Starting phenix.real_space_refine on Fri Aug 7 11:06:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyi_71022/08_2026/9oyi_71022.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyi_71022/08_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_71022/08_2026/9oyi_71022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyi_71022/08_2026/9oyi_71022.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oyi_71022/08_2026/9oyi_71022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyi_71022/08_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-2.2rc3-6140/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: 4.57, per 1000 atoms: 0.22 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: 1.89 Conformation dependent library (CDL) restraints added in 776.6 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: 2.66 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: 4.14 Time building geometry restraints manager: 2.49 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: 28499 2.09 - 4.18: 496 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.210 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.980 ------------------------------------------------------------------------------- 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 : 0.711 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 0.68029 / 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 : 0.810 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: 0.8822 time to fit residues: 499.8868 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 : 0.799 ------------------------------------------------------------------------------- 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 280 GLN A 297 GLN B 330 GLN B 360 HIS 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.167126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.124930 restraints weight = 18639.944| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.33 r_work: 0.3189 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21275 Z= 0.139 Angle : 0.593 11.554 29081 Z= 0.303 Chirality : 0.041 0.254 3349 Planarity : 0.004 0.036 3614 Dihedral : 14.384 138.321 3354 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.03 % Allowed : 8.75 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.17), residues: 2515 helix: 1.68 (0.15), residues: 1293 sheet: 1.24 (0.24), residues: 417 loop : 0.55 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 263 TYR 0.013 0.001 TYR F 284 PHE 0.014 0.001 PHE A 273 TRP 0.016 0.001 TRP C 10 HIS 0.004 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (21259) covalent geometry : angle 0.57564 / 0.30 (29057) hydrogen bonds : bond 0.04458 / 2.94 ( 1165) hydrogen bonds : angle 4.12379 / 3.01 ( 3263) metal coordination : bond 0.00434 / 0.26 ( 16) metal coordination : angle 4.98035 / 3.57 ( 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 425 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 382 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7509 (mtt180) cc_final: 0.7227 (mtt-85) REVERT: A 10 ARG cc_start: 0.8081 (tpp-160) cc_final: 0.7771 (mmt90) REVERT: A 32 GLN cc_start: 0.7967 (pt0) cc_final: 0.7064 (tp40) REVERT: A 49 GLU cc_start: 0.7445 (tt0) cc_final: 0.7047 (tt0) REVERT: A 58 ASN cc_start: 0.7680 (p0) cc_final: 0.7454 (p0) REVERT: A 69 GLN cc_start: 0.6498 (OUTLIER) cc_final: 0.5573 (mp-120) REVERT: A 122 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6843 (mt-10) REVERT: A 149 ARG cc_start: 0.7489 (ttp80) cc_final: 0.7148 (ttp-110) REVERT: A 163 ASP cc_start: 0.7605 (m-30) cc_final: 0.7391 (m-30) REVERT: A 272 LEU cc_start: 0.7419 (mt) cc_final: 0.7211 (mt) REVERT: A 274 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6912 (m-30) REVERT: B 107 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8168 (tm) REVERT: B 176 LYS cc_start: 0.8944 (mtmt) cc_final: 0.8463 (mttp) REVERT: B 208 ARG cc_start: 0.8084 (mmt180) cc_final: 0.7600 (ttm110) REVERT: B 231 GLN cc_start: 0.8203 (mt0) cc_final: 0.7710 (tt0) REVERT: B 247 ASP cc_start: 0.7434 (t70) cc_final: 0.7086 (t0) REVERT: C 9 LYS cc_start: 0.9077 (tttm) cc_final: 0.8871 (tttt) REVERT: C 86 ARG cc_start: 0.7736 (mtm110) cc_final: 0.7377 (mtm110) REVERT: C 179 ASP cc_start: 0.8337 (p0) cc_final: 0.8112 (p0) REVERT: C 180 VAL cc_start: 0.8545 (t) cc_final: 0.8331 (m) REVERT: C 263 ARG cc_start: 0.6861 (tpt-90) cc_final: 0.6531 (tpt170) REVERT: C 279 GLU cc_start: 0.8194 (tt0) cc_final: 0.7873 (tp30) REVERT: C 306 MET cc_start: 0.7152 (mtt) cc_final: 0.6634 (mtt) REVERT: C 345 ARG cc_start: 0.7768 (mtt180) cc_final: 0.7411 (mtt180) REVERT: D 160 GLN cc_start: 0.7979 (mt0) cc_final: 0.7590 (mp10) REVERT: D 208 ARG cc_start: 0.8123 (mpt-90) cc_final: 0.7420 (ttp-110) REVERT: D 248 GLN cc_start: 0.7669 (mt0) cc_final: 0.6677 (mm110) REVERT: D 265 MET cc_start: 0.8431 (mmt) cc_final: 0.7860 (mmt) REVERT: D 351 MET cc_start: 0.8679 (mtm) cc_final: 0.8477 (mtp) REVERT: E 8 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7335 (ttm-80) REVERT: E 13 LYS cc_start: 0.8417 (ttpp) cc_final: 0.8006 (ttpp) REVERT: E 57 LYS cc_start: 0.8270 (ptpt) cc_final: 0.8070 (pttp) REVERT: E 86 ASN cc_start: 0.7348 (t0) cc_final: 0.6802 (p0) REVERT: E 87 THR cc_start: 0.8279 (p) cc_final: 0.8070 (p) REVERT: E 91 ASP cc_start: 0.7121 (p0) cc_final: 0.6775 (m-30) REVERT: F 61 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7670 (mt0) REVERT: F 137 ARG cc_start: 0.7812 (tpt170) cc_final: 0.7492 (tpt170) REVERT: F 161 GLU cc_start: 0.7784 (tt0) cc_final: 0.7152 (tm-30) REVERT: F 198 LYS cc_start: 0.8019 (mttt) cc_final: 0.7198 (mppt) REVERT: F 282 ARG cc_start: 0.6379 (ttm170) cc_final: 0.5810 (ttm-80) REVERT: F 325 LEU cc_start: 0.6503 (tp) cc_final: 0.6289 (mt) REVERT: F 326 ASP cc_start: 0.6812 (m-30) cc_final: 0.6467 (m-30) REVERT: F 339 MET cc_start: 0.6649 (mtm) cc_final: 0.6337 (mtm) REVERT: G 136 LYS cc_start: 0.8377 (tttm) cc_final: 0.7846 (ttmt) REVERT: G 286 SER cc_start: 0.8530 (m) cc_final: 0.8298 (p) outliers start: 43 outliers final: 16 residues processed: 403 average time/residue: 0.8664 time to fit residues: 384.2556 Evaluate side-chains 366 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 346 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 233 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 191 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN B 360 HIS C 112 GLN C 137 ASN D 137 ASN D 204 GLN E 54 GLN E 206 GLN E 333 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.163966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120973 restraints weight = 18553.953| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.37 r_work: 0.3139 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21275 Z= 0.215 Angle : 0.641 12.966 29081 Z= 0.319 Chirality : 0.043 0.253 3349 Planarity : 0.005 0.054 3614 Dihedral : 14.409 138.962 3354 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.12 % Allowed : 10.03 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.17), residues: 2515 helix: 1.52 (0.14), residues: 1292 sheet: 1.26 (0.24), residues: 407 loop : 0.42 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 36 TYR 0.011 0.002 TYR D 341 PHE 0.010 0.002 PHE A 47 TRP 0.016 0.002 TRP C 10 HIS 0.005 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (21259) covalent geometry : angle 0.62250 / 0.32 (29057) hydrogen bonds : bond 0.04624 / 3.04 ( 1165) hydrogen bonds : angle 4.02365 / 2.93 ( 3263) metal coordination : bond 0.00530 / 0.30 ( 16) metal coordination : angle 5.37812 / 3.93 ( 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 416 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 350 time to evaluate : 0.824 Fit side-chains REVERT: A 10 ARG cc_start: 0.8051 (tpp-160) cc_final: 0.7738 (mmt90) REVERT: A 32 GLN cc_start: 0.8012 (pt0) cc_final: 0.7081 (tp40) REVERT: A 49 GLU cc_start: 0.7602 (tt0) cc_final: 0.7156 (tt0) REVERT: A 58 ASN cc_start: 0.7656 (p0) cc_final: 0.7440 (p0) REVERT: A 69 GLN cc_start: 0.6353 (OUTLIER) cc_final: 0.5172 (mp10) REVERT: A 122 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6820 (mt-10) REVERT: A 149 ARG cc_start: 0.7478 (ttp80) cc_final: 0.7110 (ttp-110) REVERT: A 274 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6964 (m-30) REVERT: B 107 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8194 (tm) REVERT: B 176 LYS cc_start: 0.8967 (mtmt) cc_final: 0.8500 (mttp) REVERT: B 208 ARG cc_start: 0.8153 (mmt180) cc_final: 0.7668 (ttm110) REVERT: B 231 GLN cc_start: 0.8313 (mt0) cc_final: 0.7748 (tt0) REVERT: B 247 ASP cc_start: 0.7545 (t70) cc_final: 0.7234 (p0) REVERT: B 327 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8182 (tp) REVERT: B 362 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.5992 (mtt180) REVERT: C 179 ASP cc_start: 0.8414 (p0) cc_final: 0.8181 (p0) REVERT: C 180 VAL cc_start: 0.8586 (t) cc_final: 0.8356 (m) REVERT: C 279 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: C 306 MET cc_start: 0.7251 (mtt) cc_final: 0.6700 (mtt) REVERT: C 318 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7699 (ptp-110) REVERT: C 337 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8164 (ttmt) REVERT: C 345 ARG cc_start: 0.7886 (mtt180) cc_final: 0.7566 (mtt180) REVERT: D 160 GLN cc_start: 0.7994 (mt0) cc_final: 0.7597 (mp10) REVERT: D 208 ARG cc_start: 0.8177 (mpt-90) cc_final: 0.7416 (ttp-110) REVERT: D 248 GLN cc_start: 0.7695 (mt0) cc_final: 0.6712 (mm110) REVERT: D 258 GLU cc_start: 0.7935 (tt0) cc_final: 0.7724 (tt0) REVERT: D 351 MET cc_start: 0.8721 (mtm) cc_final: 0.8517 (mtp) REVERT: E 8 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7293 (ttm-80) REVERT: E 13 LYS cc_start: 0.8447 (ttpp) cc_final: 0.8019 (ttpp) REVERT: E 57 LYS cc_start: 0.8309 (ptpt) cc_final: 0.8082 (pttp) REVERT: E 86 ASN cc_start: 0.7354 (t0) cc_final: 0.6817 (p0) REVERT: E 91 ASP cc_start: 0.7139 (p0) cc_final: 0.6886 (m-30) REVERT: E 94 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7235 (mtm110) REVERT: F 61 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7596 (mt0) REVERT: F 137 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7457 (tpt170) REVERT: F 161 GLU cc_start: 0.7844 (tt0) cc_final: 0.7208 (tm-30) REVERT: F 198 LYS cc_start: 0.8170 (mttt) cc_final: 0.7273 (mppt) REVERT: F 282 ARG cc_start: 0.6302 (ttm170) cc_final: 0.5700 (ttm-80) REVERT: F 326 ASP cc_start: 0.6819 (m-30) cc_final: 0.6604 (m-30) REVERT: F 339 MET cc_start: 0.6686 (mtm) cc_final: 0.6417 (mtm) REVERT: F 362 MET cc_start: 0.7476 (tpt) cc_final: 0.7261 (tpt) REVERT: G 136 LYS cc_start: 0.8368 (tttm) cc_final: 0.7795 (ttmt) outliers start: 66 outliers final: 22 residues processed: 389 average time/residue: 0.8395 time to fit residues: 360.4832 Evaluate side-chains 355 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 323 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 194 ASP 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 107 LEU 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 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 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 190 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 142 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 chunk 123 optimal weight: 0.9990 chunk 253 optimal weight: 50.0000 chunk 175 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 280 HIS E 333 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.165712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123108 restraints weight = 18455.975| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.35 r_work: 0.3162 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21275 Z= 0.157 Angle : 0.577 11.836 29081 Z= 0.289 Chirality : 0.041 0.254 3349 Planarity : 0.004 0.047 3614 Dihedral : 14.261 143.373 3354 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.22 % Allowed : 11.78 % Favored : 85.00 % 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: 1.74 (0.17), residues: 2515 helix: 1.66 (0.14), residues: 1292 sheet: 1.20 (0.25), residues: 409 loop : 0.46 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 201 TYR 0.010 0.001 TYR E 222 PHE 0.017 0.001 PHE G 230 TRP 0.017 0.001 TRP C 10 HIS 0.003 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (21259) covalent geometry : angle 0.55899 / 0.29 (29057) hydrogen bonds : bond 0.03973 / 2.61 ( 1165) hydrogen bonds : angle 3.86106 / 2.81 ( 3263) metal coordination : bond 0.00382 / 0.23 ( 16) metal coordination : angle 4.99763 / 3.62 ( 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 419 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 351 time to evaluate : 0.820 Fit side-chains REVERT: A 10 ARG cc_start: 0.8043 (tpp-160) cc_final: 0.7738 (mmt90) REVERT: A 32 GLN cc_start: 0.8022 (pt0) cc_final: 0.7079 (tp40) REVERT: A 49 GLU cc_start: 0.7545 (tt0) cc_final: 0.7121 (tt0) REVERT: A 58 ASN cc_start: 0.7613 (p0) cc_final: 0.7410 (p0) REVERT: A 69 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.6357 (mt0) REVERT: A 122 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6823 (mt-10) REVERT: A 149 ARG cc_start: 0.7492 (ttp80) cc_final: 0.7116 (ttp-110) REVERT: B 176 LYS cc_start: 0.8941 (mtmt) cc_final: 0.8475 (mttp) REVERT: B 208 ARG cc_start: 0.8131 (mmt180) cc_final: 0.7651 (ttm110) REVERT: B 231 GLN cc_start: 0.8316 (mt0) cc_final: 0.7749 (tt0) REVERT: B 247 ASP cc_start: 0.7568 (t70) cc_final: 0.7291 (p0) REVERT: B 256 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8596 (ttp) REVERT: B 327 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8158 (tp) REVERT: B 362 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6102 (mtt180) REVERT: C 179 ASP cc_start: 0.8402 (p0) cc_final: 0.8192 (p0) REVERT: C 180 VAL cc_start: 0.8527 (t) cc_final: 0.8307 (m) REVERT: C 279 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7949 (tp30) REVERT: C 306 MET cc_start: 0.7301 (mtt) cc_final: 0.6712 (mtt) REVERT: C 318 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7643 (ptp-110) REVERT: C 337 LYS cc_start: 0.8362 (mtpt) cc_final: 0.8109 (ttmt) REVERT: C 363 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6911 (ptp) REVERT: D 160 GLN cc_start: 0.8019 (mt0) cc_final: 0.7623 (mp10) REVERT: D 208 ARG cc_start: 0.8183 (mpt-90) cc_final: 0.7423 (ttp-110) REVERT: D 248 GLN cc_start: 0.7627 (mt0) cc_final: 0.6675 (mm110) REVERT: E 8 ARG cc_start: 0.8018 (ttp80) cc_final: 0.7313 (ttm-80) REVERT: E 13 LYS cc_start: 0.8436 (ttpp) cc_final: 0.7993 (ttpp) REVERT: E 57 LYS cc_start: 0.8286 (ptpt) cc_final: 0.8082 (pttp) REVERT: E 94 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7162 (mtm110) REVERT: F 61 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7565 (mt0) REVERT: F 137 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7479 (tpt170) REVERT: F 161 GLU cc_start: 0.7847 (tt0) cc_final: 0.7113 (tm-30) REVERT: F 198 LYS cc_start: 0.8151 (mttt) cc_final: 0.7272 (mppt) REVERT: F 212 ASN cc_start: 0.7573 (t0) cc_final: 0.7344 (m110) REVERT: F 326 ASP cc_start: 0.6782 (m-30) cc_final: 0.6564 (m-30) REVERT: F 339 MET cc_start: 0.6629 (mtm) cc_final: 0.6348 (mtm) REVERT: G 136 LYS cc_start: 0.8347 (tttm) cc_final: 0.7785 (ttmt) REVERT: G 202 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7548 (mm-30) REVERT: G 206 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7332 (ttm) outliers start: 68 outliers final: 31 residues processed: 389 average time/residue: 0.7894 time to fit residues: 339.7783 Evaluate side-chains 376 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 334 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 269 LEU 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 157 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 256 MET 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 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 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 206 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 103 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 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: 7.9990 chunk 124 optimal weight: 0.8980 chunk 251 optimal weight: 30.0000 chunk 145 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS C 112 GLN D 137 ASN D 204 GLN E 54 GLN E 206 GLN E 333 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.163823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119247 restraints weight = 18428.335| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.55 r_work: 0.3105 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 21275 Z= 0.248 Angle : 0.668 13.030 29081 Z= 0.330 Chirality : 0.044 0.255 3349 Planarity : 0.005 0.063 3614 Dihedral : 14.381 143.854 3354 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.55 % Allowed : 12.58 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.17), residues: 2515 helix: 1.38 (0.14), residues: 1293 sheet: 1.18 (0.24), residues: 407 loop : 0.34 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 263 TYR 0.014 0.002 TYR C 113 PHE 0.023 0.002 PHE G 230 TRP 0.015 0.002 TRP C 10 HIS 0.005 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 (21259) covalent geometry : angle 0.65125 / 0.33 (29057) hydrogen bonds : bond 0.04643 / 3.05 ( 1165) hydrogen bonds : angle 3.99005 / 2.90 ( 3263) metal coordination : bond 0.00529 / 0.31 ( 16) metal coordination : angle 5.25106 / 3.82 ( 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 414 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 339 time to evaluate : 0.683 Fit side-chains REVERT: A 10 ARG cc_start: 0.7928 (tpp-160) cc_final: 0.7624 (mmt90) REVERT: A 32 GLN cc_start: 0.7794 (pt0) cc_final: 0.6508 (tp40) REVERT: A 49 GLU cc_start: 0.7474 (tt0) cc_final: 0.6935 (tt0) REVERT: A 69 GLN cc_start: 0.6274 (OUTLIER) cc_final: 0.5176 (mp-120) REVERT: A 122 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6608 (mt-10) REVERT: A 149 ARG cc_start: 0.7147 (ttp80) cc_final: 0.6740 (ttp-110) REVERT: A 201 ARG cc_start: 0.8357 (mtt180) cc_final: 0.8093 (mtt180) REVERT: A 227 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7750 (ttpt) REVERT: B 176 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8336 (mttp) REVERT: B 208 ARG cc_start: 0.8021 (mmt180) cc_final: 0.7359 (ttm110) REVERT: B 231 GLN cc_start: 0.8352 (mt0) cc_final: 0.7527 (tt0) REVERT: B 245 ASP cc_start: 0.7630 (t0) cc_final: 0.6849 (t0) REVERT: B 247 ASP cc_start: 0.7689 (t70) cc_final: 0.7012 (p0) REVERT: B 263 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7685 (tpt-90) REVERT: B 327 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7895 (tp) REVERT: B 362 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.5886 (mtt180) REVERT: C 179 ASP cc_start: 0.8428 (p0) cc_final: 0.8206 (p0) REVERT: C 180 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8056 (m) REVERT: C 279 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7704 (tp30) REVERT: C 306 MET cc_start: 0.7197 (mtt) cc_final: 0.6629 (mtt) REVERT: C 318 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7324 (ptp-110) REVERT: C 337 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7845 (ttmt) REVERT: C 363 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6653 (ptp) REVERT: D 160 GLN cc_start: 0.7861 (mt0) cc_final: 0.7336 (mp10) REVERT: D 208 ARG cc_start: 0.7926 (mpt-90) cc_final: 0.7286 (mtp-110) REVERT: D 248 GLN cc_start: 0.7388 (mt0) cc_final: 0.6342 (mm110) REVERT: D 347 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8399 (ttt) REVERT: E 8 ARG cc_start: 0.7747 (ttp80) cc_final: 0.6805 (ttm-80) REVERT: E 13 LYS cc_start: 0.8243 (ttpp) cc_final: 0.7698 (ttpp) REVERT: E 57 LYS cc_start: 0.8169 (ptpt) cc_final: 0.7788 (pttp) REVERT: E 94 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6787 (mtm110) REVERT: F 61 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7287 (mt0) REVERT: F 137 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.6950 (tpt170) REVERT: F 161 GLU cc_start: 0.7734 (tt0) cc_final: 0.6963 (tm-30) REVERT: F 198 LYS cc_start: 0.7936 (mttt) cc_final: 0.6918 (mppt) REVERT: F 282 ARG cc_start: 0.6097 (ttm-80) cc_final: 0.5252 (ttm-80) REVERT: F 339 MET cc_start: 0.6475 (mtm) cc_final: 0.6150 (mtm) REVERT: G 136 LYS cc_start: 0.8008 (tttm) cc_final: 0.7346 (ttmt) outliers start: 75 outliers final: 33 residues processed: 381 average time/residue: 0.8061 time to fit residues: 340.1194 Evaluate side-chains 366 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 320 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 97 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 227 LYS 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 5 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 263 ARG 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 180 VAL 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 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 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 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: 3.9990 chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 51 optimal weight: 0.0970 chunk 128 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 136 GLN B 360 HIS C 112 GLN 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 = 0.3871 r_free = 0.3871 target = 0.166533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115122 restraints weight = 18400.661| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.65 r_work: 0.3158 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21275 Z= 0.130 Angle : 0.557 11.493 29081 Z= 0.279 Chirality : 0.039 0.254 3349 Planarity : 0.004 0.049 3614 Dihedral : 14.196 146.219 3354 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.79 % Allowed : 13.58 % 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: 1.79 (0.17), residues: 2515 helix: 1.72 (0.14), residues: 1289 sheet: 1.12 (0.25), residues: 417 loop : 0.49 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 263 TYR 0.010 0.001 TYR C 328 PHE 0.021 0.001 PHE G 230 TRP 0.018 0.001 TRP C 10 HIS 0.003 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (21259) covalent geometry : angle 0.53970 / 0.28 (29057) hydrogen bonds : bond 0.03737 / 2.47 ( 1165) hydrogen bonds : angle 3.79343 / 2.76 ( 3263) metal coordination : bond 0.00324 / 0.19 ( 16) metal coordination : angle 4.85123 / 3.47 ( 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 399 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 340 time to evaluate : 0.828 Fit side-chains REVERT: A 10 ARG cc_start: 0.7905 (tpp-160) cc_final: 0.7657 (mmt90) REVERT: A 18 ARG cc_start: 0.7943 (mmt90) cc_final: 0.7628 (mmt180) REVERT: A 32 GLN cc_start: 0.7789 (pt0) cc_final: 0.6495 (tp40) REVERT: A 49 GLU cc_start: 0.7382 (tt0) cc_final: 0.6835 (tt0) REVERT: A 69 GLN cc_start: 0.6018 (OUTLIER) cc_final: 0.4926 (mp10) REVERT: A 149 ARG cc_start: 0.7116 (ttp80) cc_final: 0.6643 (ttp80) REVERT: A 201 ARG cc_start: 0.8324 (mtt180) cc_final: 0.8052 (mtt180) REVERT: A 320 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7791 (m) REVERT: B 107 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7706 (tm) REVERT: B 176 LYS cc_start: 0.8872 (mtmt) cc_final: 0.8296 (mttp) REVERT: B 201 ARG cc_start: 0.7636 (tpt-90) cc_final: 0.7431 (tpm-80) REVERT: B 208 ARG cc_start: 0.7913 (mmt180) cc_final: 0.7247 (ttm110) REVERT: B 231 GLN cc_start: 0.8342 (mt0) cc_final: 0.7513 (tt0) REVERT: B 247 ASP cc_start: 0.7561 (t70) cc_final: 0.6964 (p0) REVERT: B 263 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7649 (tpt-90) REVERT: B 327 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7793 (tp) REVERT: B 362 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.5921 (mtt180) REVERT: C 179 ASP cc_start: 0.8381 (p0) cc_final: 0.8101 (p0) REVERT: C 180 VAL cc_start: 0.8267 (t) cc_final: 0.7961 (m) REVERT: C 263 ARG cc_start: 0.6334 (tpt-90) cc_final: 0.6042 (tpt170) REVERT: C 279 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7801 (tp30) REVERT: C 306 MET cc_start: 0.7222 (mtt) cc_final: 0.6639 (mtt) REVERT: C 318 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7280 (ptp-110) REVERT: C 337 LYS cc_start: 0.8076 (mtpt) cc_final: 0.7699 (ttmt) REVERT: C 363 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6644 (ptp) REVERT: D 105 ARG cc_start: 0.7609 (mtm-85) cc_final: 0.7402 (mtm-85) REVERT: D 160 GLN cc_start: 0.7813 (mt0) cc_final: 0.7297 (mp10) REVERT: D 208 ARG cc_start: 0.7923 (mpt-90) cc_final: 0.6995 (ttp-110) REVERT: D 248 GLN cc_start: 0.7275 (mt0) cc_final: 0.6244 (mm110) REVERT: D 294 MET cc_start: 0.7921 (mmm) cc_final: 0.7583 (mmm) REVERT: E 8 ARG cc_start: 0.7692 (ttp80) cc_final: 0.6788 (ttm-80) REVERT: E 13 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7596 (ttpp) REVERT: E 57 LYS cc_start: 0.8120 (ptpt) cc_final: 0.7767 (pttp) REVERT: E 91 ASP cc_start: 0.6554 (p0) cc_final: 0.6005 (m-30) REVERT: E 94 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6730 (mtm110) REVERT: E 95 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6093 (mm-30) REVERT: F 61 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7208 (mt0) REVERT: F 137 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7046 (tpt170) REVERT: F 161 GLU cc_start: 0.7694 (tt0) cc_final: 0.6861 (tm-30) REVERT: F 198 LYS cc_start: 0.7820 (mttt) cc_final: 0.6808 (mppt) REVERT: F 282 ARG cc_start: 0.5972 (ttm-80) cc_final: 0.5232 (ttm-80) REVERT: F 339 MET cc_start: 0.6433 (mtm) cc_final: 0.6126 (mtm) REVERT: G 136 LYS cc_start: 0.7910 (tttm) cc_final: 0.7243 (ttmt) REVERT: G 202 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7279 (mm-30) outliers start: 59 outliers final: 26 residues processed: 374 average time/residue: 0.7656 time to fit residues: 316.1464 Evaluate side-chains 369 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 331 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 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 327 LEU Chi-restraints excluded: chain B residue 332 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 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 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 293 THR 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 Chi-restraints excluded: chain G residue 206 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 30 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 213 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 136 GLN A 259 ASN B 360 HIS D 137 ASN D 204 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 = 0.3875 r_free = 0.3875 target = 0.166924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122417 restraints weight = 18510.992| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.52 r_work: 0.3157 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21275 Z= 0.131 Angle : 0.551 11.061 29081 Z= 0.275 Chirality : 0.039 0.254 3349 Planarity : 0.004 0.048 3614 Dihedral : 14.147 147.372 3354 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.70 % Allowed : 14.33 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.17), residues: 2515 helix: 1.82 (0.14), residues: 1295 sheet: 1.09 (0.25), residues: 419 loop : 0.53 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 263 TYR 0.013 0.001 TYR B 341 PHE 0.018 0.001 PHE G 230 TRP 0.017 0.001 TRP C 10 HIS 0.003 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (21259) covalent geometry : angle 0.53500 / 0.27 (29057) hydrogen bonds : bond 0.03595 / 2.37 ( 1165) hydrogen bonds : angle 3.73846 / 2.72 ( 3263) metal coordination : bond 0.00336 / 0.20 ( 16) metal coordination : angle 4.65380 / 3.34 ( 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 402 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 345 time to evaluate : 0.847 Fit side-chains REVERT: A 10 ARG cc_start: 0.7905 (tpp-160) cc_final: 0.7649 (mmt90) REVERT: A 18 ARG cc_start: 0.7897 (mmt90) cc_final: 0.7600 (mmt180) REVERT: A 49 GLU cc_start: 0.7395 (tt0) cc_final: 0.6841 (tt0) REVERT: A 69 GLN cc_start: 0.6343 (OUTLIER) cc_final: 0.5676 (mt0) REVERT: A 149 ARG cc_start: 0.7088 (ttp80) cc_final: 0.6605 (ttp80) REVERT: A 201 ARG cc_start: 0.8325 (mtt180) cc_final: 0.8056 (mtt180) REVERT: B 176 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8279 (mttp) REVERT: B 208 ARG cc_start: 0.7890 (mmt180) cc_final: 0.7193 (ttm110) REVERT: B 231 GLN cc_start: 0.8343 (mt0) cc_final: 0.7535 (tt0) REVERT: B 245 ASP cc_start: 0.7521 (t0) cc_final: 0.6868 (t70) REVERT: B 247 ASP cc_start: 0.7491 (t70) cc_final: 0.6972 (p0) REVERT: B 263 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7662 (tpt-90) REVERT: B 327 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7757 (tp) REVERT: C 117 ARG cc_start: 0.7640 (mtm110) cc_final: 0.7378 (mtm180) REVERT: C 179 ASP cc_start: 0.8305 (p0) cc_final: 0.8069 (p0) REVERT: C 180 VAL cc_start: 0.8252 (t) cc_final: 0.7925 (m) REVERT: C 279 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7736 (tp30) REVERT: C 306 MET cc_start: 0.7261 (mtt) cc_final: 0.6622 (mtt) REVERT: C 318 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7289 (ptp-110) REVERT: C 337 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7663 (ttmt) REVERT: C 363 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6618 (ptp) REVERT: D 160 GLN cc_start: 0.7798 (mt0) cc_final: 0.7271 (mp10) REVERT: D 193 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7238 (mm-30) REVERT: D 208 ARG cc_start: 0.7897 (mpt-90) cc_final: 0.6929 (ttp-110) REVERT: D 248 GLN cc_start: 0.7215 (mt0) cc_final: 0.6187 (mm110) REVERT: D 294 MET cc_start: 0.7891 (mmm) cc_final: 0.7561 (mmm) REVERT: E 8 ARG cc_start: 0.7673 (ttp80) cc_final: 0.6760 (ttm-80) REVERT: E 13 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7577 (ttpp) REVERT: E 57 LYS cc_start: 0.8100 (ptpt) cc_final: 0.7734 (pttp) REVERT: E 94 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6671 (mtm110) REVERT: E 95 GLU cc_start: 0.7097 (mt-10) cc_final: 0.5991 (mm-30) REVERT: E 211 GLN cc_start: 0.7817 (tp-100) cc_final: 0.6771 (mp10) REVERT: F 61 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7146 (mt0) REVERT: F 137 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7035 (tpt170) REVERT: F 161 GLU cc_start: 0.7700 (tt0) cc_final: 0.6868 (tm-30) REVERT: F 198 LYS cc_start: 0.7826 (mttt) cc_final: 0.6819 (mppt) REVERT: F 282 ARG cc_start: 0.5938 (ttm-80) cc_final: 0.5162 (ttm-80) REVERT: F 339 MET cc_start: 0.6399 (mtm) cc_final: 0.6068 (mtm) REVERT: G 136 LYS cc_start: 0.7871 (tttm) cc_final: 0.7197 (ttmt) REVERT: G 315 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8090 (ttm) outliers start: 57 outliers final: 31 residues processed: 376 average time/residue: 0.8353 time to fit residues: 346.5982 Evaluate side-chains 373 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 332 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 156 LYS Chi-restraints excluded: chain A residue 234 GLN 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 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 327 LEU Chi-restraints excluded: chain B residue 332 LEU 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 214 LEU 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 293 THR 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 Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 315 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 135 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 250 optimal weight: 40.0000 chunk 139 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 69 GLN A 136 GLN B 204 GLN B 360 HIS D 204 GLN E 333 HIS F 148 HIS F 156 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.167807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123386 restraints weight = 18424.797| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.51 r_work: 0.3179 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21275 Z= 0.118 Angle : 0.540 10.698 29081 Z= 0.269 Chirality : 0.039 0.252 3349 Planarity : 0.004 0.047 3614 Dihedral : 14.096 148.878 3354 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.32 % Allowed : 14.85 % Favored : 82.83 % 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: 1.99 (0.17), residues: 2515 helix: 1.92 (0.14), residues: 1293 sheet: 1.15 (0.25), residues: 410 loop : 0.57 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 263 TYR 0.013 0.001 TYR B 341 PHE 0.024 0.001 PHE G 230 TRP 0.016 0.001 TRP C 10 HIS 0.005 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (21259) covalent geometry : angle 0.52335 / 0.27 (29057) hydrogen bonds : bond 0.03395 / 2.25 ( 1165) hydrogen bonds : angle 3.67700 / 2.68 ( 3263) metal coordination : bond 0.00311 / 0.18 ( 16) metal coordination : angle 4.64490 / 3.35 ( 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 391 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 342 time to evaluate : 0.788 Fit side-chains REVERT: A 10 ARG cc_start: 0.7923 (tpp-160) cc_final: 0.7677 (mmt90) REVERT: A 18 ARG cc_start: 0.7893 (mmt90) cc_final: 0.7585 (mmt180) REVERT: A 49 GLU cc_start: 0.7396 (tt0) cc_final: 0.6866 (tt0) REVERT: A 149 ARG cc_start: 0.7123 (ttp80) cc_final: 0.6646 (ttp80) REVERT: A 201 ARG cc_start: 0.8362 (mtt180) cc_final: 0.8093 (mtt180) REVERT: B 176 LYS cc_start: 0.8855 (mtmt) cc_final: 0.8285 (mttp) REVERT: B 208 ARG cc_start: 0.7890 (mmt180) cc_final: 0.7207 (ttm110) REVERT: B 231 GLN cc_start: 0.8299 (mt0) cc_final: 0.7544 (tt0) REVERT: B 245 ASP cc_start: 0.7494 (t0) cc_final: 0.6894 (t70) REVERT: B 247 ASP cc_start: 0.7452 (t70) cc_final: 0.7027 (p0) REVERT: B 327 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7769 (tp) REVERT: B 362 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.5969 (mtt180) REVERT: C 161 LYS cc_start: 0.8038 (mmtm) cc_final: 0.7690 (mmtp) REVERT: C 179 ASP cc_start: 0.8316 (p0) cc_final: 0.8115 (p0) REVERT: C 180 VAL cc_start: 0.8277 (t) cc_final: 0.7976 (m) REVERT: C 279 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7875 (tp30) REVERT: C 306 MET cc_start: 0.7296 (mtt) cc_final: 0.6654 (mtt) REVERT: C 318 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7328 (ptp-110) REVERT: C 337 LYS cc_start: 0.8056 (mtpt) cc_final: 0.7690 (ttmt) REVERT: C 363 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6621 (ptp) REVERT: D 105 ARG cc_start: 0.7591 (mtm-85) cc_final: 0.7380 (mtm-85) REVERT: D 160 GLN cc_start: 0.7803 (mt0) cc_final: 0.7300 (mp10) REVERT: D 171 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8168 (mp) REVERT: D 208 ARG cc_start: 0.7919 (mpt-90) cc_final: 0.6992 (ttp-110) REVERT: D 248 GLN cc_start: 0.7248 (mt0) cc_final: 0.6200 (mm110) REVERT: D 294 MET cc_start: 0.7928 (mmm) cc_final: 0.7602 (mmm) REVERT: E 8 ARG cc_start: 0.7720 (ttp80) cc_final: 0.7502 (ttp80) REVERT: E 13 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7617 (ttpp) REVERT: E 57 LYS cc_start: 0.8119 (ptpt) cc_final: 0.7772 (pttp) REVERT: E 94 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6710 (mtm110) REVERT: E 95 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6035 (mm-30) REVERT: E 211 GLN cc_start: 0.7864 (tp-100) cc_final: 0.6816 (mp10) REVERT: F 61 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7121 (mt0) REVERT: F 137 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7086 (tpt170) REVERT: F 161 GLU cc_start: 0.7732 (tt0) cc_final: 0.6907 (tm-30) REVERT: F 198 LYS cc_start: 0.7834 (mttt) cc_final: 0.6845 (mppt) REVERT: F 282 ARG cc_start: 0.5945 (ttm-80) cc_final: 0.5146 (ttm-80) REVERT: F 326 ASP cc_start: 0.6625 (m-30) cc_final: 0.6259 (m-30) REVERT: F 339 MET cc_start: 0.6423 (mtm) cc_final: 0.6076 (mtm) REVERT: G 136 LYS cc_start: 0.7891 (tttm) cc_final: 0.7254 (ttmt) REVERT: G 315 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8081 (ttm) outliers start: 49 outliers final: 26 residues processed: 367 average time/residue: 0.8631 time to fit residues: 348.9204 Evaluate side-chains 364 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 328 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 234 GLN Chi-restraints excluded: chain B residue 5 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 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 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 171 LEU 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 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 247 VAL Chi-restraints excluded: chain F residue 293 THR 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 Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 315 MET Chi-restraints excluded: chain G residue 364 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 145 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 164 optimal weight: 0.0770 chunk 232 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 58 ASN A 69 GLN A 136 GLN B 204 GLN B 360 HIS D 137 ASN E 333 HIS F 156 ASN G 255 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.166734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115177 restraints weight = 18454.652| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.66 r_work: 0.3152 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21275 Z= 0.153 Angle : 0.569 10.994 29081 Z= 0.282 Chirality : 0.040 0.250 3349 Planarity : 0.004 0.048 3614 Dihedral : 14.113 150.196 3354 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.37 % Allowed : 15.00 % Favored : 82.64 % 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: 1.82 (0.14), residues: 1295 sheet: 1.16 (0.25), residues: 410 loop : 0.54 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 263 TYR 0.014 0.001 TYR B 341 PHE 0.014 0.001 PHE G 230 TRP 0.013 0.001 TRP C 10 HIS 0.004 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (21259) covalent geometry : angle 0.55307 / 0.28 (29057) hydrogen bonds : bond 0.03678 / 2.42 ( 1165) hydrogen bonds : angle 3.72320 / 2.71 ( 3263) metal coordination : bond 0.00349 / 0.21 ( 16) metal coordination : angle 4.66837 / 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: 50 poor density : 329 time to evaluate : 0.820 Fit side-chains REVERT: A 10 ARG cc_start: 0.7976 (tpp-160) cc_final: 0.7720 (mmt90) REVERT: A 18 ARG cc_start: 0.7921 (mmt90) cc_final: 0.7610 (mmt180) REVERT: A 49 GLU cc_start: 0.7477 (tt0) cc_final: 0.6955 (tt0) REVERT: A 149 ARG cc_start: 0.7251 (ttp80) cc_final: 0.6781 (ttp80) REVERT: B 176 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8391 (mttp) REVERT: B 208 ARG cc_start: 0.8030 (mmt180) cc_final: 0.7431 (ttm-80) REVERT: B 231 GLN cc_start: 0.8363 (mt0) cc_final: 0.7641 (tt0) REVERT: B 245 ASP cc_start: 0.7587 (t0) cc_final: 0.6898 (t70) REVERT: B 247 ASP cc_start: 0.7520 (t70) cc_final: 0.7150 (p0) REVERT: B 327 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7924 (tp) REVERT: B 362 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6089 (mtt180) REVERT: C 180 VAL cc_start: 0.8367 (t) cc_final: 0.8084 (m) REVERT: C 279 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7901 (tp30) REVERT: C 306 MET cc_start: 0.7286 (mtt) cc_final: 0.6664 (mtt) REVERT: C 318 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7438 (ptp-110) REVERT: C 337 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7847 (ttmt) REVERT: D 160 GLN cc_start: 0.7916 (mt0) cc_final: 0.7424 (mp10) REVERT: D 193 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7408 (mm-30) REVERT: D 208 ARG cc_start: 0.8051 (mpt-90) cc_final: 0.7140 (ttp-110) REVERT: D 248 GLN cc_start: 0.7382 (mt0) cc_final: 0.6338 (mm110) REVERT: D 294 MET cc_start: 0.8007 (mmm) cc_final: 0.7699 (mmm) REVERT: E 8 ARG cc_start: 0.7839 (ttp80) cc_final: 0.6956 (ttm-80) REVERT: E 13 LYS cc_start: 0.8290 (ttpp) cc_final: 0.7753 (ttpp) REVERT: E 57 LYS cc_start: 0.8197 (ptpt) cc_final: 0.7856 (pttp) REVERT: E 88 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8075 (tt) REVERT: E 94 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6877 (mtm110) REVERT: E 95 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6256 (mm-30) REVERT: E 211 GLN cc_start: 0.7969 (tp-100) cc_final: 0.6962 (mp10) REVERT: F 61 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7126 (mt0) REVERT: F 137 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7120 (tpt170) REVERT: F 161 GLU cc_start: 0.7774 (tt0) cc_final: 0.7009 (tm-30) REVERT: F 166 GLU cc_start: 0.7125 (tt0) cc_final: 0.6801 (mt-10) REVERT: F 198 LYS cc_start: 0.7988 (mttt) cc_final: 0.7012 (mppt) REVERT: F 282 ARG cc_start: 0.5974 (ttm-80) cc_final: 0.5187 (ttm-80) REVERT: F 326 ASP cc_start: 0.6588 (m-30) cc_final: 0.6309 (m-30) REVERT: F 339 MET cc_start: 0.6448 (mtm) cc_final: 0.6186 (mtm) REVERT: G 97 MET cc_start: 0.6224 (tpt) cc_final: 0.4085 (tmt) REVERT: G 136 LYS cc_start: 0.8023 (tttm) cc_final: 0.7439 (ttmt) REVERT: G 315 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8145 (ttm) outliers start: 50 outliers final: 29 residues processed: 355 average time/residue: 0.8287 time to fit residues: 324.8921 Evaluate side-chains 367 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 329 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 234 GLN Chi-restraints excluded: chain B residue 5 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 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 133 ARG 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 151 LEU 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 247 VAL Chi-restraints excluded: chain F residue 293 THR 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 206 MET Chi-restraints excluded: chain G residue 315 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 203 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 220 optimal weight: 8.9990 chunk 219 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 147 optimal weight: 0.0050 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 58 ASN A 69 GLN A 136 GLN B 204 GLN B 360 HIS E 333 HIS ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.166133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115343 restraints weight = 18635.097| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.64 r_work: 0.3167 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21275 Z= 0.135 Angle : 0.553 10.787 29081 Z= 0.275 Chirality : 0.039 0.266 3349 Planarity : 0.004 0.046 3614 Dihedral : 14.119 152.660 3354 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.94 % Allowed : 15.70 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.17), residues: 2515 helix: 1.88 (0.14), residues: 1295 sheet: 1.15 (0.26), residues: 410 loop : 0.58 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 263 TYR 0.013 0.001 TYR B 341 PHE 0.021 0.001 PHE G 230 TRP 0.015 0.001 TRP C 10 HIS 0.004 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (21259) covalent geometry : angle 0.53746 / 0.27 (29057) hydrogen bonds : bond 0.03530 / 2.33 ( 1165) hydrogen bonds : angle 3.70576 / 2.71 ( 3263) metal coordination : bond 0.00320 / 0.19 ( 16) metal coordination : angle 4.61739 / 3.32 ( 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 371 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 330 time to evaluate : 0.866 Fit side-chains REVERT: A 10 ARG cc_start: 0.7951 (tpp-160) cc_final: 0.7682 (mmt90) REVERT: A 18 ARG cc_start: 0.7866 (mmt90) cc_final: 0.7571 (mmt180) REVERT: A 49 GLU cc_start: 0.7429 (tt0) cc_final: 0.6885 (tt0) REVERT: A 149 ARG cc_start: 0.7136 (ttp80) cc_final: 0.6655 (ttp80) REVERT: B 176 LYS cc_start: 0.8880 (mtmt) cc_final: 0.8300 (mttp) REVERT: B 208 ARG cc_start: 0.7917 (mmt180) cc_final: 0.7277 (ttm-80) REVERT: B 231 GLN cc_start: 0.8287 (mt0) cc_final: 0.7533 (tt0) REVERT: B 245 ASP cc_start: 0.7483 (t0) cc_final: 0.6875 (t0) REVERT: B 247 ASP cc_start: 0.7453 (t70) cc_final: 0.6963 (p0) REVERT: B 327 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7783 (tp) REVERT: C 84 GLN cc_start: 0.7672 (mt0) cc_final: 0.7294 (mt0) REVERT: C 117 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7192 (tmm-80) REVERT: C 180 VAL cc_start: 0.8235 (t) cc_final: 0.7957 (m) REVERT: C 279 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7787 (tp30) REVERT: C 306 MET cc_start: 0.7262 (mtt) cc_final: 0.6622 (mtt) REVERT: C 318 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7321 (ptp-110) REVERT: C 337 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7694 (ttmt) REVERT: D 102 GLU cc_start: 0.7330 (mp0) cc_final: 0.6686 (mp0) REVERT: D 133 ARG cc_start: 0.7669 (mpt180) cc_final: 0.7435 (mmt90) REVERT: D 160 GLN cc_start: 0.7809 (mt0) cc_final: 0.7302 (mp10) REVERT: D 208 ARG cc_start: 0.7930 (mpt-90) cc_final: 0.6996 (ttp-110) REVERT: D 248 GLN cc_start: 0.7265 (mt0) cc_final: 0.6213 (mm110) REVERT: D 294 MET cc_start: 0.7914 (mmm) cc_final: 0.7595 (mmm) REVERT: E 8 ARG cc_start: 0.7729 (ttp80) cc_final: 0.6820 (ttm-80) REVERT: E 13 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7622 (ttpp) REVERT: E 57 LYS cc_start: 0.8112 (ptpt) cc_final: 0.7776 (pttp) REVERT: E 88 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7975 (tt) REVERT: E 94 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6718 (mtm110) REVERT: E 95 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6048 (mm-30) REVERT: E 211 GLN cc_start: 0.7859 (tp-100) cc_final: 0.6806 (mp10) REVERT: F 61 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7073 (mt0) REVERT: F 137 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7033 (tpt170) REVERT: F 161 GLU cc_start: 0.7715 (tt0) cc_final: 0.6915 (tm-30) REVERT: F 166 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6745 (mt-10) REVERT: F 198 LYS cc_start: 0.7840 (mttt) cc_final: 0.6877 (mppt) REVERT: F 282 ARG cc_start: 0.5989 (ttm-80) cc_final: 0.5192 (ttm-80) REVERT: F 326 ASP cc_start: 0.6567 (m-30) cc_final: 0.6245 (m-30) REVERT: F 339 MET cc_start: 0.6401 (mtm) cc_final: 0.6120 (mtm) REVERT: G 136 LYS cc_start: 0.7901 (tttm) cc_final: 0.7293 (ttmt) REVERT: G 315 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8067 (ttm) outliers start: 41 outliers final: 27 residues processed: 349 average time/residue: 0.8717 time to fit residues: 335.5919 Evaluate side-chains 364 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 328 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 156 LYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain B residue 5 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 327 LEU Chi-restraints excluded: chain B residue 332 LEU 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 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 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 247 VAL 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 206 MET Chi-restraints excluded: chain G residue 315 MET 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: 1.9990 chunk 67 optimal weight: 0.6980 chunk 202 optimal weight: 0.0470 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 58 ASN A 69 GLN A 136 GLN A 259 ASN B 204 GLN B 360 HIS E 333 HIS ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.167190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.115814 restraints weight = 18551.729| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.66 r_work: 0.3161 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 21275 Z= 0.150 Angle : 0.721 59.200 29081 Z= 0.397 Chirality : 0.042 0.967 3349 Planarity : 0.004 0.063 3614 Dihedral : 14.119 152.672 3354 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.99 % Allowed : 15.75 % Favored : 82.26 % 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: 1.97 (0.17), residues: 2515 helix: 1.88 (0.14), residues: 1295 sheet: 1.15 (0.26), residues: 410 loop : 0.59 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 263 TYR 0.011 0.001 TYR B 341 PHE 0.020 0.001 PHE G 230 TRP 0.015 0.001 TRP C 10 HIS 0.003 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (21259) covalent geometry : angle 0.70883 / 0.40 (29057) hydrogen bonds : bond 0.03515 / 2.32 ( 1165) hydrogen bonds : angle 3.70588 / 2.71 ( 3263) metal coordination : bond 0.00307 / 0.18 ( 16) metal coordination : angle 4.61415 / 3.31 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10249.84 seconds wall clock time: 174 minutes 37.72 seconds (10477.72 seconds total)