06_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-dev-6079/lib/python3.9/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: 4.72, per 1000 atoms: 0.23 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: 1.36 Conformation dependent library (CDL) restraints added in 988.8 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: 2.51 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: 3.94 Time building geometry restraints manager: 1.92 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=" N PRO E 332 " pdb=" CA PRO E 332 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.20e-02 6.94e+03 7.61e+00 bond pdb=" N HIS E 333 " pdb=" CA HIS E 333 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.32e-02 5.74e+03 6.60e+00 bond pdb=" C VAL E 331 " pdb=" N PRO E 332 " ideal model delta sigma weight residual 1.331 1.360 -0.029 1.20e-02 6.94e+03 5.88e+00 bond pdb=" N PRO E 332 " pdb=" CD PRO E 332 " ideal model delta sigma weight residual 1.473 1.503 -0.030 1.40e-02 5.10e+03 4.55e+00 bond pdb=" P DG H 44 " pdb=" OP2 DG H 44 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.80e+00 ... (remaining 21279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 28713 2.26 - 4.53: 336 4.53 - 6.79: 35 6.79 - 9.05: 5 9.05 - 11.31: 1 Bond angle restraints: 29090 Sorted by residual: angle pdb=" CA GLY C 45 " pdb=" C GLY C 45 " pdb=" N THR C 46 " ideal model delta sigma weight residual 114.23 117.61 -3.38 8.80e-01 1.29e+00 1.48e+01 angle pdb=" O3A AGS C 702 " pdb=" PA AGS C 702 " pdb=" O5' AGS C 702 " ideal model delta sigma weight residual 104.35 115.66 -11.31 3.00e+00 1.11e-01 1.42e+01 angle pdb=" N ILE F 184 " pdb=" CA ILE F 184 " pdb=" C ILE F 184 " ideal model delta sigma weight residual 113.20 109.86 3.34 9.60e-01 1.09e+00 1.21e+01 angle pdb=" O3' DT I 4 " pdb=" P DC I 5 " pdb=" O5' DC I 5 " ideal model delta sigma weight residual 104.00 99.16 4.84 1.50e+00 4.44e-01 1.04e+01 angle pdb=" C ASP G 48 " pdb=" N LEU G 49 " pdb=" CA LEU G 49 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 ... (remaining 29085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.49: 12296 29.49 - 58.99: 532 58.99 - 88.48: 34 88.48 - 117.97: 3 117.97 - 147.47: 3 Dihedral angle restraints: 12868 sinusoidal: 5527 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=" O1A AGS B 702 " pdb=" O3A AGS B 702 " pdb=" PA AGS B 702 " pdb=" PB AGS B 702 " ideal model delta sinusoidal sigma weight residual -67.73 79.74 -147.47 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" O1A AGS D 702 " pdb=" O3A AGS D 702 " pdb=" PA AGS D 702 " pdb=" PB AGS D 702 " ideal model delta sinusoidal sigma weight residual -67.73 74.64 -142.37 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 12865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 3295 0.109 - 0.219: 57 0.219 - 0.328: 1 0.328 - 0.438: 0 0.438 - 0.547: 6 Chirality restraints: 3359 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 2.35 -2.89 -0.55 2.00e-01 2.50e+01 7.48e+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 2.35 -2.87 -0.53 2.00e-01 2.50e+01 6.99e+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 2.35 -2.87 -0.53 2.00e-01 2.50e+01 6.90e+00 ... (remaining 3356 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.750 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 0.043 21300 Z= 0.210 Angle : 0.622 11.314 29114 Z= 0.308 Chirality : 0.047 0.547 3359 Planarity : 0.004 0.043 3618 Dihedral : 15.432 147.468 8104 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 0.00485 / 0.21 (21284) covalent geometry : angle 0.60957 / 0.31 (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 : 0.805 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: 0.8885 time to fit residues: 458.7037 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 : 0.789 ------------------------------------------------------------------------------- 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: 4.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 186 GLN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.183645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.143159 restraints weight = 19688.681| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.60 r_work: 0.3477 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21300 Z= 0.196 Angle : 0.595 10.109 29114 Z= 0.295 Chirality : 0.041 0.244 3359 Planarity : 0.004 0.047 3618 Dihedral : 14.105 146.187 3303 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.46 % Allowed : 8.93 % Favored : 88.62 % 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: 1258 sheet: 1.23 (0.25), residues: 409 loop : 0.23 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 47 TYR 0.012 0.002 TYR B 341 PHE 0.011 0.002 PHE F 128 TRP 0.013 0.002 TRP B 10 HIS 0.005 0.001 HIS D 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (21284) covalent geometry : angle 0.58032 / 0.29 (29090) hydrogen bonds : bond 0.04278 / 2.89 ( 1132) hydrogen bonds : angle 4.02166 / 2.92 ( 3175) metal coordination : bond 0.00328 / 0.20 ( 16) metal coordination : angle 4.57706 / 2.97 ( 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 404 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 352 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6811 (mt0) cc_final: 0.6311 (mm-40) REVERT: A 77 ARG cc_start: 0.7190 (mtp180) cc_final: 0.6941 (mtp180) REVERT: A 237 ARG cc_start: 0.8086 (ttm170) cc_final: 0.7794 (ttp80) REVERT: A 280 GLN cc_start: 0.8181 (tp40) cc_final: 0.7974 (mm-40) REVERT: A 288 GLU cc_start: 0.7571 (tt0) cc_final: 0.7288 (mm-30) REVERT: A 309 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8016 (tm-30) REVERT: A 325 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: B 80 ARG cc_start: 0.7609 (mtm-85) cc_final: 0.6981 (mtm-85) REVERT: B 105 ARG cc_start: 0.7559 (ttm110) cc_final: 0.6937 (mtt-85) REVERT: B 127 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7222 (mm-30) REVERT: B 144 GLU cc_start: 0.7299 (tt0) cc_final: 0.6850 (tm-30) REVERT: B 148 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7734 (mm-30) REVERT: B 169 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7105 (mmp80) REVERT: B 176 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8075 (mmtm) REVERT: B 208 ARG cc_start: 0.8189 (ttm-80) cc_final: 0.7723 (ttp-110) REVERT: B 310 GLU cc_start: 0.7960 (tt0) cc_final: 0.7742 (tm-30) REVERT: B 318 ARG cc_start: 0.8495 (ttp80) cc_final: 0.7416 (ttp-110) REVERT: C 77 ASP cc_start: 0.7970 (m-30) cc_final: 0.7636 (m-30) REVERT: C 98 ARG cc_start: 0.7882 (mtp180) cc_final: 0.7653 (mtp180) REVERT: C 112 GLN cc_start: 0.8335 (mp10) cc_final: 0.7960 (mp10) REVERT: C 141 LYS cc_start: 0.8595 (tttt) cc_final: 0.8371 (tmmt) REVERT: C 193 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8103 (mm-30) REVERT: C 235 GLN cc_start: 0.8209 (tt0) cc_final: 0.7718 (tm130) REVERT: D 102 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7480 (pm20) REVERT: D 141 LYS cc_start: 0.8775 (tptm) cc_final: 0.8509 (tptp) REVERT: D 145 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8381 (mm-30) REVERT: D 176 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8032 (mmtt) REVERT: D 318 ARG cc_start: 0.8308 (ttp-110) cc_final: 0.8098 (ttp-110) REVERT: E 8 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7618 (tpm170) REVERT: E 178 ARG cc_start: 0.8104 (mtm-85) cc_final: 0.7865 (mtm110) REVERT: E 211 GLN cc_start: 0.8336 (tp-100) cc_final: 0.7769 (mp10) REVERT: E 285 ARG cc_start: 0.8582 (mtt-85) cc_final: 0.8359 (mtt-85) REVERT: F 73 ARG cc_start: 0.8078 (tpt-90) cc_final: 0.7704 (tpp-160) REVERT: F 97 MET cc_start: 0.8803 (ttm) cc_final: 0.8451 (ttp) REVERT: F 105 ARG cc_start: 0.8088 (ttp-110) cc_final: 0.7816 (ttp-170) REVERT: F 136 LYS cc_start: 0.7943 (tttm) cc_final: 0.7701 (tttm) REVERT: F 154 TYR cc_start: 0.8479 (p90) cc_final: 0.7911 (p90) REVERT: F 322 SER cc_start: 0.7533 (t) cc_final: 0.7243 (m) REVERT: F 339 MET cc_start: 0.5217 (OUTLIER) cc_final: 0.4943 (mmm) REVERT: G 1 MET cc_start: 0.5303 (ttm) cc_final: 0.3620 (tpt) REVERT: G 48 ASP cc_start: 0.7257 (t0) cc_final: 0.6912 (t0) REVERT: G 50 GLU cc_start: 0.7564 (mt-10) cc_final: 0.6991 (mm-30) REVERT: G 149 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7331 (mt0) REVERT: G 166 GLU cc_start: 0.7837 (tt0) cc_final: 0.7494 (tt0) REVERT: G 186 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: G 198 LYS cc_start: 0.8159 (mttp) cc_final: 0.7409 (mptt) REVERT: G 215 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7490 (ttm110) REVERT: G 257 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: G 277 LYS cc_start: 0.8124 (ptpp) cc_final: 0.7524 (ttmm) REVERT: G 282 ARG cc_start: 0.8453 (mtt90) cc_final: 0.7931 (mtp85) REVERT: G 301 GLU cc_start: 0.7696 (tt0) cc_final: 0.7303 (mt-10) REVERT: J 10 GLN cc_start: 0.8663 (tt0) cc_final: 0.8369 (tt0) outliers start: 52 outliers final: 16 residues processed: 375 average time/residue: 0.8514 time to fit residues: 350.8863 Evaluate side-chains 354 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 330 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 GLU 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 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 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 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 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 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: 8.9990 chunk 128 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 232 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 157 optimal weight: 0.3980 chunk 47 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 291 ASN B 112 GLN B 330 GLN C 78 ASN E 52 GLN E 206 GLN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.180144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.138582 restraints weight = 19762.310| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.64 r_work: 0.3443 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21300 Z= 0.151 Angle : 0.542 8.402 29114 Z= 0.269 Chirality : 0.038 0.193 3359 Planarity : 0.004 0.048 3618 Dihedral : 14.037 142.765 3303 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.36 % Allowed : 10.58 % Favored : 87.06 % 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: 1.80 (0.17), residues: 2518 helix: 1.88 (0.15), residues: 1257 sheet: 1.25 (0.25), residues: 401 loop : 0.24 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 245 TYR 0.019 0.001 TYR E 47 PHE 0.010 0.001 PHE F 128 TRP 0.013 0.001 TRP B 10 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (21284) covalent geometry : angle 0.52784 / 0.27 (29090) hydrogen bonds : bond 0.03758 / 2.54 ( 1132) hydrogen bonds : angle 3.77509 / 2.76 ( 3175) metal coordination : bond 0.00226 / 0.14 ( 16) metal coordination : angle 4.26452 / 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 395 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 345 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6742 (mt0) cc_final: 0.6224 (mm-40) REVERT: A 77 ARG cc_start: 0.7067 (mtp180) cc_final: 0.6822 (mtp180) REVERT: A 198 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7670 (p) REVERT: A 237 ARG cc_start: 0.8083 (ttm170) cc_final: 0.7680 (ttp80) REVERT: A 280 GLN cc_start: 0.8018 (tp40) cc_final: 0.7799 (mm-40) REVERT: A 288 GLU cc_start: 0.7399 (tt0) cc_final: 0.7131 (mm-30) REVERT: A 309 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8085 (tm-30) REVERT: A 325 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: B 80 ARG cc_start: 0.7520 (mtm-85) cc_final: 0.7016 (mtm-85) REVERT: B 105 ARG cc_start: 0.7414 (ttm110) cc_final: 0.6717 (mtt-85) REVERT: B 127 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7165 (mm-30) REVERT: B 144 GLU cc_start: 0.7194 (tt0) cc_final: 0.6715 (tm-30) REVERT: B 148 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 169 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.6819 (mmp80) REVERT: B 176 LYS cc_start: 0.8867 (mtmt) cc_final: 0.7939 (mmtp) REVERT: B 201 ARG cc_start: 0.8119 (tmt-80) cc_final: 0.7525 (tpm170) REVERT: B 208 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7563 (ttp-110) REVERT: B 277 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6343 (tm-30) REVERT: B 310 GLU cc_start: 0.7834 (tt0) cc_final: 0.7571 (tm-30) REVERT: B 318 ARG cc_start: 0.8446 (ttp80) cc_final: 0.7366 (ttp-110) REVERT: C 98 ARG cc_start: 0.7879 (mtp180) cc_final: 0.7669 (mtp180) REVERT: C 112 GLN cc_start: 0.8281 (mp10) cc_final: 0.7891 (mp10) REVERT: C 141 LYS cc_start: 0.8541 (tttt) cc_final: 0.8290 (tmmt) REVERT: C 193 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8027 (mm-30) REVERT: C 235 GLN cc_start: 0.8164 (tt0) cc_final: 0.7656 (tm130) REVERT: D 94 ASP cc_start: 0.8351 (t0) cc_final: 0.8149 (t0) REVERT: D 102 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7369 (pm20) REVERT: D 141 LYS cc_start: 0.8680 (tptm) cc_final: 0.8377 (tptp) REVERT: D 145 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8282 (mm-30) REVERT: D 176 LYS cc_start: 0.8514 (mtpt) cc_final: 0.7906 (mmtt) REVERT: E 8 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7546 (ttm170) REVERT: E 178 ARG cc_start: 0.8086 (mtm-85) cc_final: 0.7832 (mtm110) REVERT: E 253 MET cc_start: 0.8776 (tpp) cc_final: 0.8575 (ttm) REVERT: E 285 ARG cc_start: 0.8515 (mtt-85) cc_final: 0.8289 (mtt-85) REVERT: F 73 ARG cc_start: 0.7909 (tpt-90) cc_final: 0.7554 (tpp-160) REVERT: F 97 MET cc_start: 0.8786 (ttm) cc_final: 0.8393 (ttp) REVERT: F 105 ARG cc_start: 0.7935 (ttp-110) cc_final: 0.7645 (ttp-170) REVERT: F 154 TYR cc_start: 0.8406 (p90) cc_final: 0.7817 (p90) REVERT: F 322 SER cc_start: 0.7467 (t) cc_final: 0.7155 (m) REVERT: G 1 MET cc_start: 0.5247 (ttm) cc_final: 0.3587 (tpt) REVERT: G 48 ASP cc_start: 0.7093 (t0) cc_final: 0.6703 (t0) REVERT: G 50 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6885 (mm-30) REVERT: G 82 LEU cc_start: -0.0281 (OUTLIER) cc_final: -0.0495 (tp) REVERT: G 149 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7276 (mt0) REVERT: G 166 GLU cc_start: 0.7633 (tt0) cc_final: 0.7404 (tt0) REVERT: G 198 LYS cc_start: 0.8127 (mttp) cc_final: 0.7227 (mptt) REVERT: G 215 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7262 (ttm110) REVERT: G 257 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: G 277 LYS cc_start: 0.8090 (ptpp) cc_final: 0.7407 (ttmm) REVERT: G 282 ARG cc_start: 0.8397 (mtt180) cc_final: 0.7789 (mtp85) REVERT: G 301 GLU cc_start: 0.7620 (tt0) cc_final: 0.7159 (mt-10) REVERT: J 10 GLN cc_start: 0.8601 (tt0) cc_final: 0.8340 (tt0) outliers start: 50 outliers final: 13 residues processed: 368 average time/residue: 0.8503 time to fit residues: 344.3825 Evaluate side-chains 344 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 322 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 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 148 GLU 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 E residue 102 GLU Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 82 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 179 optimal weight: 0.4980 chunk 244 optimal weight: 9.9990 chunk 238 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 234 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 263 GLN A 291 ASN B 110 ASN B 112 GLN B 269 ASN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.178903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137577 restraints weight = 19658.753| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.49 r_work: 0.3457 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21300 Z= 0.190 Angle : 0.576 10.101 29114 Z= 0.284 Chirality : 0.040 0.242 3359 Planarity : 0.004 0.048 3618 Dihedral : 14.094 144.433 3303 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.40 % Allowed : 10.82 % Favored : 85.78 % 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: 1.69 (0.17), residues: 2518 helix: 1.79 (0.15), residues: 1257 sheet: 1.38 (0.26), residues: 384 loop : 0.11 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 47 TYR 0.016 0.002 TYR E 47 PHE 0.011 0.001 PHE F 128 TRP 0.013 0.001 TRP B 10 HIS 0.005 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (21284) covalent geometry : angle 0.56221 / 0.28 (29090) hydrogen bonds : bond 0.03943 / 2.66 ( 1132) hydrogen bonds : angle 3.75394 / 2.74 ( 3175) metal coordination : bond 0.00253 / 0.15 ( 16) metal coordination : angle 4.35109 / 2.84 ( 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 406 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 334 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6835 (mt0) cc_final: 0.6299 (mm-40) REVERT: A 77 ARG cc_start: 0.7088 (mtp180) cc_final: 0.6824 (mtp180) REVERT: A 186 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: A 198 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7744 (p) REVERT: A 237 ARG cc_start: 0.8146 (ttm170) cc_final: 0.7733 (ttp80) REVERT: A 280 GLN cc_start: 0.8066 (tp40) cc_final: 0.7841 (mm-40) REVERT: A 307 ARG cc_start: 0.8452 (mtm110) cc_final: 0.8222 (mtm110) REVERT: A 309 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: A 325 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: B 80 ARG cc_start: 0.7547 (mtm-85) cc_final: 0.7095 (mtm-85) REVERT: B 105 ARG cc_start: 0.7498 (ttm110) cc_final: 0.6752 (mtt-85) REVERT: B 127 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7183 (mm-30) REVERT: B 144 GLU cc_start: 0.7226 (tt0) cc_final: 0.6765 (tm-30) REVERT: B 148 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7612 (mm-30) REVERT: B 169 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.6738 (mmp80) REVERT: B 176 LYS cc_start: 0.8890 (mtmt) cc_final: 0.8011 (mmtm) REVERT: B 204 GLN cc_start: 0.8272 (mt0) cc_final: 0.7979 (mt0) REVERT: B 208 ARG cc_start: 0.8086 (ttm-80) cc_final: 0.7658 (ttp-110) REVERT: B 277 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6392 (tm-30) REVERT: B 310 GLU cc_start: 0.7870 (tt0) cc_final: 0.7627 (tm-30) REVERT: B 318 ARG cc_start: 0.8478 (ttp80) cc_final: 0.7475 (ttm110) REVERT: C 98 ARG cc_start: 0.7869 (mtp180) cc_final: 0.7663 (mtp180) REVERT: C 112 GLN cc_start: 0.8310 (mp10) cc_final: 0.7939 (mp10) REVERT: C 141 LYS cc_start: 0.8559 (tttt) cc_final: 0.8316 (tmmt) REVERT: C 193 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8025 (mm-30) REVERT: C 235 GLN cc_start: 0.8165 (tt0) cc_final: 0.7683 (tm130) REVERT: C 367 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: D 94 ASP cc_start: 0.8346 (t0) cc_final: 0.8007 (t0) REVERT: D 102 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7467 (pm20) REVERT: D 141 LYS cc_start: 0.8696 (tptm) cc_final: 0.8405 (tptp) REVERT: D 145 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8296 (mm-30) REVERT: D 176 LYS cc_start: 0.8577 (mtpt) cc_final: 0.7965 (mmtt) REVERT: D 347 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8283 (ttt) REVERT: E 8 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7548 (tpm170) REVERT: E 178 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7838 (mtm110) REVERT: E 184 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: E 253 MET cc_start: 0.8779 (tpp) cc_final: 0.8572 (ttm) REVERT: E 285 ARG cc_start: 0.8543 (mtt-85) cc_final: 0.8314 (mtt-85) REVERT: F 2 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8240 (ttmm) REVERT: F 73 ARG cc_start: 0.7939 (tpt-90) cc_final: 0.7610 (tpp-160) REVERT: F 97 MET cc_start: 0.8843 (ttm) cc_final: 0.8414 (ttp) REVERT: F 105 ARG cc_start: 0.7929 (ttp-110) cc_final: 0.7675 (ttp-170) REVERT: F 149 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8487 (mt0) REVERT: F 154 TYR cc_start: 0.8433 (p90) cc_final: 0.7791 (p90) REVERT: F 198 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7133 (pptt) REVERT: F 322 SER cc_start: 0.7470 (t) cc_final: 0.7116 (m) REVERT: F 339 MET cc_start: 0.5073 (mmm) cc_final: 0.4841 (mmt) REVERT: G 1 MET cc_start: 0.5153 (ttm) cc_final: 0.3500 (tpt) REVERT: G 48 ASP cc_start: 0.7112 (t0) cc_final: 0.6819 (t0) REVERT: G 50 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6888 (mm-30) REVERT: G 149 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7338 (mt0) REVERT: G 166 GLU cc_start: 0.7681 (tt0) cc_final: 0.7460 (tt0) REVERT: G 198 LYS cc_start: 0.8172 (mttp) cc_final: 0.7321 (mptt) REVERT: G 215 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7372 (ttm110) REVERT: G 257 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: G 277 LYS cc_start: 0.8100 (ptpp) cc_final: 0.7446 (ttmm) REVERT: G 282 ARG cc_start: 0.8363 (mtt180) cc_final: 0.7840 (mtp85) REVERT: G 301 GLU cc_start: 0.7593 (tt0) cc_final: 0.7209 (mt-10) REVERT: J 10 GLN cc_start: 0.8629 (tt0) cc_final: 0.8324 (tt0) outliers start: 72 outliers final: 25 residues processed: 373 average time/residue: 0.8479 time to fit residues: 348.7254 Evaluate side-chains 365 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 325 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 309 GLU Chi-restraints excluded: chain A residue 325 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 46 THR 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 C residue 367 GLU 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 2 LYS Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 198 LYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 80 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 245 optimal weight: 10.0000 chunk 114 optimal weight: 0.0470 chunk 34 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 291 ASN B 112 GLN B 269 ASN C 78 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 = 0.4066 r_free = 0.4066 target = 0.182081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.140678 restraints weight = 19615.863| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.66 r_work: 0.3461 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21300 Z= 0.106 Angle : 0.490 6.894 29114 Z= 0.245 Chirality : 0.037 0.135 3359 Planarity : 0.004 0.048 3618 Dihedral : 13.949 140.028 3303 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.50 % Allowed : 12.00 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.17), residues: 2518 helix: 2.10 (0.15), residues: 1264 sheet: 1.43 (0.26), residues: 386 loop : 0.25 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 215 TYR 0.010 0.001 TYR E 47 PHE 0.009 0.001 PHE F 128 TRP 0.013 0.001 TRP B 10 HIS 0.003 0.001 HIS G 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (21284) covalent geometry : angle 0.47482 / 0.24 (29090) hydrogen bonds : bond 0.03100 / 2.10 ( 1132) hydrogen bonds : angle 3.55201 / 2.60 ( 3175) metal coordination : bond 0.00188 / 0.12 ( 16) metal coordination : angle 4.18413 / 2.71 ( 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 401 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 348 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6817 (mt0) cc_final: 0.6256 (mm-40) REVERT: A 77 ARG cc_start: 0.7009 (mtp180) cc_final: 0.6777 (mtp180) REVERT: A 181 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8686 (tt) REVERT: A 198 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7628 (p) REVERT: A 237 ARG cc_start: 0.8058 (ttm170) cc_final: 0.7648 (ttp80) REVERT: A 239 GLU cc_start: 0.7137 (tt0) cc_final: 0.6809 (pt0) REVERT: A 307 ARG cc_start: 0.8406 (mtm110) cc_final: 0.8144 (mtm110) REVERT: A 309 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: A 325 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: B 80 ARG cc_start: 0.7454 (mtm-85) cc_final: 0.7021 (mtm-85) REVERT: B 105 ARG cc_start: 0.7398 (ttm110) cc_final: 0.6684 (mtt-85) REVERT: B 127 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7116 (mm-30) REVERT: B 144 GLU cc_start: 0.7215 (tt0) cc_final: 0.6759 (tm-30) REVERT: B 148 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 169 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.6687 (mmp80) REVERT: B 176 LYS cc_start: 0.8852 (mtmt) cc_final: 0.7953 (mmtp) REVERT: B 204 GLN cc_start: 0.8228 (mt0) cc_final: 0.7946 (mt0) REVERT: B 208 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.7625 (ttp-110) REVERT: B 277 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6298 (tm-30) REVERT: B 310 GLU cc_start: 0.7816 (tt0) cc_final: 0.7596 (tm-30) REVERT: B 318 ARG cc_start: 0.8507 (ttp80) cc_final: 0.7445 (ttp-110) REVERT: C 112 GLN cc_start: 0.8246 (mp10) cc_final: 0.7810 (mp10) REVERT: C 141 LYS cc_start: 0.8500 (tttt) cc_final: 0.8281 (tmmt) REVERT: C 193 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8008 (mm-30) REVERT: C 235 GLN cc_start: 0.8182 (tt0) cc_final: 0.7679 (tm130) REVERT: C 367 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: D 94 ASP cc_start: 0.8315 (t0) cc_final: 0.7860 (t0) REVERT: D 102 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7446 (pm20) REVERT: D 141 LYS cc_start: 0.8635 (tptm) cc_final: 0.8347 (tptm) REVERT: D 145 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8258 (mm-30) REVERT: D 176 LYS cc_start: 0.8491 (mtpt) cc_final: 0.7892 (mmtt) REVERT: D 344 ASP cc_start: 0.8245 (p0) cc_final: 0.8025 (p0) REVERT: D 347 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8144 (ttt) REVERT: E 8 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7597 (ttm170) REVERT: E 178 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7861 (mtm110) REVERT: E 285 ARG cc_start: 0.8499 (mtt-85) cc_final: 0.8281 (mtt-85) REVERT: F 73 ARG cc_start: 0.7935 (tpt-90) cc_final: 0.7583 (tpp-160) REVERT: F 97 MET cc_start: 0.8820 (ttm) cc_final: 0.8418 (ttp) REVERT: F 105 ARG cc_start: 0.7928 (ttp-110) cc_final: 0.7660 (ttp-170) REVERT: F 149 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8319 (mt0) REVERT: F 154 TYR cc_start: 0.8427 (p90) cc_final: 0.7794 (p90) REVERT: F 198 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7053 (pptt) REVERT: F 339 MET cc_start: 0.5051 (mmm) cc_final: 0.4820 (mmt) REVERT: G 1 MET cc_start: 0.5161 (ttm) cc_final: 0.3461 (tpt) REVERT: G 48 ASP cc_start: 0.6877 (t0) cc_final: 0.6605 (t0) REVERT: G 50 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6894 (mm-30) REVERT: G 149 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7294 (mt0) REVERT: G 166 GLU cc_start: 0.7731 (tt0) cc_final: 0.7461 (tt0) REVERT: G 198 LYS cc_start: 0.8188 (mttp) cc_final: 0.7333 (mptt) REVERT: G 250 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7362 (mmtp) REVERT: G 257 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: G 277 LYS cc_start: 0.8044 (ptpp) cc_final: 0.7440 (ttmm) REVERT: G 282 ARG cc_start: 0.8366 (mtt180) cc_final: 0.7843 (mtp85) REVERT: G 301 GLU cc_start: 0.7583 (tt0) cc_final: 0.7235 (mt-10) REVERT: J 10 GLN cc_start: 0.8617 (tt0) cc_final: 0.8375 (tt0) outliers start: 53 outliers final: 13 residues processed: 366 average time/residue: 0.8919 time to fit residues: 357.9512 Evaluate side-chains 348 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 323 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 A residue 325 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 46 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 367 GLU 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 220 LEU Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 298 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 250 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 chunk 202 optimal weight: 20.0000 chunk 75 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 263 GLN B 110 ASN B 112 GLN B 269 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.179916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138389 restraints weight = 19638.864| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.62 r_work: 0.3430 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21300 Z= 0.164 Angle : 0.540 8.747 29114 Z= 0.267 Chirality : 0.039 0.211 3359 Planarity : 0.004 0.047 3618 Dihedral : 14.015 141.490 3303 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.79 % Allowed : 12.85 % Favored : 84.36 % 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: 2.01 (0.15), residues: 1259 sheet: 1.42 (0.26), residues: 386 loop : 0.23 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 215 TYR 0.014 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 D 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (21284) covalent geometry : angle 0.52715 / 0.27 (29090) hydrogen bonds : bond 0.03547 / 2.40 ( 1132) hydrogen bonds : angle 3.60082 / 2.63 ( 3175) metal coordination : bond 0.00227 / 0.15 ( 16) metal coordination : angle 4.11744 / 2.70 ( 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 385 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 326 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6849 (mt0) cc_final: 0.6268 (mm-40) REVERT: A 77 ARG cc_start: 0.7055 (mtp180) cc_final: 0.6810 (mtp180) REVERT: A 181 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8740 (tt) REVERT: A 198 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7665 (p) REVERT: A 237 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7678 (ttp80) REVERT: A 307 ARG cc_start: 0.8455 (mtm110) cc_final: 0.8225 (mtm110) REVERT: A 309 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: A 325 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: B 80 ARG cc_start: 0.7540 (mtm-85) cc_final: 0.7099 (mtm-85) REVERT: B 105 ARG cc_start: 0.7474 (ttm110) cc_final: 0.6755 (mtt-85) REVERT: B 127 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7186 (mm-30) REVERT: B 144 GLU cc_start: 0.7247 (tt0) cc_final: 0.6779 (tm-30) REVERT: B 148 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 169 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.6668 (mmp80) REVERT: B 176 LYS cc_start: 0.8867 (mtmt) cc_final: 0.7967 (mmtp) REVERT: B 204 GLN cc_start: 0.8239 (mt0) cc_final: 0.7972 (mt0) REVERT: B 208 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7659 (ttp-110) REVERT: B 277 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6327 (tm-30) REVERT: B 310 GLU cc_start: 0.7850 (tt0) cc_final: 0.7638 (tm-30) REVERT: B 318 ARG cc_start: 0.8483 (ttp80) cc_final: 0.7489 (ttm110) REVERT: C 112 GLN cc_start: 0.8324 (mp10) cc_final: 0.7889 (mp10) REVERT: C 193 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8035 (mm-30) REVERT: C 235 GLN cc_start: 0.8205 (tt0) cc_final: 0.7717 (tm130) REVERT: D 94 ASP cc_start: 0.8361 (t0) cc_final: 0.7891 (t0) REVERT: D 102 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7450 (pm20) REVERT: D 141 LYS cc_start: 0.8649 (tptm) cc_final: 0.8365 (tptm) REVERT: D 145 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8309 (mm-30) REVERT: D 176 LYS cc_start: 0.8537 (mtpt) cc_final: 0.7916 (mmtt) REVERT: D 347 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8133 (ttt) REVERT: E 8 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7570 (ttm170) REVERT: E 178 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7820 (mtm110) REVERT: E 285 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.8309 (mtt-85) REVERT: F 73 ARG cc_start: 0.7989 (tpt-90) cc_final: 0.7662 (tpp-160) REVERT: F 97 MET cc_start: 0.8828 (ttm) cc_final: 0.8440 (ttp) REVERT: F 105 ARG cc_start: 0.7952 (ttp-110) cc_final: 0.7661 (ttp-170) REVERT: F 149 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8357 (mt0) REVERT: F 154 TYR cc_start: 0.8444 (p90) cc_final: 0.7803 (p90) REVERT: F 198 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7130 (pptt) REVERT: F 339 MET cc_start: 0.5125 (mmm) cc_final: 0.4836 (mmt) REVERT: G 1 MET cc_start: 0.5124 (ttm) cc_final: 0.3520 (tpt) REVERT: G 48 ASP cc_start: 0.7001 (t0) cc_final: 0.6754 (t0) REVERT: G 50 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6922 (mm-30) REVERT: G 149 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7300 (mt0) REVERT: G 166 GLU cc_start: 0.7769 (tt0) cc_final: 0.7537 (tt0) REVERT: G 198 LYS cc_start: 0.8207 (mttp) cc_final: 0.7356 (mptt) REVERT: G 202 GLU cc_start: 0.7635 (tp30) cc_final: 0.7428 (mm-30) REVERT: G 250 LYS cc_start: 0.8110 (mtpt) cc_final: 0.7360 (mmtp) REVERT: G 257 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: G 277 LYS cc_start: 0.8087 (ptpp) cc_final: 0.7470 (ttmm) REVERT: G 282 ARG cc_start: 0.8402 (mtt180) cc_final: 0.7856 (mtp85) REVERT: G 301 GLU cc_start: 0.7542 (tt0) cc_final: 0.7173 (mt-10) REVERT: J 10 GLN cc_start: 0.8615 (tt0) cc_final: 0.8359 (tt0) outliers start: 59 outliers final: 21 residues processed: 357 average time/residue: 0.8662 time to fit residues: 339.7980 Evaluate side-chains 349 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 318 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 A residue 325 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 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 131 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 142 optimal weight: 0.5980 chunk 47 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 175 optimal weight: 8.9990 chunk 77 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN B 269 ASN C 129 HIS ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 HIS G 175 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.181591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140595 restraints weight = 19742.388| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.72 r_work: 0.3463 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21300 Z= 0.113 Angle : 0.495 6.798 29114 Z= 0.248 Chirality : 0.037 0.145 3359 Planarity : 0.004 0.047 3618 Dihedral : 13.940 140.571 3303 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.17 % Allowed : 13.75 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.17), residues: 2518 helix: 2.17 (0.15), residues: 1260 sheet: 1.45 (0.26), residues: 386 loop : 0.31 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 205 TYR 0.011 0.001 TYR E 47 PHE 0.009 0.001 PHE F 128 TRP 0.012 0.001 TRP D 10 HIS 0.003 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (21284) covalent geometry : angle 0.48154 / 0.25 (29090) hydrogen bonds : bond 0.03087 / 2.09 ( 1132) hydrogen bonds : angle 3.50865 / 2.57 ( 3175) metal coordination : bond 0.00188 / 0.13 ( 16) metal coordination : angle 4.07592 / 2.65 ( 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 375 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 329 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6793 (mt0) cc_final: 0.6174 (mm-40) REVERT: A 77 ARG cc_start: 0.7015 (mtp180) cc_final: 0.6789 (mtp180) REVERT: A 181 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8709 (tt) REVERT: A 198 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7614 (p) REVERT: A 239 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6860 (pt0) REVERT: A 307 ARG cc_start: 0.8419 (mtm110) cc_final: 0.8187 (mtm110) REVERT: A 325 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: B 80 ARG cc_start: 0.7420 (mtm-85) cc_final: 0.6969 (mtm-85) REVERT: B 105 ARG cc_start: 0.7426 (ttm110) cc_final: 0.6687 (mtt-85) REVERT: B 127 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7135 (mm-30) REVERT: B 144 GLU cc_start: 0.7230 (tt0) cc_final: 0.6769 (tm-30) REVERT: B 148 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7595 (mm-30) REVERT: B 169 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.6658 (mmp80) REVERT: B 176 LYS cc_start: 0.8822 (mtmt) cc_final: 0.7948 (mmtp) REVERT: B 204 GLN cc_start: 0.8192 (mt0) cc_final: 0.7945 (mt0) REVERT: B 208 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7621 (ttp-110) REVERT: B 277 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6263 (tm-30) REVERT: B 310 GLU cc_start: 0.7797 (tt0) cc_final: 0.7572 (tm-30) REVERT: B 318 ARG cc_start: 0.8509 (ttp80) cc_final: 0.7444 (ttp-110) REVERT: C 112 GLN cc_start: 0.8261 (mp10) cc_final: 0.7826 (mp10) REVERT: C 193 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8037 (mm-30) REVERT: C 235 GLN cc_start: 0.8157 (tt0) cc_final: 0.7667 (tm130) REVERT: D 1 MET cc_start: 0.5021 (pp-130) cc_final: 0.4362 (ptm) REVERT: D 94 ASP cc_start: 0.8327 (t0) cc_final: 0.7973 (t0) REVERT: D 102 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7468 (pm20) REVERT: D 141 LYS cc_start: 0.8638 (tptm) cc_final: 0.8354 (tptm) REVERT: D 145 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8253 (mm-30) REVERT: D 176 LYS cc_start: 0.8504 (mtpt) cc_final: 0.7923 (mmtt) REVERT: D 347 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8104 (ttt) REVERT: E 8 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7610 (ttm170) REVERT: E 178 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.7822 (mtm110) REVERT: E 285 ARG cc_start: 0.8490 (mtt-85) cc_final: 0.8273 (mtt-85) REVERT: F 73 ARG cc_start: 0.7955 (tpt-90) cc_final: 0.7601 (tpp-160) REVERT: F 97 MET cc_start: 0.8814 (ttm) cc_final: 0.8436 (ttp) REVERT: F 105 ARG cc_start: 0.7900 (ttp-110) cc_final: 0.7635 (ttp-170) REVERT: F 154 TYR cc_start: 0.8419 (p90) cc_final: 0.7780 (p90) REVERT: F 339 MET cc_start: 0.5194 (mmm) cc_final: 0.4863 (mmp) REVERT: G 1 MET cc_start: 0.5095 (ttm) cc_final: 0.3458 (tpt) REVERT: G 48 ASP cc_start: 0.6852 (t0) cc_final: 0.6648 (t0) REVERT: G 50 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6851 (mm-30) REVERT: G 149 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7277 (mt0) REVERT: G 166 GLU cc_start: 0.7698 (tt0) cc_final: 0.7443 (tt0) REVERT: G 184 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6972 (mm) REVERT: G 198 LYS cc_start: 0.8184 (mttp) cc_final: 0.7338 (mptt) REVERT: G 250 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7424 (mmtp) REVERT: G 257 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: G 277 LYS cc_start: 0.8029 (ptpp) cc_final: 0.7465 (ttmm) REVERT: G 282 ARG cc_start: 0.8385 (mtt180) cc_final: 0.7844 (mtp85) REVERT: G 301 GLU cc_start: 0.7517 (tt0) cc_final: 0.7183 (mt-10) REVERT: J 10 GLN cc_start: 0.8602 (tt0) cc_final: 0.8335 (tt0) outliers start: 46 outliers final: 20 residues processed: 354 average time/residue: 0.8457 time to fit residues: 330.6087 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 : 0.965 ------------------------------------------------------------------------------- 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 239 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 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 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 131 THR Chi-restraints excluded: chain E residue 292 ASP 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 184 ILE 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: 0.6980 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN B 110 ASN B 112 GLN B 269 ASN C 78 ASN D 110 ASN E 61 HIS E 267 ASN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 HIS G 175 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.182030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.140907 restraints weight = 19468.080| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.60 r_work: 0.3478 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21300 Z= 0.112 Angle : 0.497 6.654 29114 Z= 0.248 Chirality : 0.037 0.152 3359 Planarity : 0.004 0.050 3618 Dihedral : 13.901 141.030 3303 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.27 % Allowed : 13.75 % Favored : 83.99 % 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: 2.19 (0.17), residues: 2518 helix: 2.24 (0.15), residues: 1261 sheet: 1.48 (0.26), residues: 386 loop : 0.33 (0.22), residues: 871 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 0.005 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (21284) covalent geometry : angle 0.48356 / 0.25 (29090) hydrogen bonds : bond 0.03017 / 2.04 ( 1132) hydrogen bonds : angle 3.46332 / 2.54 ( 3175) metal coordination : bond 0.00155 / 0.11 ( 16) metal coordination : angle 3.95604 / 2.60 ( 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 373 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 325 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6856 (mt0) cc_final: 0.6126 (mm-40) REVERT: A 77 ARG cc_start: 0.6996 (mtp180) cc_final: 0.6765 (mtp180) REVERT: A 181 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8691 (tt) REVERT: A 198 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7468 (p) REVERT: A 239 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6800 (pt0) REVERT: A 307 ARG cc_start: 0.8421 (mtm110) cc_final: 0.8167 (mtm110) REVERT: A 325 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: B 80 ARG cc_start: 0.7373 (mtm-85) cc_final: 0.6901 (mtm-85) REVERT: B 84 GLN cc_start: 0.7645 (mt0) cc_final: 0.7168 (mm110) REVERT: B 105 ARG cc_start: 0.7343 (ttm110) cc_final: 0.6625 (mtt-85) REVERT: B 127 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7134 (mm-30) REVERT: B 144 GLU cc_start: 0.7218 (tt0) cc_final: 0.6755 (tm-30) REVERT: B 148 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7566 (mm-30) REVERT: B 169 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.6601 (mmp80) REVERT: B 176 LYS cc_start: 0.8787 (mtmt) cc_final: 0.7888 (mmtp) REVERT: B 204 GLN cc_start: 0.8179 (mt0) cc_final: 0.7936 (mt0) REVERT: B 208 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7587 (ttp-110) REVERT: B 277 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6160 (tm-30) REVERT: B 310 GLU cc_start: 0.7812 (tt0) cc_final: 0.7551 (tm-30) REVERT: B 318 ARG cc_start: 0.8480 (ttp80) cc_final: 0.7388 (ttp-110) REVERT: C 112 GLN cc_start: 0.8273 (mp10) cc_final: 0.7826 (mp10) REVERT: C 193 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8003 (mm-30) REVERT: C 235 GLN cc_start: 0.8165 (tt0) cc_final: 0.7661 (tm130) REVERT: C 258 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7008 (pt0) REVERT: D 1 MET cc_start: 0.4875 (pp-130) cc_final: 0.4129 (ptm) REVERT: D 94 ASP cc_start: 0.8329 (t0) cc_final: 0.7872 (t0) REVERT: D 102 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7351 (pm20) REVERT: D 141 LYS cc_start: 0.8623 (tptm) cc_final: 0.8328 (tptm) REVERT: D 145 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8246 (mm-30) REVERT: D 176 LYS cc_start: 0.8511 (mtpt) cc_final: 0.7878 (mmtt) REVERT: D 347 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8087 (ttt) REVERT: E 8 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7559 (ttm170) REVERT: E 178 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7854 (mtm110) REVERT: E 285 ARG cc_start: 0.8486 (mtt-85) cc_final: 0.8267 (mtt-85) REVERT: F 73 ARG cc_start: 0.7951 (tpt-90) cc_final: 0.7611 (tpp-160) REVERT: F 97 MET cc_start: 0.8789 (ttm) cc_final: 0.8425 (ttp) REVERT: F 105 ARG cc_start: 0.7906 (ttp-110) cc_final: 0.7607 (ttp-170) REVERT: F 136 LYS cc_start: 0.7838 (tptp) cc_final: 0.7606 (tttm) REVERT: F 154 TYR cc_start: 0.8421 (p90) cc_final: 0.7776 (p90) REVERT: F 198 LYS cc_start: 0.8153 (mtmt) cc_final: 0.7005 (pptt) REVERT: F 245 ARG cc_start: 0.6322 (mmp-170) cc_final: 0.6115 (mmp80) REVERT: F 339 MET cc_start: 0.5169 (mmm) cc_final: 0.4859 (mmp) REVERT: G 1 MET cc_start: 0.5106 (ttm) cc_final: 0.3440 (tpt) REVERT: G 50 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6833 (mm-30) REVERT: G 127 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7108 (tm-30) REVERT: G 149 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7258 (mt0) REVERT: G 166 GLU cc_start: 0.7698 (tt0) cc_final: 0.7439 (tt0) REVERT: G 198 LYS cc_start: 0.8164 (mttp) cc_final: 0.7322 (mptt) REVERT: G 250 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7415 (mmtp) REVERT: G 257 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: G 277 LYS cc_start: 0.8012 (ptpp) cc_final: 0.7446 (ttmm) REVERT: G 282 ARG cc_start: 0.8393 (mtt180) cc_final: 0.7805 (mtp85) REVERT: G 301 GLU cc_start: 0.7504 (tt0) cc_final: 0.7145 (mt-10) REVERT: J 10 GLN cc_start: 0.8586 (tt0) cc_final: 0.8335 (tt0) outliers start: 48 outliers final: 24 residues processed: 349 average time/residue: 0.8579 time to fit residues: 330.3830 Evaluate side-chains 345 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 312 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 239 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 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 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 252 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain D residue 77 ASP 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 D residue 347 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 88 optimal weight: 2.9990 chunk 158 optimal weight: 0.0060 chunk 221 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN B 112 GLN B 269 ASN C 129 HIS E 267 ASN F 191 HIS G 175 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.185775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145737 restraints weight = 19646.106| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.60 r_work: 0.3502 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21300 Z= 0.129 Angle : 0.520 7.109 29114 Z= 0.261 Chirality : 0.037 0.163 3359 Planarity : 0.004 0.060 3618 Dihedral : 13.931 141.298 3303 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.08 % Allowed : 14.41 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.17), residues: 2518 helix: 2.19 (0.15), residues: 1261 sheet: 1.48 (0.26), residues: 386 loop : 0.34 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG F 205 TYR 0.013 0.001 TYR E 47 PHE 0.009 0.001 PHE F 128 TRP 0.010 0.001 TRP B 10 HIS 0.003 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (21284) covalent geometry : angle 0.50761 / 0.26 (29090) hydrogen bonds : bond 0.03155 / 2.13 ( 1132) hydrogen bonds : angle 3.48511 / 2.55 ( 3175) metal coordination : bond 0.00172 / 0.12 ( 16) metal coordination : angle 3.98652 / 2.60 ( 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 372 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 328 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6921 (mt0) cc_final: 0.6240 (mm-40) REVERT: A 18 ARG cc_start: 0.7944 (mmm160) cc_final: 0.7478 (mtp-110) REVERT: A 77 ARG cc_start: 0.7103 (mtp180) cc_final: 0.6877 (mtp180) REVERT: A 181 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8764 (tt) REVERT: A 239 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6823 (pt0) REVERT: A 307 ARG cc_start: 0.8486 (mtm110) cc_final: 0.8239 (mtm110) REVERT: A 325 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: B 80 ARG cc_start: 0.7536 (mtm-85) cc_final: 0.7046 (mtm-85) REVERT: B 84 GLN cc_start: 0.7729 (mt0) cc_final: 0.7277 (mm110) REVERT: B 105 ARG cc_start: 0.7585 (ttm110) cc_final: 0.6941 (mtt-85) REVERT: B 127 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7182 (mm-30) REVERT: B 144 GLU cc_start: 0.7320 (tt0) cc_final: 0.6887 (tm-30) REVERT: B 148 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7668 (mm-30) REVERT: B 169 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.6622 (mmp80) REVERT: B 176 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8001 (mmtp) REVERT: B 201 ARG cc_start: 0.8134 (tmt-80) cc_final: 0.7647 (tpm170) REVERT: B 208 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7727 (ttp-110) REVERT: B 277 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6351 (tm-30) REVERT: B 310 GLU cc_start: 0.7921 (tt0) cc_final: 0.7707 (tm-30) REVERT: B 318 ARG cc_start: 0.8521 (ttp80) cc_final: 0.7475 (ttp-110) REVERT: C 112 GLN cc_start: 0.8341 (mp10) cc_final: 0.7927 (mp10) REVERT: C 235 GLN cc_start: 0.8226 (tt0) cc_final: 0.7741 (tm130) REVERT: C 258 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7248 (pt0) REVERT: D 1 MET cc_start: 0.5045 (pp-130) cc_final: 0.4325 (ptm) REVERT: D 94 ASP cc_start: 0.8392 (t0) cc_final: 0.8045 (t0) REVERT: D 102 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7506 (pm20) REVERT: D 141 LYS cc_start: 0.8727 (tptm) cc_final: 0.8456 (tptm) REVERT: D 145 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8353 (mm-30) REVERT: D 176 LYS cc_start: 0.8570 (mtpt) cc_final: 0.7997 (mmtt) REVERT: E 8 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7660 (ttm170) REVERT: E 285 ARG cc_start: 0.8564 (mtt-85) cc_final: 0.8352 (mtt-85) REVERT: F 73 ARG cc_start: 0.8060 (tpt-90) cc_final: 0.7720 (tpp-160) REVERT: F 97 MET cc_start: 0.8806 (ttm) cc_final: 0.8512 (ttp) REVERT: F 105 ARG cc_start: 0.8017 (ttp-110) cc_final: 0.7767 (ttp-170) REVERT: F 154 TYR cc_start: 0.8481 (p90) cc_final: 0.7862 (p90) REVERT: F 198 LYS cc_start: 0.8277 (mtmt) cc_final: 0.7175 (pptt) REVERT: F 245 ARG cc_start: 0.6421 (mmp-170) cc_final: 0.6182 (mmp80) REVERT: F 326 ASP cc_start: 0.6478 (m-30) cc_final: 0.5994 (m-30) REVERT: F 339 MET cc_start: 0.5295 (mmm) cc_final: 0.4889 (mmt) REVERT: G 1 MET cc_start: 0.5157 (ttm) cc_final: 0.3480 (tpt) REVERT: G 50 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7015 (mm-30) REVERT: G 149 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7340 (mt0) REVERT: G 166 GLU cc_start: 0.7856 (tt0) cc_final: 0.7581 (tt0) REVERT: G 198 LYS cc_start: 0.8144 (mttp) cc_final: 0.7459 (mptt) REVERT: G 250 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7456 (mmtp) REVERT: G 257 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: G 277 LYS cc_start: 0.8024 (ptpp) cc_final: 0.7559 (ttmm) REVERT: G 282 ARG cc_start: 0.8431 (mtt180) cc_final: 0.7933 (mtp85) REVERT: G 301 GLU cc_start: 0.7551 (tt0) cc_final: 0.7243 (mt-10) REVERT: J 10 GLN cc_start: 0.8651 (tt0) cc_final: 0.8435 (tt0) outliers start: 44 outliers final: 27 residues processed: 353 average time/residue: 0.8545 time to fit residues: 331.1731 Evaluate side-chains 356 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 322 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 239 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 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 B residue 337 LYS Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 311 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 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 2 LYS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 51 MET 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 68 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 226 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 263 GLN B 110 ASN B 112 GLN B 269 ASN C 129 HIS E 267 ASN F 191 HIS G 175 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.185992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.145949 restraints weight = 19672.145| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.60 r_work: 0.3511 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21300 Z= 0.122 Angle : 0.514 7.271 29114 Z= 0.258 Chirality : 0.037 0.156 3359 Planarity : 0.004 0.053 3618 Dihedral : 13.926 141.166 3303 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.84 % Allowed : 15.02 % Favored : 83.14 % 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: 2.16 (0.17), residues: 2518 helix: 2.21 (0.15), residues: 1262 sheet: 1.38 (0.26), residues: 383 loop : 0.38 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 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 0.004 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (21284) covalent geometry : angle 0.50116 / 0.26 (29090) hydrogen bonds : bond 0.03097 / 2.09 ( 1132) hydrogen bonds : angle 3.47256 / 2.54 ( 3175) metal coordination : bond 0.00166 / 0.12 ( 16) metal coordination : angle 3.97368 / 2.59 ( 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 372 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 333 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6911 (mt0) cc_final: 0.6199 (mm-40) REVERT: A 18 ARG cc_start: 0.7947 (mmm160) cc_final: 0.7484 (mtp-110) REVERT: A 77 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6873 (mtp180) REVERT: A 181 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8753 (tt) REVERT: A 239 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6792 (pt0) REVERT: A 307 ARG cc_start: 0.8468 (mtm110) cc_final: 0.8209 (mtm110) REVERT: A 325 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: B 80 ARG cc_start: 0.7522 (mtm-85) cc_final: 0.7040 (mtm-85) REVERT: B 84 GLN cc_start: 0.7710 (mt0) cc_final: 0.7252 (mm110) REVERT: B 105 ARG cc_start: 0.7558 (ttm110) cc_final: 0.6927 (mtt-85) REVERT: B 127 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7166 (mm-30) REVERT: B 144 GLU cc_start: 0.7316 (tt0) cc_final: 0.6881 (tm-30) REVERT: B 148 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7655 (mm-30) REVERT: B 169 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.6610 (mmp80) REVERT: B 176 LYS cc_start: 0.8817 (mtmt) cc_final: 0.7972 (mmtp) REVERT: B 204 GLN cc_start: 0.8312 (mt0) cc_final: 0.8054 (mt0) REVERT: B 208 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.7707 (ttp-110) REVERT: B 277 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6311 (tm-30) REVERT: B 310 GLU cc_start: 0.7898 (tt0) cc_final: 0.7661 (tm-30) REVERT: B 318 ARG cc_start: 0.8506 (ttp80) cc_final: 0.7464 (ttp-110) REVERT: C 112 GLN cc_start: 0.8321 (mp10) cc_final: 0.7967 (mp10) REVERT: C 235 GLN cc_start: 0.8209 (tt0) cc_final: 0.7726 (tm130) REVERT: C 258 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7236 (pt0) REVERT: D 1 MET cc_start: 0.4838 (pp-130) cc_final: 0.4209 (ptm) REVERT: D 94 ASP cc_start: 0.8378 (t0) cc_final: 0.7931 (t0) REVERT: D 102 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7495 (pm20) REVERT: D 141 LYS cc_start: 0.8702 (tptm) cc_final: 0.8435 (tptm) REVERT: D 145 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8333 (mm-30) REVERT: D 176 LYS cc_start: 0.8554 (mtpt) cc_final: 0.7986 (mmtt) REVERT: D 274 ARG cc_start: 0.7825 (ttm-80) cc_final: 0.7298 (mtm-85) REVERT: E 8 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7677 (ttm170) REVERT: E 285 ARG cc_start: 0.8547 (mtt-85) cc_final: 0.8329 (mtt-85) REVERT: F 73 ARG cc_start: 0.8044 (tpt-90) cc_final: 0.7691 (tpp-160) REVERT: F 97 MET cc_start: 0.8777 (ttm) cc_final: 0.8498 (ttp) REVERT: F 105 ARG cc_start: 0.8019 (ttp-110) cc_final: 0.7752 (ttp-170) REVERT: F 154 TYR cc_start: 0.8472 (p90) cc_final: 0.7851 (p90) REVERT: F 198 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7211 (pptt) REVERT: F 326 ASP cc_start: 0.6501 (m-30) cc_final: 0.6016 (m-30) REVERT: F 339 MET cc_start: 0.5307 (mmm) cc_final: 0.4904 (mmt) REVERT: G 1 MET cc_start: 0.5126 (ttm) cc_final: 0.3449 (tpt) REVERT: G 50 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6986 (mm-30) REVERT: G 149 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7329 (mt0) REVERT: G 166 GLU cc_start: 0.7825 (tt0) cc_final: 0.7577 (tt0) REVERT: G 198 LYS cc_start: 0.8153 (mttp) cc_final: 0.7449 (mptt) REVERT: G 250 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7462 (mmtp) REVERT: G 257 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: G 277 LYS cc_start: 0.8055 (ptpp) cc_final: 0.7602 (ttmm) REVERT: G 282 ARG cc_start: 0.8415 (mtt180) cc_final: 0.7913 (mtp85) REVERT: G 301 GLU cc_start: 0.7531 (tt0) cc_final: 0.7235 (mt-10) REVERT: J 10 GLN cc_start: 0.8615 (tt0) cc_final: 0.8345 (tt0) outliers start: 39 outliers final: 28 residues processed: 355 average time/residue: 0.8168 time to fit residues: 318.7584 Evaluate side-chains 356 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 321 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 239 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 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 B residue 337 LYS Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain D residue 77 ASP 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 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 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 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 224 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 232 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 201 optimal weight: 0.1980 chunk 29 optimal weight: 5.9990 chunk 166 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN B 112 GLN B 269 ASN D 110 ASN E 267 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.187201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.147063 restraints weight = 19647.703| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.48 r_work: 0.3553 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2036 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= 0.106 Angle : 0.496 7.539 29114 Z= 0.249 Chirality : 0.036 0.145 3359 Planarity : 0.004 0.068 3618 Dihedral : 13.859 140.873 3303 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.70 % Allowed : 15.16 % Favored : 83.14 % 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: 2.23 (0.17), residues: 2518 helix: 2.24 (0.15), residues: 1274 sheet: 1.39 (0.27), residues: 383 loop : 0.43 (0.23), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG F 205 TYR 0.011 0.001 TYR E 47 PHE 0.009 0.001 PHE F 128 TRP 0.012 0.001 TRP D 10 HIS 0.002 0.000 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (21284) covalent geometry : angle 0.48336 / 0.25 (29090) hydrogen bonds : bond 0.02878 / 1.94 ( 1132) hydrogen bonds : angle 3.41996 / 2.51 ( 3175) metal coordination : bond 0.00171 / 0.13 ( 16) metal coordination : angle 3.89989 / 2.53 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9726.86 seconds wall clock time: 165 minutes 40.48 seconds (9940.48 seconds total)