Starting phenix.real_space_refine on Sat Jul 4 13:50:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyi_71022/07_2026/9oyi_71022.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyi_71022/07_2026/9oyi_71022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oyi_71022/07_2026/9oyi_71022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyi_71022/07_2026/9oyi_71022.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oyi_71022/07_2026/9oyi_71022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyi_71022/07_2026/9oyi_71022.map" } resolution = 2.54 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 111 5.16 5 C 12924 2.51 5 N 3719 2.21 5 O 3978 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-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20794 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: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2840 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 16, 'TRANS': 348} Chain: "C" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2865 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "D" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2799 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "E" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2602 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "F" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2835 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 20, 'TRANS': 344} Chain: "G" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2844 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 345} Chain: "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: "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: "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 78.600 86.850 113.331 1.00 41.17 S ATOM 3269 SG CYS B 73 82.327 86.070 113.496 1.00 58.73 S ATOM 3286 SG CYS B 76 80.128 83.913 115.137 1.00 68.96 S ATOM 3308 SG CYS B 79 80.034 84.127 111.100 1.00 42.99 S ATOM 6049 SG CYS C 64 101.021 56.986 85.464 1.00 33.44 S ATOM 6109 SG CYS C 73 102.567 54.470 83.654 1.00 37.76 S ATOM 6126 SG CYS C 76 99.334 53.213 85.846 1.00 36.42 S ATOM 6148 SG CYS C 79 98.922 55.356 82.979 1.00 42.82 S ATOM 8914 SG CYS D 64 78.529 30.110 54.808 1.00 35.71 S ATOM 8974 SG CYS D 73 76.498 27.553 52.933 1.00 44.68 S ATOM 8991 SG CYS D 76 75.434 28.170 56.484 1.00 39.70 S ATOM 9013 SG CYS D 79 74.923 30.879 54.097 1.00 30.75 S ATOM 11637 SG CYS E 50 32.778 34.883 48.101 1.00 35.73 S ATOM 11706 SG CYS E 59 29.237 33.770 48.856 1.00 49.11 S ATOM 11726 SG CYS E 62 31.652 33.861 51.732 1.00 44.87 S ATOM 11747 SG CYS E 65 30.705 37.105 50.202 1.00 41.44 S Time building chain proxies: 4.86, per 1000 atoms: 0.23 Number of scatterers: 20794 At special positions: 0 Unit cell: (113.436, 125.028, 149.04, 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 111 16.00 P 55 15.00 Mg 3 11.99 O 3978 8.00 N 3719 7.00 C 12924 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: 1.96 Conformation dependent library (CDL) restraints added in 877.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 64 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 76 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 79 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 76 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 79 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 64 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 73 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 79 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 73 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 76 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 64 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 65 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 59 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 62 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " Number of angles added : 24 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 14 sheets defined 56.0% alpha, 15.0% beta 17 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 8 through 15 removed outlier: 3.746A pdb=" N GLN A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 45 Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.507A pdb=" N ILE A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.878A pdb=" N GLN A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 124 through 130 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 204 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: 3.654A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 253 " --> pdb=" O THR A 249 " (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 315 Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.650A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.617A pdb=" N VAL B 18 " --> pdb=" O PHE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 removed outlier: 4.145A pdb=" N ALA B 27 " --> pdb=" O HIS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 64 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 100 through 110 removed outlier: 3.923A pdb=" N ASN B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 132 through 145 removed outlier: 4.239A 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 163 through 169 removed outlier: 3.664A pdb=" N LEU B 167 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 169 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 195 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.926A pdb=" N GLU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 229 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 260 through 274 Processing helix chain 'B' and resid 277 through 298 Processing helix chain 'B' and resid 299 through 302 removed outlier: 3.620A pdb=" N LEU B 302 " --> pdb=" O PRO B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 321 through 339 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 344 through 358 Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.572A pdb=" N VAL C 18 " --> pdb=" O PHE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 35 Processing helix chain 'C' and resid 50 through 64 Processing helix chain 'C' and resid 76 through 84 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 145 removed outlier: 4.746A pdb=" N LYS C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 163 through 169 removed outlier: 3.726A pdb=" N ARG C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 195 Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.996A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 245 through 259 Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 277 through 298 Processing helix chain 'C' and resid 299 through 302 removed outlier: 4.038A 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: 3.748A 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 35 Processing helix chain 'D' and resid 50 through 64 Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 132 through 145 removed outlier: 4.722A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N THR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 163 through 170 removed outlier: 3.588A pdb=" N ARG D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 195 Processing helix chain 'D' and resid 199 through 211 removed outlier: 3.816A pdb=" N GLU D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 245 through 259 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: 3.894A 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 Processing helix chain 'D' and resid 309 through 320 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: 3.656A pdb=" N ALA D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 20 removed outlier: 4.709A pdb=" N ASP E 10 " --> pdb=" O TRP E 6 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER E 17 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR E 18 " --> pdb=" O LEU E 14 " (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 Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 121 through 134 removed outlier: 3.613A pdb=" N LEU E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 152 through 159 removed outlier: 3.640A pdb=" N ARG E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 178 removed outlier: 3.618A 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 204 Processing helix chain 'E' and resid 208 through 227 Proline residue: E 225 - end of helix Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 240 through 260 Processing helix chain 'E' and resid 270 through 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: 4.495A 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 143 removed outlier: 3.786A pdb=" N THR F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 146 No H-bonds generated for 'chain 'F' and resid 144 through 146' Processing helix chain 'F' and resid 152 through 156 Processing helix chain 'F' and resid 196 through 207 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.675A pdb=" N LEU F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 332 Processing helix chain 'G' and resid 7 through 18 removed outlier: 3.634A pdb=" N LYS G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) Proline residue: G 13 - end of helix Processing helix chain 'G' and resid 29 through 33 removed outlier: 4.316A pdb=" N LEU G 33 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 81 Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.597A pdb=" N THR G 142 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 4.775A 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 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: 6.420A pdb=" N ILE A 2 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N THR A 138 " --> pdb=" O ILE A 2 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU A 4 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ARG A 77 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU A 49 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.420A pdb=" N GLU A 161 " --> pdb=" O LEU A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.162A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA B 40 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N PHE B 173 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 42 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU B 175 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER B 44 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AA5, first strand: chain 'C' and resid 90 through 94 removed outlier: 6.259A pdb=" N LYS C 121 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU C 153 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TYR C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA C 155 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE C 125 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR C 41 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR C 156 " --> pdb=" O TYR C 41 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE C 43 " --> pdb=" O THR C 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 90 through 94 removed outlier: 6.209A pdb=" N LYS D 121 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU D 153 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA D 155 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE D 125 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR D 41 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N THR D 156 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N PHE D 43 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA D 40 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 7.824A 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) Processing sheet with id=AA7, first strand: chain 'E' and resid 76 through 79 removed outlier: 6.463A pdb=" N LYS E 110 " --> pdb=" O TRP E 140 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N PHE E 142 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL E 112 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ALA E 144 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL E 114 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.672A pdb=" N ASN G 295 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY G 280 " --> pdb=" O ASN G 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.550A pdb=" N ASN F 32 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N THR F 47 " --> pdb=" O ASN F 32 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR F 41 " --> pdb=" O ALA F 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 309 through 310 removed outlier: 15.666A pdb=" N SER F 181 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 15.779A pdb=" N THR F 172 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 14.479A pdb=" N VAL F 170 " --> pdb=" O PRO F 183 " (cutoff:3.500A) removed outlier: 13.773A pdb=" N GLY F 185 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N ARG F 168 " --> pdb=" O GLY F 185 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N SER F 187 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N GLU F 166 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLY F 164 " --> pdb=" O PRO F 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 303 through 307 removed outlier: 3.873A pdb=" N MET F 315 " --> pdb=" O VAL F 285 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 2 through 6 Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 68 Processing sheet with id=AB5, first strand: chain 'G' and resid 254 through 259 removed outlier: 4.555A pdb=" N ASP G 351 " --> pdb=" O ALA G 357 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ALA G 357 " --> pdb=" O ASP G 351 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLU G 165 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 9.153A pdb=" N GLN G 186 " --> pdb=" O GLU G 163 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLU G 163 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N LEU G 188 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N GLU G 161 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 13.544A pdb=" N SER G 190 " --> pdb=" O LEU G 159 " (cutoff:3.500A) removed outlier: 14.199A pdb=" N LEU G 159 " --> pdb=" O SER G 190 " (cutoff:3.500A) removed outlier: 13.444A pdb=" N SER G 192 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 13.096A pdb=" N GLY G 157 " --> pdb=" O SER G 192 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7129 1.36 - 1.51: 5810 1.51 - 1.65: 8136 1.65 - 1.80: 116 1.80 - 1.95: 68 Bond restraints: 21259 Sorted by residual: bond pdb=" O2G AGS B 702 " pdb=" PG AGS B 702 " ideal model delta sigma weight residual 1.604 1.499 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" O3B AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sigma weight residual 1.673 1.575 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" O3A AGS D 702 " pdb=" PA AGS D 702 " ideal model delta sigma weight residual 1.664 1.571 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" O3B AGS D 702 " pdb=" PB AGS D 702 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" O3A AGS C 702 " pdb=" PA AGS C 702 " ideal model delta sigma weight residual 1.664 1.580 0.084 2.00e-02 2.50e+03 1.74e+01 ... (remaining 21254 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 28500 2.09 - 4.18: 495 4.18 - 6.27: 45 6.27 - 8.36: 11 8.36 - 10.45: 6 Bond angle restraints: 29057 Sorted by residual: angle pdb=" N3 DT I 4 " pdb=" C4 DT I 4 " pdb=" O4 DT I 4 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT I 8 " pdb=" C4 DT I 8 " pdb=" O4 DT I 8 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT H 29 " pdb=" C4 DT H 29 " pdb=" O4 DT H 29 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT H 25 " pdb=" C4 DT H 25 " pdb=" O4 DT H 25 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT I 14 " pdb=" C4 DT I 14 " pdb=" O4 DT I 14 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 ... (remaining 29052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.36: 12331 28.36 - 56.73: 516 56.73 - 85.09: 48 85.09 - 113.46: 8 113.46 - 141.82: 2 Dihedral angle restraints: 12905 sinusoidal: 5573 harmonic: 7332 Sorted by residual: dihedral pdb=" CA ALA D 116 " pdb=" C ALA D 116 " pdb=" N ARG D 117 " pdb=" CA ARG D 117 " ideal model delta harmonic sigma weight residual -180.00 -159.18 -20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA VAL D 19 " pdb=" C VAL D 19 " pdb=" N GLY D 20 " pdb=" CA GLY D 20 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PHE C 120 " pdb=" C PHE C 120 " pdb=" N LYS C 121 " pdb=" CA LYS C 121 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 12902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3298 0.115 - 0.231: 38 0.231 - 0.346: 3 0.346 - 0.462: 0 0.462 - 0.577: 10 Chirality restraints: 3349 Sorted by residual: chirality pdb=" P DC H 31 " pdb=" OP1 DC H 31 " pdb=" OP2 DC H 31 " pdb=" O5' DC H 31 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.58 2.00e-01 2.50e+01 8.32e+00 chirality pdb=" P DT H 30 " pdb=" OP1 DT H 30 " pdb=" OP2 DT H 30 " pdb=" O5' DT H 30 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" P DC H 32 " pdb=" OP1 DC H 32 " pdb=" OP2 DC H 32 " pdb=" O5' DC H 32 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.55 2.00e-01 2.50e+01 7.69e+00 ... (remaining 3346 not shown) Planarity restraints: 3614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 47 " -0.231 9.50e-02 1.11e+02 1.04e-01 6.68e+00 pdb=" NE ARG C 47 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 47 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 47 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 47 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 73 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C CYS C 73 " -0.042 2.00e-02 2.50e+03 pdb=" O CYS C 73 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY C 74 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 47 " -0.197 9.50e-02 1.11e+02 8.84e-02 4.95e+00 pdb=" NE ARG D 47 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG D 47 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 47 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 47 " -0.005 2.00e-02 2.50e+03 ... (remaining 3611 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 27 2.42 - 3.04: 12389 3.04 - 3.66: 31808 3.66 - 4.28: 49929 4.28 - 4.90: 82030 Nonbonded interactions: 176183 Sorted by model distance: nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 703 " model vdw 1.797 2.170 nonbonded pdb=" OG1 THR B 52 " pdb="MG MG B 703 " model vdw 1.814 2.170 nonbonded pdb=" OG1 THR D 52 " pdb="MG MG D 703 " model vdw 1.822 2.170 nonbonded pdb=" S1G AGS C 702 " pdb="MG MG C 703 " model vdw 2.056 2.530 nonbonded pdb=" O2G AGS D 702 " pdb="MG MG D 703 " model vdw 2.102 2.170 ... (remaining 176178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 361 or resid 701 through 703)) selection = (chain 'C' and (resid 2 through 361 or resid 701 through 703)) selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 365) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 26.640 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 21275 Z= 0.298 Angle : 0.710 16.319 29081 Z= 0.394 Chirality : 0.051 0.577 3349 Planarity : 0.005 0.104 3614 Dihedral : 15.052 141.823 8147 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 1.55 (0.17), residues: 2515 helix: 1.46 (0.15), residues: 1254 sheet: 1.34 (0.24), residues: 424 loop : 0.35 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 47 TYR 0.015 0.002 TYR E 222 PHE 0.022 0.002 PHE B 136 TRP 0.010 0.002 TRP C 10 HIS 0.005 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.30 (21259) covalent geometry : angle 0.67960 / 0.39 (29057) hydrogen bonds : bond 0.14787 / 9.76 ( 1165) hydrogen bonds : angle 5.38100 / 3.90 ( 3263) metal coordination : bond 0.00996 / 0.46 ( 16) metal coordination : angle 7.20448 / 5.29 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8147 (tpp-160) cc_final: 0.7814 (mmt90) REVERT: A 18 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7511 (mmt180) REVERT: A 32 GLN cc_start: 0.8056 (pt0) cc_final: 0.7397 (tp40) REVERT: A 58 ASN cc_start: 0.7787 (p0) cc_final: 0.7538 (p0) REVERT: A 122 GLU cc_start: 0.7268 (mt-10) cc_final: 0.7034 (mt-10) REVERT: A 149 ARG cc_start: 0.7577 (ttp80) cc_final: 0.7204 (ttp80) REVERT: A 163 ASP cc_start: 0.7670 (m-30) cc_final: 0.7452 (m-30) REVERT: B 176 LYS cc_start: 0.8968 (mtmt) cc_final: 0.8575 (mttp) REVERT: B 208 ARG cc_start: 0.7994 (mmt180) cc_final: 0.7758 (ttm110) REVERT: B 231 GLN cc_start: 0.8089 (mt0) cc_final: 0.7761 (tt0) REVERT: C 9 LYS cc_start: 0.9043 (tttm) cc_final: 0.8829 (tttt) REVERT: C 77 ASP cc_start: 0.7824 (m-30) cc_final: 0.7610 (m-30) REVERT: C 100 LYS cc_start: 0.7634 (mmpt) cc_final: 0.7275 (mttp) REVERT: C 179 ASP cc_start: 0.8172 (p0) cc_final: 0.7966 (p0) REVERT: C 306 MET cc_start: 0.7331 (mtt) cc_final: 0.6839 (mtt) REVERT: C 345 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7556 (mtt-85) REVERT: D 148 GLU cc_start: 0.7932 (mp0) cc_final: 0.7730 (mp0) REVERT: D 208 ARG cc_start: 0.8142 (mpt-90) cc_final: 0.7863 (mtp85) REVERT: D 248 GLN cc_start: 0.7789 (mt0) cc_final: 0.7155 (mm110) REVERT: E 8 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7854 (ttp80) REVERT: E 13 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8242 (ttpp) REVERT: E 37 ASP cc_start: 0.7103 (p0) cc_final: 0.6596 (p0) REVERT: E 86 ASN cc_start: 0.7286 (t0) cc_final: 0.6969 (p0) REVERT: E 90 VAL cc_start: 0.8726 (p) cc_final: 0.8447 (t) REVERT: F 161 GLU cc_start: 0.7645 (tt0) cc_final: 0.7196 (tm-30) REVERT: F 198 LYS cc_start: 0.8060 (mttt) cc_final: 0.7435 (mppt) REVERT: F 282 ARG cc_start: 0.6318 (ttm170) cc_final: 0.5979 (ttm-80) REVERT: F 326 ASP cc_start: 0.7097 (m-30) cc_final: 0.6565 (m-30) REVERT: F 336 VAL cc_start: 0.7367 (t) cc_final: 0.6914 (m) REVERT: F 339 MET cc_start: 0.6926 (mtm) cc_final: 0.6655 (mtm) REVERT: G 48 ASP cc_start: 0.7074 (t0) cc_final: 0.6863 (t0) REVERT: G 136 LYS cc_start: 0.8415 (tttm) cc_final: 0.8038 (ttmt) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.8785 time to fit residues: 497.1939 Evaluate side-chains 377 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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: 7.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 247 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN A 105 HIS A 136 GLN A 157 GLN A 280 GLN A 297 GLN C 112 GLN C 137 ASN D 204 GLN E 54 GLN E 56 HIS E 66 GLN E 206 GLN E 333 HIS F 16 GLN F 320 ASN G 265 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125031 restraints weight = 18657.589| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.32 r_work: 0.3183 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21275 Z= 0.139 Angle : 0.594 11.414 29081 Z= 0.303 Chirality : 0.041 0.252 3349 Planarity : 0.004 0.037 3614 Dihedral : 14.406 139.119 3354 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.13 % Allowed : 8.94 % Favored : 88.93 % 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: 1.79 (0.17), residues: 2515 helix: 1.67 (0.15), residues: 1291 sheet: 1.24 (0.24), residues: 417 loop : 0.53 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 263 TYR 0.015 0.001 TYR F 284 PHE 0.014 0.001 PHE A 273 TRP 0.017 0.001 TRP C 10 HIS 0.004 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (21259) covalent geometry : angle 0.57683 / 0.30 (29057) hydrogen bonds : bond 0.04413 / 2.91 ( 1165) hydrogen bonds : angle 4.11013 / 3.00 ( 3263) metal coordination : bond 0.00418 / 0.24 ( 16) metal coordination : angle 4.95105 / 3.56 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 383 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7452 (pmm) cc_final: 0.7250 (ptp) REVERT: A 3 ARG cc_start: 0.7476 (mtt180) cc_final: 0.7176 (mtt-85) REVERT: A 10 ARG cc_start: 0.8043 (tpp-160) cc_final: 0.7734 (mmt90) REVERT: A 32 GLN cc_start: 0.7911 (pt0) cc_final: 0.6941 (tp40) REVERT: A 49 GLU cc_start: 0.7418 (tt0) cc_final: 0.6996 (tt0) REVERT: A 58 ASN cc_start: 0.7648 (p0) cc_final: 0.7424 (p0) REVERT: A 69 GLN cc_start: 0.6419 (OUTLIER) cc_final: 0.5472 (mp-120) REVERT: A 122 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6780 (mt-10) REVERT: A 149 ARG cc_start: 0.7427 (ttp80) cc_final: 0.7073 (ttp-110) REVERT: A 163 ASP cc_start: 0.7583 (m-30) cc_final: 0.7363 (m-30) REVERT: A 272 LEU cc_start: 0.7358 (mt) cc_final: 0.7155 (mt) REVERT: A 274 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6837 (m-30) REVERT: B 107 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8067 (tm) REVERT: B 176 LYS cc_start: 0.8929 (mtmt) cc_final: 0.8420 (mttp) REVERT: B 208 ARG cc_start: 0.8043 (mmt180) cc_final: 0.7510 (ttm110) REVERT: B 231 GLN cc_start: 0.8195 (mt0) cc_final: 0.7662 (tt0) REVERT: B 247 ASP cc_start: 0.7442 (t70) cc_final: 0.6986 (t0) REVERT: B 360 HIS cc_start: 0.8427 (p90) cc_final: 0.8058 (p90) REVERT: C 9 LYS cc_start: 0.9036 (tttm) cc_final: 0.8833 (tttt) REVERT: C 179 ASP cc_start: 0.8325 (p0) cc_final: 0.8105 (p0) REVERT: C 180 VAL cc_start: 0.8507 (t) cc_final: 0.8282 (m) REVERT: C 263 ARG cc_start: 0.6784 (tpt-90) cc_final: 0.6460 (tpt170) REVERT: C 279 GLU cc_start: 0.8165 (tt0) cc_final: 0.7832 (tp30) REVERT: C 306 MET cc_start: 0.7120 (mtt) cc_final: 0.6526 (mtt) REVERT: C 345 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7374 (mtt180) REVERT: D 160 GLN cc_start: 0.7944 (mt0) cc_final: 0.7522 (mp10) REVERT: D 208 ARG cc_start: 0.8064 (mpt-90) cc_final: 0.7317 (ttp-110) REVERT: D 248 GLN cc_start: 0.7597 (mt0) cc_final: 0.6579 (mm110) REVERT: D 265 MET cc_start: 0.8374 (mmt) cc_final: 0.7797 (mmt) REVERT: D 351 MET cc_start: 0.8631 (mtm) cc_final: 0.8421 (mtp) REVERT: E 8 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7234 (ttm-80) REVERT: E 13 LYS cc_start: 0.8371 (ttpp) cc_final: 0.7924 (ttpp) REVERT: E 57 LYS cc_start: 0.8237 (ptpt) cc_final: 0.8018 (pttp) REVERT: E 86 ASN cc_start: 0.7314 (t0) cc_final: 0.6725 (p0) REVERT: E 87 THR cc_start: 0.8197 (p) cc_final: 0.7981 (p) REVERT: E 91 ASP cc_start: 0.7048 (p0) cc_final: 0.6651 (m-30) REVERT: E 276 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7037 (mm-30) REVERT: F 61 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7573 (mt0) REVERT: F 137 ARG cc_start: 0.7739 (tpt170) cc_final: 0.7424 (tpt170) REVERT: F 161 GLU cc_start: 0.7747 (tt0) cc_final: 0.7068 (tm-30) REVERT: F 198 LYS cc_start: 0.7930 (mttt) cc_final: 0.7061 (mppt) REVERT: F 282 ARG cc_start: 0.6344 (ttm170) cc_final: 0.5768 (ttm-80) REVERT: F 325 LEU cc_start: 0.6422 (tp) cc_final: 0.6192 (mt) REVERT: F 326 ASP cc_start: 0.6698 (m-30) cc_final: 0.6366 (m-30) REVERT: F 339 MET cc_start: 0.6636 (mtm) cc_final: 0.6311 (mtm) REVERT: G 136 LYS cc_start: 0.8310 (tttm) cc_final: 0.7744 (ttmt) REVERT: G 286 SER cc_start: 0.8499 (m) cc_final: 0.8257 (p) REVERT: G 316 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7460 (tm-30) outliers start: 45 outliers final: 16 residues processed: 405 average time/residue: 0.8620 time to fit residues: 384.9245 Evaluate side-chains 365 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 344 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 364 MET Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 316 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 203 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 191 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 259 ASN C 112 GLN D 204 GLN E 54 GLN E 206 GLN E 333 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.167155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124924 restraints weight = 18602.226| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.34 r_work: 0.3179 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21275 Z= 0.139 Angle : 0.558 11.555 29081 Z= 0.282 Chirality : 0.040 0.232 3349 Planarity : 0.004 0.041 3614 Dihedral : 14.298 140.941 3354 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.74 % Allowed : 10.22 % Favored : 87.04 % 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: 1.90 (0.17), residues: 2515 helix: 1.77 (0.15), residues: 1300 sheet: 1.28 (0.25), residues: 414 loop : 0.55 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 263 TYR 0.010 0.001 TYR F 284 PHE 0.009 0.001 PHE G 230 TRP 0.015 0.001 TRP C 10 HIS 0.003 0.001 HIS G 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (21259) covalent geometry : angle 0.53902 / 0.28 (29057) hydrogen bonds : bond 0.03988 / 2.64 ( 1165) hydrogen bonds : angle 3.88576 / 2.83 ( 3263) metal coordination : bond 0.00402 / 0.23 ( 16) metal coordination : angle 5.00509 / 3.66 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 356 time to evaluate : 0.795 Fit side-chains REVERT: A 1 MET cc_start: 0.7331 (pmm) cc_final: 0.7080 (ptp) REVERT: A 10 ARG cc_start: 0.7995 (tpp-160) cc_final: 0.7679 (mmt90) REVERT: A 32 GLN cc_start: 0.7929 (pt0) cc_final: 0.6928 (tp40) REVERT: A 49 GLU cc_start: 0.7529 (tt0) cc_final: 0.7056 (tt0) REVERT: A 58 ASN cc_start: 0.7578 (p0) cc_final: 0.7367 (p0) REVERT: A 69 GLN cc_start: 0.6212 (OUTLIER) cc_final: 0.5115 (mp10) REVERT: A 122 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6742 (mt-10) REVERT: A 149 ARG cc_start: 0.7421 (ttp80) cc_final: 0.7038 (ttp-110) REVERT: A 163 ASP cc_start: 0.7660 (m-30) cc_final: 0.7447 (m-30) REVERT: A 201 ARG cc_start: 0.8483 (mtt180) cc_final: 0.8275 (mtt180) REVERT: A 274 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6804 (m-30) REVERT: B 176 LYS cc_start: 0.8909 (mtmt) cc_final: 0.8409 (mttp) REVERT: B 208 ARG cc_start: 0.8121 (mmt180) cc_final: 0.7570 (ttm110) REVERT: B 231 GLN cc_start: 0.8229 (mt0) cc_final: 0.7680 (tt0) REVERT: B 247 ASP cc_start: 0.7421 (t70) cc_final: 0.7137 (p0) REVERT: B 327 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8070 (tp) REVERT: B 362 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6069 (mtt180) REVERT: C 179 ASP cc_start: 0.8387 (p0) cc_final: 0.8172 (p0) REVERT: C 180 VAL cc_start: 0.8486 (t) cc_final: 0.8275 (m) REVERT: C 279 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: C 306 MET cc_start: 0.7200 (mtt) cc_final: 0.6594 (mtt) REVERT: C 318 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7561 (ptp-110) REVERT: C 337 LYS cc_start: 0.8318 (mtpt) cc_final: 0.8047 (ttmt) REVERT: D 160 GLN cc_start: 0.7953 (mt0) cc_final: 0.7516 (mp10) REVERT: D 208 ARG cc_start: 0.8093 (mpt-90) cc_final: 0.7312 (ttp-110) REVERT: D 248 GLN cc_start: 0.7546 (mt0) cc_final: 0.6502 (mm110) REVERT: D 258 GLU cc_start: 0.7804 (tt0) cc_final: 0.7588 (tt0) REVERT: D 265 MET cc_start: 0.8338 (mmt) cc_final: 0.7830 (mmt) REVERT: E 8 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7171 (ttm-80) REVERT: E 13 LYS cc_start: 0.8378 (ttpp) cc_final: 0.7928 (ttpp) REVERT: E 57 LYS cc_start: 0.8233 (ptpt) cc_final: 0.8006 (pttp) REVERT: E 86 ASN cc_start: 0.7315 (t0) cc_final: 0.6705 (p0) REVERT: E 91 ASP cc_start: 0.7023 (p0) cc_final: 0.6547 (m-30) REVERT: E 94 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7092 (mtm110) REVERT: E 95 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6452 (mm-30) REVERT: F 53 MET cc_start: 0.8532 (mtt) cc_final: 0.8329 (mmt) REVERT: F 61 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: F 137 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7352 (tpt170) REVERT: F 161 GLU cc_start: 0.7800 (tt0) cc_final: 0.7064 (tm-30) REVERT: F 198 LYS cc_start: 0.8012 (mttt) cc_final: 0.7063 (mppt) REVERT: F 282 ARG cc_start: 0.6170 (ttm170) cc_final: 0.5613 (ttm-80) REVERT: F 326 ASP cc_start: 0.6658 (m-30) cc_final: 0.6316 (m-30) REVERT: F 339 MET cc_start: 0.6580 (mtm) cc_final: 0.6298 (mtm) REVERT: G 1 MET cc_start: 0.5392 (ttt) cc_final: 0.4997 (ttp) REVERT: G 136 LYS cc_start: 0.8263 (tttm) cc_final: 0.7682 (ttmt) REVERT: G 277 LYS cc_start: 0.8134 (ptpp) cc_final: 0.7647 (pttt) REVERT: G 316 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7511 (tm-30) outliers start: 58 outliers final: 22 residues processed: 387 average time/residue: 0.8413 time to fit residues: 359.7981 Evaluate side-chains 364 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 332 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 137 ARG Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 364 MET Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 316 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 142 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 97 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 253 optimal weight: 50.0000 chunk 175 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN A 136 GLN A 157 GLN B 360 HIS C 112 GLN D 137 ASN E 54 GLN E 206 GLN E 280 HIS E 333 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.166697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124166 restraints weight = 18487.816| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.34 r_work: 0.3168 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21275 Z= 0.151 Angle : 0.561 11.379 29081 Z= 0.282 Chirality : 0.040 0.237 3349 Planarity : 0.004 0.044 3614 Dihedral : 14.233 143.129 3354 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.98 % Allowed : 11.68 % Favored : 85.34 % 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: 1.91 (0.17), residues: 2515 helix: 1.80 (0.14), residues: 1296 sheet: 1.26 (0.25), residues: 414 loop : 0.52 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 117 TYR 0.010 0.001 TYR C 113 PHE 0.019 0.001 PHE G 230 TRP 0.014 0.001 TRP C 10 HIS 0.003 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (21259) covalent geometry : angle 0.54407 / 0.28 (29057) hydrogen bonds : bond 0.03859 / 2.54 ( 1165) hydrogen bonds : angle 3.81147 / 2.77 ( 3263) metal coordination : bond 0.00365 / 0.21 ( 16) metal coordination : angle 4.84947 / 3.51 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 357 time to evaluate : 0.852 Fit side-chains REVERT: A 10 ARG cc_start: 0.8007 (tpp-160) cc_final: 0.7699 (mmt90) REVERT: A 32 GLN cc_start: 0.7957 (pt0) cc_final: 0.6943 (tp40) REVERT: A 49 GLU cc_start: 0.7548 (tt0) cc_final: 0.7067 (tt0) REVERT: A 69 GLN cc_start: 0.6422 (OUTLIER) cc_final: 0.5200 (mp-120) REVERT: A 149 ARG cc_start: 0.7422 (ttp80) cc_final: 0.7034 (ttp-110) REVERT: A 201 ARG cc_start: 0.8527 (mtt180) cc_final: 0.8259 (mtt180) REVERT: B 107 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8089 (tm) REVERT: B 176 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8416 (mttp) REVERT: B 208 ARG cc_start: 0.8123 (mmt180) cc_final: 0.7576 (ttm110) REVERT: B 231 GLN cc_start: 0.8239 (mt0) cc_final: 0.7655 (tt0) REVERT: B 247 ASP cc_start: 0.7566 (t70) cc_final: 0.7232 (p0) REVERT: B 327 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8092 (tp) REVERT: B 362 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6037 (mtt180) REVERT: C 179 ASP cc_start: 0.8403 (p0) cc_final: 0.8185 (p0) REVERT: C 180 VAL cc_start: 0.8486 (t) cc_final: 0.8268 (m) REVERT: C 279 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7994 (tp30) REVERT: C 306 MET cc_start: 0.7200 (mtt) cc_final: 0.6668 (mtt) REVERT: C 318 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7538 (ptp-110) REVERT: C 337 LYS cc_start: 0.8322 (mtpt) cc_final: 0.8042 (ttmt) REVERT: C 363 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6856 (ptp) REVERT: D 160 GLN cc_start: 0.7962 (mt0) cc_final: 0.7542 (mp10) REVERT: D 208 ARG cc_start: 0.8110 (mpt-90) cc_final: 0.7317 (ttp-110) REVERT: D 248 GLN cc_start: 0.7540 (mt0) cc_final: 0.6530 (mm110) REVERT: D 258 GLU cc_start: 0.7876 (tt0) cc_final: 0.7655 (tt0) REVERT: D 347 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8490 (ttt) REVERT: E 8 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7185 (ttm-80) REVERT: E 13 LYS cc_start: 0.8384 (ttpp) cc_final: 0.7891 (ttpp) REVERT: E 57 LYS cc_start: 0.8246 (ptpt) cc_final: 0.8003 (pttp) REVERT: E 86 ASN cc_start: 0.7328 (t0) cc_final: 0.6746 (p0) REVERT: E 94 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7061 (mtm110) REVERT: E 95 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6470 (mm-30) REVERT: F 53 MET cc_start: 0.8510 (mtt) cc_final: 0.8248 (mmt) REVERT: F 61 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7449 (mt0) REVERT: F 137 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7394 (tpt170) REVERT: F 161 GLU cc_start: 0.7816 (tt0) cc_final: 0.7115 (tm-30) REVERT: F 198 LYS cc_start: 0.8041 (mttt) cc_final: 0.7089 (mppt) REVERT: F 212 ASN cc_start: 0.7468 (t0) cc_final: 0.7224 (m110) REVERT: F 326 ASP cc_start: 0.6666 (m-30) cc_final: 0.6345 (m-30) REVERT: F 339 MET cc_start: 0.6603 (mtm) cc_final: 0.6286 (mtm) REVERT: G 136 LYS cc_start: 0.8244 (tttm) cc_final: 0.7671 (ttmt) REVERT: G 206 MET cc_start: 0.7947 (ttp) cc_final: 0.7567 (ttm) REVERT: G 316 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7430 (tm-30) outliers start: 63 outliers final: 27 residues processed: 393 average time/residue: 0.8382 time to fit residues: 363.7395 Evaluate side-chains 378 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 339 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 137 ARG Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 316 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 103 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 251 optimal weight: 30.0000 chunk 145 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 69 GLN A 136 GLN B 360 HIS C 112 GLN C 137 ASN D 204 GLN E 54 GLN E 333 HIS F 156 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.163516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121544 restraints weight = 18427.613| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.31 r_work: 0.3128 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 21275 Z= 0.242 Angle : 0.651 12.450 29081 Z= 0.323 Chirality : 0.044 0.236 3349 Planarity : 0.005 0.057 3614 Dihedral : 14.333 144.015 3354 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.36 % Allowed : 12.49 % Favored : 84.15 % 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: 1.62 (0.17), residues: 2515 helix: 1.51 (0.14), residues: 1294 sheet: 1.21 (0.24), residues: 409 loop : 0.44 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 263 TYR 0.013 0.002 TYR C 113 PHE 0.024 0.002 PHE G 230 TRP 0.014 0.002 TRP C 10 HIS 0.005 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 (21259) covalent geometry : angle 0.63452 / 0.32 (29057) hydrogen bonds : bond 0.04515 / 2.96 ( 1165) hydrogen bonds : angle 3.94100 / 2.86 ( 3263) metal coordination : bond 0.00516 / 0.30 ( 16) metal coordination : angle 5.17354 / 3.77 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 335 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8013 (tpp-160) cc_final: 0.7684 (mmt90) REVERT: A 32 GLN cc_start: 0.8000 (pt0) cc_final: 0.6931 (tp40) REVERT: A 49 GLU cc_start: 0.7565 (tt0) cc_final: 0.7048 (tt0) REVERT: A 149 ARG cc_start: 0.7388 (ttp80) cc_final: 0.7004 (ttp-110) REVERT: A 201 ARG cc_start: 0.8556 (mtt180) cc_final: 0.8289 (mtt180) REVERT: A 274 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6895 (m-30) REVERT: B 80 ARG cc_start: 0.7380 (ttp-110) cc_final: 0.7081 (ttp-110) REVERT: B 107 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8059 (tm) REVERT: B 176 LYS cc_start: 0.8963 (mtmt) cc_final: 0.8463 (mttp) REVERT: B 208 ARG cc_start: 0.8136 (mmt180) cc_final: 0.7584 (ttm110) REVERT: B 231 GLN cc_start: 0.8378 (mt0) cc_final: 0.7708 (tt0) REVERT: B 245 ASP cc_start: 0.7674 (t0) cc_final: 0.6912 (t0) REVERT: B 247 ASP cc_start: 0.7671 (t70) cc_final: 0.7291 (p0) REVERT: B 263 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7865 (tpt-90) REVERT: B 327 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8153 (tp) REVERT: B 362 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6039 (mtt180) REVERT: C 179 ASP cc_start: 0.8436 (p0) cc_final: 0.8208 (p0) REVERT: C 180 VAL cc_start: 0.8518 (t) cc_final: 0.8278 (m) REVERT: C 263 ARG cc_start: 0.6648 (tpt-90) cc_final: 0.6365 (tpt170) REVERT: C 279 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7947 (tp30) REVERT: C 306 MET cc_start: 0.7253 (mtt) cc_final: 0.6743 (mtt) REVERT: C 318 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7564 (ptp-110) REVERT: C 337 LYS cc_start: 0.8397 (mtpt) cc_final: 0.8082 (mtpm) REVERT: C 363 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6826 (ptp) REVERT: D 160 GLN cc_start: 0.7995 (mt0) cc_final: 0.7553 (mp10) REVERT: D 208 ARG cc_start: 0.8116 (mpt-90) cc_final: 0.7294 (ttp-110) REVERT: D 248 GLN cc_start: 0.7585 (mt0) cc_final: 0.6581 (mm110) REVERT: E 8 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7169 (ttm-80) REVERT: E 13 LYS cc_start: 0.8438 (ttpp) cc_final: 0.7988 (ttpp) REVERT: E 57 LYS cc_start: 0.8294 (ptpt) cc_final: 0.8026 (pttp) REVERT: E 94 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7091 (mtm110) REVERT: F 53 MET cc_start: 0.8539 (mtt) cc_final: 0.8256 (mmt) REVERT: F 61 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7443 (mt0) REVERT: F 137 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7236 (tpt170) REVERT: F 161 GLU cc_start: 0.7815 (tt0) cc_final: 0.7136 (tm-30) REVERT: F 198 LYS cc_start: 0.8142 (mttt) cc_final: 0.7227 (mppt) REVERT: F 212 ASN cc_start: 0.7578 (t0) cc_final: 0.7297 (m110) REVERT: F 326 ASP cc_start: 0.6686 (m-30) cc_final: 0.6471 (m-30) REVERT: F 339 MET cc_start: 0.6611 (mtm) cc_final: 0.6249 (mtm) REVERT: G 136 LYS cc_start: 0.8244 (tttm) cc_final: 0.7650 (ttmt) REVERT: G 206 MET cc_start: 0.7879 (ttp) cc_final: 0.7506 (ttm) outliers start: 71 outliers final: 35 residues processed: 376 average time/residue: 0.8179 time to fit residues: 339.4405 Evaluate side-chains 372 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 326 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 137 ARG Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 364 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 172 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 179 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN B 360 HIS C 112 GLN D 204 GLN E 54 GLN E 206 GLN E 333 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.165858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.123225 restraints weight = 18418.997| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.35 r_work: 0.3160 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21275 Z= 0.146 Angle : 0.560 11.435 29081 Z= 0.281 Chirality : 0.040 0.236 3349 Planarity : 0.004 0.049 3614 Dihedral : 14.203 146.190 3354 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.89 % Allowed : 13.48 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.17), residues: 2515 helix: 1.73 (0.14), residues: 1291 sheet: 1.18 (0.25), residues: 417 loop : 0.52 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 263 TYR 0.010 0.001 TYR C 113 PHE 0.022 0.001 PHE G 230 TRP 0.017 0.001 TRP C 10 HIS 0.003 0.001 HIS G 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (21259) covalent geometry : angle 0.54257 / 0.28 (29057) hydrogen bonds : bond 0.03808 / 2.51 ( 1165) hydrogen bonds : angle 3.79281 / 2.76 ( 3263) metal coordination : bond 0.00336 / 0.20 ( 16) metal coordination : angle 4.83845 / 3.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 346 time to evaluate : 0.509 Fit side-chains REVERT: A 10 ARG cc_start: 0.7991 (tpp-160) cc_final: 0.7739 (mmt90) REVERT: A 18 ARG cc_start: 0.8005 (mmt90) cc_final: 0.7659 (mmt180) REVERT: A 32 GLN cc_start: 0.8049 (pt0) cc_final: 0.6986 (tp40) REVERT: A 49 GLU cc_start: 0.7496 (tt0) cc_final: 0.7024 (tt0) REVERT: A 149 ARG cc_start: 0.7387 (ttp80) cc_final: 0.6955 (ttp80) REVERT: A 201 ARG cc_start: 0.8559 (mtt180) cc_final: 0.8290 (mtt180) REVERT: A 274 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6888 (m-30) REVERT: B 80 ARG cc_start: 0.7381 (ttp-110) cc_final: 0.7066 (ttp-110) REVERT: B 176 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8429 (mttp) REVERT: B 208 ARG cc_start: 0.8126 (mmt180) cc_final: 0.7569 (ttm110) REVERT: B 231 GLN cc_start: 0.8323 (mt0) cc_final: 0.7689 (tt0) REVERT: B 247 ASP cc_start: 0.7568 (t70) cc_final: 0.7240 (p0) REVERT: B 256 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8553 (ttp) REVERT: B 263 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7853 (tpt-90) REVERT: B 327 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8094 (tp) REVERT: B 362 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6048 (mtt180) REVERT: C 179 ASP cc_start: 0.8425 (p0) cc_final: 0.8170 (p0) REVERT: C 180 VAL cc_start: 0.8466 (t) cc_final: 0.8217 (m) REVERT: C 263 ARG cc_start: 0.6663 (tpt-90) cc_final: 0.6407 (tpt170) REVERT: C 279 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: C 306 MET cc_start: 0.7331 (mtt) cc_final: 0.6801 (mtt) REVERT: C 318 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7541 (ptp-110) REVERT: C 337 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8050 (ttmt) REVERT: C 363 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6831 (ptp) REVERT: D 160 GLN cc_start: 0.7977 (mt0) cc_final: 0.7547 (mp10) REVERT: D 208 ARG cc_start: 0.8129 (mpt-90) cc_final: 0.7356 (ttp-110) REVERT: D 248 GLN cc_start: 0.7523 (mt0) cc_final: 0.6544 (mm110) REVERT: E 8 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7182 (ttm-80) REVERT: E 13 LYS cc_start: 0.8412 (ttpp) cc_final: 0.7923 (ttpp) REVERT: E 57 LYS cc_start: 0.8283 (ptpt) cc_final: 0.8021 (pttp) REVERT: E 91 ASP cc_start: 0.6909 (p0) cc_final: 0.6460 (m-30) REVERT: E 94 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7093 (mtm110) REVERT: E 95 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6481 (mm-30) REVERT: F 53 MET cc_start: 0.8528 (mtt) cc_final: 0.8257 (mmt) REVERT: F 61 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7425 (mt0) REVERT: F 137 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7261 (tpt170) REVERT: F 161 GLU cc_start: 0.7827 (tt0) cc_final: 0.7155 (tm-30) REVERT: F 198 LYS cc_start: 0.8068 (mttt) cc_final: 0.7168 (mppt) REVERT: F 212 ASN cc_start: 0.7501 (t0) cc_final: 0.7261 (m110) REVERT: F 282 ARG cc_start: 0.6102 (ttm-80) cc_final: 0.5309 (ttm-80) REVERT: F 326 ASP cc_start: 0.6728 (m-30) cc_final: 0.6492 (m-30) REVERT: F 339 MET cc_start: 0.6588 (mtm) cc_final: 0.6226 (mtm) REVERT: G 136 LYS cc_start: 0.8206 (tttm) cc_final: 0.7614 (ttmt) REVERT: G 202 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7518 (mm-30) REVERT: G 206 MET cc_start: 0.7881 (ttp) cc_final: 0.7552 (ttm) outliers start: 61 outliers final: 26 residues processed: 377 average time/residue: 0.7343 time to fit residues: 306.4020 Evaluate side-chains 374 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 337 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 137 ARG Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 172 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 30 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 136 GLN B 204 GLN B 360 HIS D 204 GLN E 333 HIS F 156 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.165900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.114224 restraints weight = 18481.770| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.66 r_work: 0.3131 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21275 Z= 0.168 Angle : 0.584 11.630 29081 Z= 0.291 Chirality : 0.041 0.235 3349 Planarity : 0.004 0.049 3614 Dihedral : 14.226 147.452 3354 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.79 % Allowed : 13.86 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.17), residues: 2515 helix: 1.68 (0.14), residues: 1294 sheet: 1.15 (0.25), residues: 419 loop : 0.51 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 263 TYR 0.013 0.001 TYR C 113 PHE 0.023 0.001 PHE G 230 TRP 0.016 0.001 TRP C 10 HIS 0.004 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (21259) covalent geometry : angle 0.56780 / 0.29 (29057) hydrogen bonds : bond 0.03921 / 2.58 ( 1165) hydrogen bonds : angle 3.80000 / 2.76 ( 3263) metal coordination : bond 0.00381 / 0.23 ( 16) metal coordination : angle 4.81932 / 3.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 345 time to evaluate : 0.944 Fit side-chains REVERT: A 10 ARG cc_start: 0.7924 (tpp-160) cc_final: 0.7675 (mmt90) REVERT: A 18 ARG cc_start: 0.7939 (mmt90) cc_final: 0.7630 (mmt180) REVERT: A 49 GLU cc_start: 0.7456 (tt0) cc_final: 0.6918 (tt0) REVERT: A 149 ARG cc_start: 0.7160 (ttp80) cc_final: 0.6687 (ttp80) REVERT: A 201 ARG cc_start: 0.8423 (mtt180) cc_final: 0.8123 (mtt180) REVERT: A 320 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7831 (m) REVERT: B 80 ARG cc_start: 0.7175 (ttp-110) cc_final: 0.6962 (ttp-110) REVERT: B 176 LYS cc_start: 0.8901 (mtmt) cc_final: 0.8326 (mttp) REVERT: B 208 ARG cc_start: 0.7993 (mmt180) cc_final: 0.7322 (ttm110) REVERT: B 231 GLN cc_start: 0.8333 (mt0) cc_final: 0.7550 (tt0) REVERT: B 247 ASP cc_start: 0.7552 (t70) cc_final: 0.7015 (p0) REVERT: B 256 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8396 (ttp) REVERT: B 263 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7678 (tpt-90) REVERT: B 327 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7870 (tp) REVERT: B 362 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.6007 (mtt180) REVERT: C 179 ASP cc_start: 0.8410 (p0) cc_final: 0.8136 (p0) REVERT: C 180 VAL cc_start: 0.8331 (t) cc_final: 0.8033 (m) REVERT: C 279 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7913 (tp30) REVERT: C 306 MET cc_start: 0.7210 (mtt) cc_final: 0.6608 (mtt) REVERT: C 318 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7378 (ptp-110) REVERT: C 337 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7823 (ttmt) REVERT: C 363 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6667 (ptp) REVERT: D 160 GLN cc_start: 0.7865 (mt0) cc_final: 0.7353 (mp10) REVERT: D 208 ARG cc_start: 0.7986 (mpt-90) cc_final: 0.7055 (ttp-110) REVERT: D 248 GLN cc_start: 0.7325 (mt0) cc_final: 0.6283 (mm110) REVERT: E 8 ARG cc_start: 0.7744 (ttp80) cc_final: 0.6840 (ttm-80) REVERT: E 13 LYS cc_start: 0.8243 (ttpp) cc_final: 0.7660 (ttpp) REVERT: E 57 LYS cc_start: 0.8158 (ptpt) cc_final: 0.7793 (pttp) REVERT: E 94 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6766 (mtm110) REVERT: E 95 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6175 (mm-30) REVERT: E 211 GLN cc_start: 0.7891 (tp-100) cc_final: 0.6820 (mp10) REVERT: F 53 MET cc_start: 0.8563 (mtt) cc_final: 0.8130 (mmt) REVERT: F 61 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7232 (mt0) REVERT: F 137 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7042 (tpt170) REVERT: F 161 GLU cc_start: 0.7770 (tt0) cc_final: 0.6982 (tm-30) REVERT: F 198 LYS cc_start: 0.7920 (mttt) cc_final: 0.6916 (mppt) REVERT: F 212 ASN cc_start: 0.7476 (t0) cc_final: 0.7206 (m110) REVERT: F 282 ARG cc_start: 0.5925 (ttm-80) cc_final: 0.5218 (ttm-80) REVERT: F 326 ASP cc_start: 0.6481 (m-30) cc_final: 0.6275 (m-30) REVERT: F 339 MET cc_start: 0.6447 (mtm) cc_final: 0.6183 (mtm) REVERT: G 136 LYS cc_start: 0.7971 (tttm) cc_final: 0.7336 (ttmt) REVERT: G 206 MET cc_start: 0.7748 (ttp) cc_final: 0.7420 (ttm) outliers start: 59 outliers final: 28 residues processed: 376 average time/residue: 0.7960 time to fit residues: 330.2467 Evaluate side-chains 371 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 332 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 137 ARG Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 364 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 172 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 135 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 250 optimal weight: 40.0000 chunk 139 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 184 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 136 GLN B 204 GLN B 360 HIS D 204 GLN E 333 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.167213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.125078 restraints weight = 18494.092| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.33 r_work: 0.3181 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21275 Z= 0.121 Angle : 0.538 10.717 29081 Z= 0.269 Chirality : 0.039 0.234 3349 Planarity : 0.004 0.046 3614 Dihedral : 14.117 149.664 3354 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.18 % Allowed : 14.90 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.17), residues: 2515 helix: 1.88 (0.14), residues: 1295 sheet: 1.15 (0.25), residues: 408 loop : 0.53 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 263 TYR 0.009 0.001 TYR C 328 PHE 0.022 0.001 PHE G 230 TRP 0.017 0.001 TRP C 10 HIS 0.004 0.001 HIS G 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (21259) covalent geometry : angle 0.52123 / 0.27 (29057) hydrogen bonds : bond 0.03469 / 2.29 ( 1165) hydrogen bonds : angle 3.70141 / 2.69 ( 3263) metal coordination : bond 0.00303 / 0.18 ( 16) metal coordination : angle 4.60467 / 3.29 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 349 time to evaluate : 0.841 Fit side-chains REVERT: A 10 ARG cc_start: 0.8036 (tpp-160) cc_final: 0.7780 (mmt90) REVERT: A 18 ARG cc_start: 0.7928 (mmt90) cc_final: 0.7591 (mmt180) REVERT: A 49 GLU cc_start: 0.7452 (tt0) cc_final: 0.6987 (tt0) REVERT: A 136 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.6969 (tm130) REVERT: A 149 ARG cc_start: 0.7372 (ttp80) cc_final: 0.6942 (ttp80) REVERT: A 201 ARG cc_start: 0.8525 (mtt180) cc_final: 0.8262 (mtt180) REVERT: A 227 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7928 (ttpt) REVERT: A 274 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6797 (m-30) REVERT: B 80 ARG cc_start: 0.7324 (ttp-110) cc_final: 0.7089 (ttp-110) REVERT: B 176 LYS cc_start: 0.8914 (mtmt) cc_final: 0.8421 (mttp) REVERT: B 208 ARG cc_start: 0.8077 (mmt180) cc_final: 0.7523 (ttm110) REVERT: B 231 GLN cc_start: 0.8361 (mt0) cc_final: 0.7740 (tt0) REVERT: B 247 ASP cc_start: 0.7445 (t70) cc_final: 0.7205 (p0) REVERT: B 327 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8054 (tp) REVERT: B 362 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6043 (mtt180) REVERT: C 179 ASP cc_start: 0.8348 (p0) cc_final: 0.8139 (p0) REVERT: C 180 VAL cc_start: 0.8452 (t) cc_final: 0.8197 (m) REVERT: C 279 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7908 (tp30) REVERT: C 306 MET cc_start: 0.7342 (mtt) cc_final: 0.6754 (mtt) REVERT: C 318 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7549 (ptp-110) REVERT: C 337 LYS cc_start: 0.8316 (mtpt) cc_final: 0.8021 (ttmt) REVERT: C 363 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6778 (ptp) REVERT: D 102 GLU cc_start: 0.7492 (mp0) cc_final: 0.6863 (mp0) REVERT: D 133 ARG cc_start: 0.7888 (mpt180) cc_final: 0.7675 (mmt90) REVERT: D 160 GLN cc_start: 0.7954 (mt0) cc_final: 0.7543 (mp10) REVERT: D 208 ARG cc_start: 0.8081 (mpt-90) cc_final: 0.7322 (ttp-110) REVERT: D 248 GLN cc_start: 0.7450 (mt0) cc_final: 0.6460 (mm110) REVERT: D 294 MET cc_start: 0.8072 (mmm) cc_final: 0.7780 (mmm) REVERT: E 8 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7191 (ttm-80) REVERT: E 13 LYS cc_start: 0.8357 (ttpp) cc_final: 0.7895 (ttpp) REVERT: E 57 LYS cc_start: 0.8270 (ptpt) cc_final: 0.8007 (pttp) REVERT: E 94 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7064 (mtm110) REVERT: E 95 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6464 (mm-30) REVERT: E 211 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7212 (mp10) REVERT: F 53 MET cc_start: 0.8515 (mtt) cc_final: 0.8173 (mmt) REVERT: F 61 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7280 (mt0) REVERT: F 137 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7255 (tpt170) REVERT: F 161 GLU cc_start: 0.7815 (tt0) cc_final: 0.7129 (tm-30) REVERT: F 198 LYS cc_start: 0.8052 (mttt) cc_final: 0.7184 (mppt) REVERT: F 205 ARG cc_start: 0.7814 (ttm110) cc_final: 0.7597 (ttm110) REVERT: F 212 ASN cc_start: 0.7494 (t0) cc_final: 0.7250 (m110) REVERT: F 282 ARG cc_start: 0.6128 (ttm-80) cc_final: 0.5383 (ttm-80) REVERT: F 326 ASP cc_start: 0.6880 (m-30) cc_final: 0.6637 (m-30) REVERT: F 339 MET cc_start: 0.6562 (mtm) cc_final: 0.6301 (mtm) REVERT: G 136 LYS cc_start: 0.8174 (tttm) cc_final: 0.7605 (ttmt) REVERT: G 206 MET cc_start: 0.7876 (ttp) cc_final: 0.7618 (ttm) outliers start: 46 outliers final: 21 residues processed: 371 average time/residue: 0.8130 time to fit residues: 333.4811 Evaluate side-chains 365 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 333 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 137 ARG Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 172 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 145 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 chunk 232 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 58 ASN B 204 GLN B 360 HIS E 206 GLN E 333 HIS ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.166042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.123387 restraints weight = 18496.882| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.36 r_work: 0.3158 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21275 Z= 0.164 Angle : 0.576 10.996 29081 Z= 0.286 Chirality : 0.040 0.232 3349 Planarity : 0.004 0.045 3614 Dihedral : 14.158 150.838 3354 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.22 % Allowed : 14.85 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.17), residues: 2515 helix: 1.78 (0.14), residues: 1295 sheet: 1.21 (0.25), residues: 410 loop : 0.51 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 263 TYR 0.016 0.001 TYR B 341 PHE 0.031 0.001 PHE G 230 TRP 0.014 0.001 TRP C 10 HIS 0.004 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (21259) covalent geometry : angle 0.56070 / 0.29 (29057) hydrogen bonds : bond 0.03765 / 2.48 ( 1165) hydrogen bonds : angle 3.74438 / 2.72 ( 3263) metal coordination : bond 0.00358 / 0.22 ( 16) metal coordination : angle 4.67426 / 3.38 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 332 time to evaluate : 0.806 Fit side-chains REVERT: A 10 ARG cc_start: 0.8037 (tpp-160) cc_final: 0.7768 (mmt90) REVERT: A 18 ARG cc_start: 0.7967 (mmt90) cc_final: 0.7633 (mmt180) REVERT: A 49 GLU cc_start: 0.7505 (tt0) cc_final: 0.7013 (tt0) REVERT: A 149 ARG cc_start: 0.7344 (ttp80) cc_final: 0.6908 (ttp80) REVERT: A 201 ARG cc_start: 0.8525 (mtt180) cc_final: 0.8252 (mtt180) REVERT: A 227 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7902 (ttpt) REVERT: B 80 ARG cc_start: 0.7351 (ttp-110) cc_final: 0.7088 (ttp-110) REVERT: B 176 LYS cc_start: 0.8937 (mtmt) cc_final: 0.8422 (mttp) REVERT: B 208 ARG cc_start: 0.8071 (mmt180) cc_final: 0.7498 (ttm110) REVERT: B 231 GLN cc_start: 0.8340 (mt0) cc_final: 0.7702 (tt0) REVERT: B 245 ASP cc_start: 0.7625 (t0) cc_final: 0.6954 (t0) REVERT: B 247 ASP cc_start: 0.7473 (t70) cc_final: 0.7209 (p0) REVERT: B 327 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8066 (tp) REVERT: B 362 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6119 (mtt180) REVERT: C 179 ASP cc_start: 0.8367 (p0) cc_final: 0.8166 (p0) REVERT: C 180 VAL cc_start: 0.8452 (t) cc_final: 0.8194 (m) REVERT: C 279 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: C 306 MET cc_start: 0.7380 (mtt) cc_final: 0.6772 (mtt) REVERT: C 318 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7563 (ptp-110) REVERT: C 337 LYS cc_start: 0.8345 (mtpt) cc_final: 0.8036 (ttmt) REVERT: D 102 GLU cc_start: 0.7417 (mp0) cc_final: 0.6845 (mp0) REVERT: D 133 ARG cc_start: 0.7908 (mpt180) cc_final: 0.7693 (mmt90) REVERT: D 160 GLN cc_start: 0.7952 (mt0) cc_final: 0.7522 (mp10) REVERT: D 208 ARG cc_start: 0.8093 (mpt-90) cc_final: 0.7291 (ttp-110) REVERT: D 248 GLN cc_start: 0.7449 (mt0) cc_final: 0.6468 (mm110) REVERT: D 294 MET cc_start: 0.8081 (mmm) cc_final: 0.7791 (mmm) REVERT: E 8 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7147 (ttm-80) REVERT: E 13 LYS cc_start: 0.8380 (ttpp) cc_final: 0.7906 (ttpp) REVERT: E 57 LYS cc_start: 0.8275 (ptpt) cc_final: 0.7998 (pttp) REVERT: E 88 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8225 (tt) REVERT: E 94 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7050 (mtm110) REVERT: E 95 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6462 (mm-30) REVERT: E 211 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7178 (mp10) REVERT: F 53 MET cc_start: 0.8541 (mtt) cc_final: 0.8181 (mmt) REVERT: F 61 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7277 (mt0) REVERT: F 137 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7174 (tpt170) REVERT: F 161 GLU cc_start: 0.7838 (tt0) cc_final: 0.7155 (tm-30) REVERT: F 166 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6692 (mt-10) REVERT: F 198 LYS cc_start: 0.8065 (mttt) cc_final: 0.7157 (mppt) REVERT: F 282 ARG cc_start: 0.6100 (ttm-80) cc_final: 0.5307 (ttm-80) REVERT: F 326 ASP cc_start: 0.6830 (m-30) cc_final: 0.6569 (m-30) REVERT: F 339 MET cc_start: 0.6539 (mtm) cc_final: 0.6267 (mtm) REVERT: G 136 LYS cc_start: 0.8153 (tttm) cc_final: 0.7591 (ttmt) REVERT: G 206 MET cc_start: 0.7885 (ttp) cc_final: 0.7630 (ttm) outliers start: 47 outliers final: 27 residues processed: 355 average time/residue: 0.8497 time to fit residues: 331.6109 Evaluate side-chains 361 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 324 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 137 ARG Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 364 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 203 optimal weight: 10.0000 chunk 50 optimal weight: 0.0980 chunk 201 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 219 optimal weight: 0.0570 chunk 7 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 overall best weight: 1.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS E 206 GLN E 333 HIS ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.166099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123437 restraints weight = 18625.008| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.36 r_work: 0.3150 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.178 21275 Z= 0.185 Angle : 0.724 59.198 29081 Z= 0.396 Chirality : 0.041 0.509 3349 Planarity : 0.004 0.045 3614 Dihedral : 14.159 150.875 3354 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.94 % Allowed : 15.33 % Favored : 82.73 % Cbeta Deviations : 0.04 % 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: 1.87 (0.17), residues: 2515 helix: 1.78 (0.14), residues: 1295 sheet: 1.21 (0.25), residues: 410 loop : 0.53 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 263 TYR 0.014 0.001 TYR B 341 PHE 0.032 0.001 PHE G 230 TRP 0.014 0.001 TRP C 10 HIS 0.004 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (21259) covalent geometry : angle 0.71132 / 0.40 (29057) hydrogen bonds : bond 0.03740 / 2.46 ( 1165) hydrogen bonds : angle 3.74476 / 2.73 ( 3263) metal coordination : bond 0.00338 / 0.20 ( 16) metal coordination : angle 4.67269 / 3.38 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 324 time to evaluate : 0.740 Fit side-chains REVERT: A 10 ARG cc_start: 0.8057 (tpp-160) cc_final: 0.7788 (mmt90) REVERT: A 18 ARG cc_start: 0.7969 (mmt90) cc_final: 0.7633 (mmt180) REVERT: A 49 GLU cc_start: 0.7520 (tt0) cc_final: 0.7036 (tt0) REVERT: A 149 ARG cc_start: 0.7374 (ttp80) cc_final: 0.6946 (ttp80) REVERT: A 201 ARG cc_start: 0.8544 (mtt180) cc_final: 0.8273 (mtt180) REVERT: A 227 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7928 (ttpt) REVERT: B 80 ARG cc_start: 0.7380 (ttp-110) cc_final: 0.7118 (ttp-110) REVERT: B 176 LYS cc_start: 0.8944 (mtmt) cc_final: 0.8438 (mttp) REVERT: B 208 ARG cc_start: 0.8122 (mmt180) cc_final: 0.7579 (ttm110) REVERT: B 231 GLN cc_start: 0.8351 (mt0) cc_final: 0.7726 (tt0) REVERT: B 245 ASP cc_start: 0.7640 (t0) cc_final: 0.7006 (t70) REVERT: B 263 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7980 (tpt-90) REVERT: B 327 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8090 (tp) REVERT: B 362 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6133 (mtt180) REVERT: C 179 ASP cc_start: 0.8366 (p0) cc_final: 0.8166 (p0) REVERT: C 180 VAL cc_start: 0.8465 (t) cc_final: 0.8211 (m) REVERT: C 279 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7953 (tp30) REVERT: C 306 MET cc_start: 0.7392 (mtt) cc_final: 0.6784 (mtt) REVERT: C 318 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7588 (ptp-110) REVERT: C 337 LYS cc_start: 0.8359 (mtpt) cc_final: 0.8060 (ttmt) REVERT: D 102 GLU cc_start: 0.7445 (mp0) cc_final: 0.6881 (mp0) REVERT: D 133 ARG cc_start: 0.7930 (mpt180) cc_final: 0.7718 (mmt90) REVERT: D 160 GLN cc_start: 0.7957 (mt0) cc_final: 0.7549 (mp10) REVERT: D 208 ARG cc_start: 0.8111 (mpt-90) cc_final: 0.7340 (ttp-110) REVERT: D 248 GLN cc_start: 0.7485 (mt0) cc_final: 0.6509 (mm110) REVERT: E 8 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7185 (ttm-80) REVERT: E 13 LYS cc_start: 0.8406 (ttpp) cc_final: 0.7941 (ttpp) REVERT: E 57 LYS cc_start: 0.8278 (ptpt) cc_final: 0.8012 (pttp) REVERT: E 88 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8238 (tt) REVERT: E 94 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7085 (mtm110) REVERT: E 95 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6510 (mm-30) REVERT: E 211 GLN cc_start: 0.8094 (tp-100) cc_final: 0.7215 (mp10) REVERT: F 53 MET cc_start: 0.8536 (mtt) cc_final: 0.8184 (mmt) REVERT: F 61 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7289 (mt0) REVERT: F 137 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7203 (tpt170) REVERT: F 161 GLU cc_start: 0.7843 (tt0) cc_final: 0.7170 (tm-30) REVERT: F 166 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6677 (mt-10) REVERT: F 198 LYS cc_start: 0.8088 (mttt) cc_final: 0.7196 (mppt) REVERT: F 282 ARG cc_start: 0.6148 (ttm-80) cc_final: 0.5353 (ttm-80) REVERT: F 326 ASP cc_start: 0.6898 (m-30) cc_final: 0.6630 (m-30) REVERT: F 339 MET cc_start: 0.6568 (mtm) cc_final: 0.6297 (mtm) REVERT: G 136 LYS cc_start: 0.8172 (tttm) cc_final: 0.7625 (ttmt) REVERT: G 206 MET cc_start: 0.7899 (ttp) cc_final: 0.7645 (ttm) outliers start: 41 outliers final: 26 residues processed: 343 average time/residue: 0.7970 time to fit residues: 301.2398 Evaluate side-chains 357 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 320 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 137 ARG Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 364 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 195 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 135 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 202 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS E 206 GLN E 333 HIS ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.165347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.122653 restraints weight = 18579.187| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.36 r_work: 0.3162 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.178 21275 Z= 0.185 Angle : 0.724 59.198 29081 Z= 0.396 Chirality : 0.041 0.509 3349 Planarity : 0.004 0.045 3614 Dihedral : 14.159 150.875 3354 Min Nonbonded Distance : 1.535 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.80 % Allowed : 15.52 % Favored : 82.69 % Cbeta Deviations : 0.04 % 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: 1.87 (0.17), residues: 2515 helix: 1.78 (0.14), residues: 1295 sheet: 1.21 (0.25), residues: 410 loop : 0.53 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 263 TYR 0.014 0.001 TYR B 341 PHE 0.032 0.001 PHE G 230 TRP 0.014 0.001 TRP C 10 HIS 0.004 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (21259) covalent geometry : angle 0.71132 / 0.40 (29057) hydrogen bonds : bond 0.03740 / 2.46 ( 1165) hydrogen bonds : angle 3.74476 / 2.73 ( 3263) metal coordination : bond 0.00338 / 0.20 ( 16) metal coordination : angle 4.67269 / 3.38 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9795.40 seconds wall clock time: 166 minutes 49.29 seconds (10009.29 seconds total)