Starting phenix.real_space_refine on Thu Jun 4 17:16:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyg_71018/06_2026/9oyg_71018_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyg_71018/06_2026/9oyg_71018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oyg_71018/06_2026/9oyg_71018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyg_71018/06_2026/9oyg_71018.map" model { file = "/net/cci-nas-00/data/ceres_data/9oyg_71018/06_2026/9oyg_71018_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyg_71018/06_2026/9oyg_71018_trim.cif" } resolution = 2.95 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= 0.009 sd= 0.583 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 7 5.49 5 Mg 1 5.21 5 S 71 5.16 5 C 8878 2.51 5 N 2552 2.21 5 O 2600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14113 Number of models: 1 Model: "" Number of chains: 10 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: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2832 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 16, 'TRANS': 347} Chain breaks: 1 Chain: "C" Number of atoms: 2838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2838 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 17, 'TRANS': 347} Chain: "D" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2781 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 14, 'TRANS': 343} 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: "J" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 244 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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 63.603 102.977 96.523 1.00118.53 S ATOM 3269 SG CYS B 73 64.240 106.433 95.440 1.00118.38 S ATOM 3286 SG CYS B 76 67.313 104.130 96.298 1.00134.65 S ATOM 3308 SG CYS B 79 65.003 103.454 93.225 1.00130.22 S ATOM 6014 SG CYS C 64 85.148 98.270 40.213 1.00133.74 S ATOM 6074 SG CYS C 73 87.616 98.115 37.269 1.00131.48 S ATOM 6091 SG CYS C 76 88.703 96.655 40.275 1.00132.05 S ATOM 6113 SG CYS C 79 85.695 94.942 38.600 1.00138.02 S ATOM 8861 SG CYS D 64 80.473 48.045 15.059 1.00225.47 S ATOM 8921 SG CYS D 73 79.981 45.792 11.916 1.00236.74 S ATOM 8938 SG CYS D 76 81.902 44.381 14.588 1.00233.85 S ATOM 8960 SG CYS D 79 78.454 45.152 15.547 1.00235.24 S ATOM 11584 SG CYS E 50 52.531 13.141 52.331 1.00136.85 S ATOM 11653 SG CYS E 59 51.273 10.418 54.250 1.00142.62 S ATOM 11673 SG CYS E 62 54.320 12.276 55.706 1.00129.64 S ATOM 11694 SG CYS E 65 51.332 14.252 55.701 1.00137.78 S Time building chain proxies: 3.71, per 1000 atoms: 0.26 Number of scatterers: 14113 At special positions: 0 Unit cell: (105.984, 127.512, 120.06, 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 71 16.00 P 7 15.00 Mg 1 11.99 O 2600 8.00 N 2552 7.00 C 8878 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: 1.34 Conformation dependent library (CDL) restraints added in 602.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 64 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 79 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 76 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 76 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 64 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 79 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 79 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 76 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 73 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 64 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 62 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 65 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 59 " Number of angles added : 24 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 7 sheets defined 66.7% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 4.124A pdb=" N ARG A 10 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 46 removed outlier: 3.652A pdb=" N LEU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 69 Processing helix chain 'A' and resid 90 through 104 removed outlier: 3.814A pdb=" N GLU A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 removed outlier: 3.889A pdb=" N ASN A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 130 removed outlier: 3.915A pdb=" N THR A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 130 " --> pdb=" O TRP A 126 " (cutoff:3.500A) No H-bonds generated for '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 208 removed outlier: 3.971A pdb=" N GLN A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.816A pdb=" N TRP A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 239 Processing helix chain 'A' and resid 242 through 265 removed outlier: 3.913A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 279 through 293 removed outlier: 4.657A pdb=" N GLY A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N MET A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 316 Processing helix chain 'A' and resid 319 through 332 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.566A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 4 No H-bonds generated for 'chain 'B' and resid 2 through 4' Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 21 through 35 removed outlier: 3.871A pdb=" N ALA B 27 " --> pdb=" O HIS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 76 through 85 removed outlier: 3.777A pdb=" N GLU B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 109 through 113 removed outlier: 4.226A pdb=" N GLN B 112 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 131 Processing helix chain 'B' and resid 132 through 145 removed outlier: 4.189A pdb=" N ALA B 138 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.841A pdb=" N GLU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 249 through 259 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 277 through 298 removed outlier: 3.728A pdb=" N LEU B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 321 through 339 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 344 through 358 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 21 through 35 Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.834A pdb=" N GLU C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 110 removed outlier: 3.965A pdb=" N THR C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 132 through 145 Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 179 through 194 Processing helix chain 'C' and resid 199 through 210 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 274 Processing helix chain 'C' and resid 277 through 298 Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 309 through 318 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 21 through 35 removed outlier: 4.024A pdb=" N LEU D 25 " --> pdb=" O GLN D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 63 removed outlier: 3.641A pdb=" N ASN D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 84 removed outlier: 3.576A pdb=" N ILE D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 132 through 145 removed outlier: 3.692A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 3.729A 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: 3.536A pdb=" N ARG D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 199 through 210 Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.934A pdb=" N ALA D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 277 through 298 Processing helix chain 'D' and resid 299 through 302 removed outlier: 3.839A pdb=" N LEU D 302 " --> pdb=" O PRO D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 299 through 302' Processing helix chain 'D' and resid 303 through 307 removed outlier: 3.551A pdb=" N MET D 306 " --> pdb=" O GLY D 303 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D 307 " --> pdb=" O ASN D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 307' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 321 through 339 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'E' and resid 6 through 20 removed outlier: 4.152A pdb=" N ASP E 10 " --> pdb=" O TRP E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 89 through 102 removed outlier: 3.804A pdb=" N VAL E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 121 through 134 Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 152 through 159 Processing helix chain 'E' and resid 168 through 178 Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 197 through 206 removed outlier: 3.828A pdb=" N PHE E 205 " --> pdb=" O ALA E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 227 Proline residue: E 225 - end of helix Processing helix chain 'E' and resid 228 through 231 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 removed outlier: 3.512A pdb=" N VAL E 274 " --> pdb=" O VAL E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 303 Processing helix chain 'E' and resid 307 through 323 Processing helix chain 'J' and resid 4 through 13 Processing helix chain 'J' and resid 21 through 25 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 54 removed outlier: 6.997A pdb=" N GLN A 78 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ILE A 111 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU A 80 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ARG A 113 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 82 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 114 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 135 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.077A 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 93 removed outlier: 6.607A pdb=" N ILE B 91 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP B 126 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE B 93 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N TYR B 41 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR B 156 " --> pdb=" O TYR B 41 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE B 43 " --> pdb=" O THR B 156 " (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: 6.510A pdb=" N ILE C 91 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP C 126 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE C 93 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LYS C 121 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU C 153 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA C 155 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE C 125 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA C 40 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N PHE C 173 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU C 42 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU C 175 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER C 44 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 152 through 156 removed outlier: 5.954A pdb=" N TYR D 41 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR D 156 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N PHE D 43 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.668A pdb=" N TYR E 77 " --> pdb=" O TRP E 113 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA E 26 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N HIS E 162 " --> pdb=" O ALA E 26 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU E 28 " --> pdb=" O HIS E 162 " (cutoff:3.500A) 792 hydrogen bonds defined for protein. 2316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 4963 1.37 - 1.51: 4159 1.51 - 1.66: 5133 1.66 - 1.80: 92 1.80 - 1.95: 22 Bond restraints: 14369 Sorted by residual: bond pdb=" C4 ADP D 702 " pdb=" C5 ADP D 702 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C4 ADP B 702 " pdb=" C5 ADP B 702 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C5 ADP B 702 " pdb=" C6 ADP B 702 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C5 ADP D 702 " pdb=" C6 ADP D 702 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" N VAL D 19 " pdb=" CA VAL D 19 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.18e+00 ... (remaining 14364 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 19196 2.18 - 4.37: 283 4.37 - 6.55: 30 6.55 - 8.74: 10 8.74 - 10.92: 11 Bond angle restraints: 19530 Sorted by residual: angle pdb=" C ARG B 98 " pdb=" N THR B 99 " pdb=" CA THR B 99 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" N GLU D 22 " pdb=" CA GLU D 22 " pdb=" C GLU D 22 " ideal model delta sigma weight residual 113.23 108.32 4.91 1.24e+00 6.50e-01 1.57e+01 angle pdb=" C HIS B 360 " pdb=" CA HIS B 360 " pdb=" CB HIS B 360 " ideal model delta sigma weight residual 109.20 114.94 -5.74 1.50e+00 4.44e-01 1.47e+01 angle pdb=" N ALA D 16 " pdb=" CA ALA D 16 " pdb=" C ALA D 16 " ideal model delta sigma weight residual 112.97 108.97 4.00 1.06e+00 8.90e-01 1.42e+01 angle pdb=" C1' ADP B 702 " pdb=" C2' ADP B 702 " pdb=" C3' ADP B 702 " ideal model delta sigma weight residual 111.00 100.08 10.92 3.00e+00 1.11e-01 1.33e+01 ... (remaining 19525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.18: 8452 29.18 - 58.35: 261 58.35 - 87.53: 38 87.53 - 116.70: 3 116.70 - 145.88: 4 Dihedral angle restraints: 8758 sinusoidal: 3552 harmonic: 5206 Sorted by residual: dihedral pdb=" C2' ADP D 702 " pdb=" C1' ADP D 702 " pdb=" N9 ADP D 702 " pdb=" C4 ADP D 702 " ideal model delta sinusoidal sigma weight residual 91.55 -122.58 -145.88 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" O2A ADP D 702 " pdb=" O3A ADP D 702 " pdb=" PA ADP D 702 " pdb=" PB ADP D 702 " ideal model delta sinusoidal sigma weight residual 300.00 175.39 124.61 1 2.00e+01 2.50e-03 3.76e+01 dihedral pdb=" O1B ADP D 702 " pdb=" O3A ADP D 702 " pdb=" PB ADP D 702 " pdb=" PA ADP D 702 " ideal model delta sinusoidal sigma weight residual 300.00 179.91 120.09 1 2.00e+01 2.50e-03 3.60e+01 ... (remaining 8755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1702 0.044 - 0.088: 463 0.088 - 0.132: 93 0.132 - 0.177: 5 0.177 - 0.221: 4 Chirality restraints: 2267 Sorted by residual: chirality pdb=" CB VAL D 19 " pdb=" CA VAL D 19 " pdb=" CG1 VAL D 19 " pdb=" CG2 VAL D 19 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA VAL D 18 " pdb=" N VAL D 18 " pdb=" C VAL D 18 " pdb=" CB VAL D 18 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C3' ADP B 702 " pdb=" C2' ADP B 702 " pdb=" C4' ADP B 702 " pdb=" O3' ADP B 702 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 8.97e-01 ... (remaining 2264 not shown) Planarity restraints: 2524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 213 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO A 214 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 214 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 214 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 99 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C THR B 99 " 0.033 2.00e-02 2.50e+03 pdb=" O THR B 99 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS B 100 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 146 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO B 147 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 147 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 147 " -0.023 5.00e-02 4.00e+02 ... (remaining 2521 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 6 2.56 - 3.15: 11201 3.15 - 3.73: 22305 3.73 - 4.32: 29320 4.32 - 4.90: 49613 Nonbonded interactions: 112445 Sorted by model distance: nonbonded pdb=" O2B AGS C 702 " pdb="MG MG C 703 " model vdw 1.977 2.170 nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 703 " model vdw 1.991 2.170 nonbonded pdb=" O3G AGS C 702 " pdb="MG MG C 703 " model vdw 2.368 2.170 nonbonded pdb=" O ILE E 289 " pdb=" OD1 ASP E 292 " model vdw 2.513 3.040 nonbonded pdb=" O2A AGS C 702 " pdb="MG MG C 703 " model vdw 2.536 2.170 ... (remaining 112440 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 5 through 361) selection = (chain 'C' and (resid 5 through 246 or resid 248 through 361)) selection = (chain 'D' and (resid 5 through 246 or resid 248 through 361)) } 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: 2.240 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.090 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 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:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 14385 Z= 0.225 Angle : 0.734 13.561 19554 Z= 0.364 Chirality : 0.041 0.221 2267 Planarity : 0.004 0.050 2524 Dihedral : 14.443 145.877 5374 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.13 % Allowed : 2.83 % Favored : 97.03 % 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: 1.60 (0.20), residues: 1780 helix: 1.59 (0.16), residues: 1070 sheet: 0.21 (0.44), residues: 131 loop : 0.45 (0.28), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 47 TYR 0.016 0.002 TYR A 172 PHE 0.013 0.002 PHE C 136 TRP 0.020 0.002 TRP A 279 HIS 0.012 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.22 (14369) covalent geometry : angle 0.69614 / 0.36 (19530) hydrogen bonds : bond 0.15520 / 10.53 ( 792) hydrogen bonds : angle 5.13178 / 3.74 ( 2316) metal coordination : bond 0.01082 / 0.82 ( 16) metal coordination : angle 6.68327 / 4.20 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 413 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5541 (tmm) cc_final: 0.4395 (tpt) REVERT: A 71 MET cc_start: 0.6584 (tpt) cc_final: 0.6108 (tpt) REVERT: A 197 LEU cc_start: 0.8522 (mp) cc_final: 0.8085 (mp) REVERT: A 342 ASP cc_start: 0.8806 (m-30) cc_final: 0.8488 (m-30) REVERT: B 172 GLN cc_start: 0.9023 (tt0) cc_final: 0.8821 (tt0) REVERT: B 222 ASP cc_start: 0.8831 (t0) cc_final: 0.8602 (t0) REVERT: B 298 SER cc_start: 0.8578 (t) cc_final: 0.8199 (p) REVERT: C 94 ASP cc_start: 0.8420 (t70) cc_final: 0.8182 (t0) REVERT: C 190 ILE cc_start: 0.8914 (mt) cc_final: 0.8671 (mm) REVERT: C 288 LEU cc_start: 0.8994 (mt) cc_final: 0.8766 (mt) REVERT: C 353 LEU cc_start: 0.8677 (mt) cc_final: 0.8428 (mt) REVERT: D 28 LEU cc_start: 0.8238 (mt) cc_final: 0.8032 (mt) REVERT: D 32 LEU cc_start: 0.8276 (mt) cc_final: 0.7757 (tt) REVERT: D 182 GLN cc_start: 0.8950 (mt0) cc_final: 0.8696 (mt0) REVERT: D 194 GLU cc_start: 0.8522 (tp30) cc_final: 0.8208 (tp30) REVERT: D 246 ASP cc_start: 0.8403 (t70) cc_final: 0.8173 (t0) REVERT: D 324 ASP cc_start: 0.8371 (m-30) cc_final: 0.8081 (m-30) REVERT: E 57 LYS cc_start: 0.9065 (mttt) cc_final: 0.8788 (mppt) REVERT: E 59 CYS cc_start: 0.4711 (m) cc_final: 0.3926 (t) REVERT: E 86 ASN cc_start: 0.8330 (t0) cc_final: 0.8050 (t0) REVERT: E 185 ASP cc_start: 0.8454 (m-30) cc_final: 0.8227 (m-30) REVERT: J 26 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8946 (mm-40) outliers start: 2 outliers final: 0 residues processed: 413 average time/residue: 0.7367 time to fit residues: 327.4683 Evaluate side-chains 302 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 266 HIS B 63 ASN B 110 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 248 GLN D 39 HIS D 223 GLN D 231 GLN D 269 ASN D 330 GLN E 240 GLN E 287 GLN E 324 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.106998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.073882 restraints weight = 30987.055| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.41 r_work: 0.2798 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14385 Z= 0.157 Angle : 0.728 12.811 19554 Z= 0.334 Chirality : 0.041 0.232 2267 Planarity : 0.005 0.051 2524 Dihedral : 8.542 144.155 1998 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.17 % Allowed : 14.83 % Favored : 82.00 % 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: 1.77 (0.20), residues: 1780 helix: 1.79 (0.16), residues: 1092 sheet: 0.29 (0.45), residues: 131 loop : 0.29 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 10 TYR 0.022 0.002 TYR B 113 PHE 0.014 0.002 PHE B 136 TRP 0.020 0.002 TRP A 150 HIS 0.010 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (14369) covalent geometry : angle 0.68616 / 0.33 (19530) hydrogen bonds : bond 0.04500 / 2.99 ( 792) hydrogen bonds : angle 4.15539 / 3.01 ( 2316) metal coordination : bond 0.00613 / 0.37 ( 16) metal coordination : angle 6.96678 / 4.61 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5493 (tmm) cc_final: 0.4390 (tpt) REVERT: A 71 MET cc_start: 0.6593 (tpt) cc_final: 0.6107 (tpt) REVERT: A 81 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.9002 (tm) REVERT: A 342 ASP cc_start: 0.8795 (m-30) cc_final: 0.8584 (m-30) REVERT: B 38 HIS cc_start: 0.6998 (t-90) cc_final: 0.6614 (t-90) REVERT: B 60 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8577 (tttt) REVERT: B 148 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8112 (tm-30) REVERT: B 149 HIS cc_start: 0.8267 (m90) cc_final: 0.7993 (m90) REVERT: B 298 SER cc_start: 0.8645 (t) cc_final: 0.8274 (p) REVERT: B 357 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8662 (tt) REVERT: C 94 ASP cc_start: 0.8442 (t70) cc_final: 0.8210 (t0) REVERT: C 106 ASP cc_start: 0.8633 (t0) cc_final: 0.8361 (t0) REVERT: C 141 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8743 (mttp) REVERT: D 32 LEU cc_start: 0.8346 (mt) cc_final: 0.7835 (tt) REVERT: D 130 MET cc_start: 0.5813 (ptt) cc_final: 0.5056 (pmm) REVERT: D 173 PHE cc_start: 0.7824 (m-80) cc_final: 0.7457 (m-10) REVERT: D 194 GLU cc_start: 0.8497 (tp30) cc_final: 0.8211 (tp30) REVERT: D 208 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8067 (ttp80) REVERT: E 57 LYS cc_start: 0.9062 (mttt) cc_final: 0.8826 (mppt) REVERT: E 59 CYS cc_start: 0.4769 (m) cc_final: 0.3986 (t) REVERT: E 67 LEU cc_start: 0.8397 (mm) cc_final: 0.8143 (mm) REVERT: E 86 ASN cc_start: 0.8396 (t0) cc_final: 0.8105 (t0) REVERT: J 26 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8950 (mm-40) outliers start: 47 outliers final: 12 residues processed: 336 average time/residue: 0.7423 time to fit residues: 268.6058 Evaluate side-chains 308 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 293 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 264 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 40.0000 chunk 18 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 68 optimal weight: 0.0070 chunk 148 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 167 optimal weight: 0.0770 chunk 41 optimal weight: 9.9990 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 GLN D 304 ASN E 24 HIS E 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.106241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.073921 restraints weight = 30877.777| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.32 r_work: 0.2772 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14385 Z= 0.186 Angle : 0.754 13.266 19554 Z= 0.341 Chirality : 0.042 0.204 2267 Planarity : 0.005 0.053 2524 Dihedral : 8.489 144.296 1998 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.11 % Allowed : 16.12 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.20), residues: 1780 helix: 1.72 (0.16), residues: 1096 sheet: 0.01 (0.43), residues: 126 loop : 0.24 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 11 TYR 0.014 0.002 TYR B 113 PHE 0.012 0.002 PHE C 120 TRP 0.042 0.002 TRP A 150 HIS 0.010 0.001 HIS D 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (14369) covalent geometry : angle 0.71436 / 0.34 (19530) hydrogen bonds : bond 0.04382 / 2.91 ( 792) hydrogen bonds : angle 4.00391 / 2.88 ( 2316) metal coordination : bond 0.00576 / 0.35 ( 16) metal coordination : angle 6.94841 / 4.65 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 296 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5093 (tmm) cc_final: 0.3851 (tpt) REVERT: A 71 MET cc_start: 0.6437 (tpt) cc_final: 0.5968 (tpt) REVERT: A 81 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.7759 (tm) REVERT: A 334 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7823 (ttmm) REVERT: B 60 LYS cc_start: 0.8962 (ttmm) cc_final: 0.8583 (tttt) REVERT: B 148 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8119 (tm-30) REVERT: B 149 HIS cc_start: 0.8268 (m90) cc_final: 0.7993 (m90) REVERT: B 222 ASP cc_start: 0.8929 (t0) cc_final: 0.8645 (t0) REVERT: B 256 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7943 (ttm) REVERT: B 298 SER cc_start: 0.8671 (t) cc_final: 0.8283 (p) REVERT: B 357 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8715 (tp) REVERT: C 106 ASP cc_start: 0.8404 (t0) cc_final: 0.8012 (t0) REVERT: C 141 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8795 (mttp) REVERT: C 248 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7899 (tp40) REVERT: C 354 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8584 (mm) REVERT: D 32 LEU cc_start: 0.8309 (mt) cc_final: 0.7827 (tt) REVERT: D 194 GLU cc_start: 0.8504 (tp30) cc_final: 0.8208 (tp30) REVERT: D 208 ARG cc_start: 0.8666 (ttp80) cc_final: 0.8049 (ttp80) REVERT: D 246 ASP cc_start: 0.8116 (t0) cc_final: 0.7884 (t0) REVERT: E 57 LYS cc_start: 0.9026 (mttt) cc_final: 0.8820 (mppt) REVERT: E 59 CYS cc_start: 0.4881 (m) cc_final: 0.4115 (t) REVERT: E 67 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8222 (mm) REVERT: E 86 ASN cc_start: 0.8395 (t0) cc_final: 0.8114 (t0) outliers start: 61 outliers final: 15 residues processed: 326 average time/residue: 0.7794 time to fit residues: 273.2215 Evaluate side-chains 313 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 290 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 264 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 149 optimal weight: 0.0000 chunk 44 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN A 259 ASN B 110 ASN ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN D 223 GLN D 231 GLN E 24 HIS E 259 HIS E 287 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.107216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.075068 restraints weight = 31049.086| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.35 r_work: 0.2799 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14385 Z= 0.135 Angle : 0.713 12.856 19554 Z= 0.322 Chirality : 0.040 0.178 2267 Planarity : 0.005 0.073 2524 Dihedral : 8.321 144.501 1998 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.59 % Allowed : 17.73 % Favored : 77.68 % 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: 1.75 (0.20), residues: 1780 helix: 1.81 (0.16), residues: 1102 sheet: -0.08 (0.42), residues: 128 loop : 0.27 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 146 TYR 0.015 0.001 TYR B 113 PHE 0.015 0.001 PHE A 127 TRP 0.056 0.002 TRP A 150 HIS 0.013 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (14369) covalent geometry : angle 0.67587 / 0.32 (19530) hydrogen bonds : bond 0.03786 / 2.51 ( 792) hydrogen bonds : angle 3.89189 / 2.80 ( 2316) metal coordination : bond 0.00531 / 0.31 ( 16) metal coordination : angle 6.48349 / 4.42 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 310 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5388 (tmm) cc_final: 0.4228 (tpt) REVERT: A 71 MET cc_start: 0.6460 (tpt) cc_final: 0.5991 (tpt) REVERT: A 202 VAL cc_start: 0.7039 (OUTLIER) cc_final: 0.6618 (t) REVERT: B 60 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8499 (tttt) REVERT: B 110 ASN cc_start: 0.7614 (t0) cc_final: 0.7341 (t160) REVERT: B 148 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8118 (tm-30) REVERT: B 149 HIS cc_start: 0.8291 (m90) cc_final: 0.7854 (m90) REVERT: B 151 LYS cc_start: 0.8421 (mmmt) cc_final: 0.7957 (mmmt) REVERT: B 222 ASP cc_start: 0.8877 (t0) cc_final: 0.8591 (t0) REVERT: B 256 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7777 (ttm) REVERT: B 298 SER cc_start: 0.8654 (t) cc_final: 0.8242 (p) REVERT: C 6 LEU cc_start: 0.9223 (mt) cc_final: 0.8966 (tt) REVERT: C 141 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8784 (mttp) REVERT: C 248 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7864 (tp40) REVERT: C 277 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: D 32 LEU cc_start: 0.8334 (mt) cc_final: 0.7996 (tp) REVERT: D 194 GLU cc_start: 0.8487 (tp30) cc_final: 0.8076 (mm-30) REVERT: D 208 ARG cc_start: 0.8637 (ttp80) cc_final: 0.8057 (ttp80) REVERT: D 246 ASP cc_start: 0.8152 (t0) cc_final: 0.7939 (t0) REVERT: E 57 LYS cc_start: 0.9035 (mttt) cc_final: 0.8812 (mppt) REVERT: E 59 CYS cc_start: 0.4691 (m) cc_final: 0.3915 (t) REVERT: E 67 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8226 (mm) REVERT: E 86 ASN cc_start: 0.8391 (t0) cc_final: 0.8101 (t0) outliers start: 68 outliers final: 23 residues processed: 346 average time/residue: 0.7399 time to fit residues: 275.9262 Evaluate side-chains 320 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 291 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 164 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 128 optimal weight: 0.2980 chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS D 39 HIS D 182 GLN D 231 GLN E 24 HIS E 259 HIS E 287 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.107057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.074950 restraints weight = 30851.885| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.35 r_work: 0.2795 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14385 Z= 0.144 Angle : 0.738 13.443 19554 Z= 0.334 Chirality : 0.041 0.299 2267 Planarity : 0.005 0.083 2524 Dihedral : 8.250 145.018 1998 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.52 % Allowed : 19.96 % Favored : 75.52 % 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: 1.78 (0.20), residues: 1780 helix: 1.82 (0.16), residues: 1097 sheet: 0.04 (0.43), residues: 128 loop : 0.30 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 80 TYR 0.024 0.001 TYR E 47 PHE 0.012 0.001 PHE D 173 TRP 0.053 0.002 TRP A 150 HIS 0.009 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (14369) covalent geometry : angle 0.69321 / 0.33 (19530) hydrogen bonds : bond 0.03812 / 2.51 ( 792) hydrogen bonds : angle 3.88359 / 2.79 ( 2316) metal coordination : bond 0.00624 / 0.42 ( 16) metal coordination : angle 7.29935 / 4.80 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 298 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5131 (tmm) cc_final: 0.4008 (tpt) REVERT: A 71 MET cc_start: 0.6420 (tpt) cc_final: 0.5956 (tpt) REVERT: A 82 LEU cc_start: 0.9229 (pt) cc_final: 0.8895 (tm) REVERT: B 60 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8549 (tttt) REVERT: B 110 ASN cc_start: 0.7605 (t0) cc_final: 0.7301 (t160) REVERT: B 148 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8137 (tm-30) REVERT: B 149 HIS cc_start: 0.8333 (m90) cc_final: 0.7904 (m90) REVERT: B 151 LYS cc_start: 0.8375 (mmmt) cc_final: 0.8009 (mmmt) REVERT: B 222 ASP cc_start: 0.8903 (t0) cc_final: 0.8630 (t0) REVERT: B 256 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7913 (ttm) REVERT: B 298 SER cc_start: 0.8640 (t) cc_final: 0.8245 (p) REVERT: C 36 ARG cc_start: 0.8548 (ttm110) cc_final: 0.8182 (ptp-110) REVERT: C 94 ASP cc_start: 0.8443 (t0) cc_final: 0.8078 (t0) REVERT: C 141 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8826 (mttp) REVERT: C 274 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8000 (ttp-170) REVERT: C 277 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: D 32 LEU cc_start: 0.8318 (mt) cc_final: 0.7972 (tp) REVERT: D 130 MET cc_start: 0.5445 (ptt) cc_final: 0.5084 (ptt) REVERT: D 194 GLU cc_start: 0.8467 (tp30) cc_final: 0.8143 (tp30) REVERT: D 208 ARG cc_start: 0.8643 (ttp80) cc_final: 0.8062 (ttp80) REVERT: E 13 LYS cc_start: 0.9024 (ttpp) cc_final: 0.8756 (tttm) REVERT: E 57 LYS cc_start: 0.9033 (mttt) cc_final: 0.8831 (mppt) REVERT: E 59 CYS cc_start: 0.4701 (m) cc_final: 0.3923 (t) REVERT: E 67 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8232 (mm) REVERT: E 86 ASN cc_start: 0.8373 (t0) cc_final: 0.8100 (t0) outliers start: 67 outliers final: 24 residues processed: 334 average time/residue: 0.7152 time to fit residues: 257.8602 Evaluate side-chains 317 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 288 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 164 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 148 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 136 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 167 ASN A 259 ASN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN D 231 GLN E 24 HIS E 287 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.106977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.075001 restraints weight = 30642.921| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.34 r_work: 0.2792 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14385 Z= 0.143 Angle : 0.746 15.076 19554 Z= 0.338 Chirality : 0.041 0.278 2267 Planarity : 0.005 0.063 2524 Dihedral : 8.171 145.519 1998 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.98 % Allowed : 21.58 % Favored : 74.44 % 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 (0.20), residues: 1780 helix: 1.81 (0.16), residues: 1091 sheet: 0.12 (0.43), residues: 136 loop : 0.34 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 80 TYR 0.018 0.001 TYR E 47 PHE 0.007 0.001 PHE C 120 TRP 0.059 0.002 TRP A 150 HIS 0.006 0.001 HIS B 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (14369) covalent geometry : angle 0.70833 / 0.34 (19530) hydrogen bonds : bond 0.03712 / 2.45 ( 792) hydrogen bonds : angle 3.90162 / 2.79 ( 2316) metal coordination : bond 0.00645 / 0.43 ( 16) metal coordination : angle 6.68005 / 4.45 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 297 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5356 (tmm) cc_final: 0.4370 (tpt) REVERT: A 71 MET cc_start: 0.6405 (tpt) cc_final: 0.5951 (tpt) REVERT: A 81 LEU cc_start: 0.8719 (tm) cc_final: 0.8440 (tm) REVERT: A 82 LEU cc_start: 0.9288 (pt) cc_final: 0.8898 (tm) REVERT: A 171 CYS cc_start: 0.8888 (t) cc_final: 0.8487 (m) REVERT: A 334 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7746 (ttmm) REVERT: B 60 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8485 (tttt) REVERT: B 110 ASN cc_start: 0.7573 (t0) cc_final: 0.7280 (t160) REVERT: B 148 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8169 (tm-30) REVERT: B 149 HIS cc_start: 0.8314 (m90) cc_final: 0.7864 (m90) REVERT: B 151 LYS cc_start: 0.8348 (mmmt) cc_final: 0.7892 (mmtt) REVERT: B 256 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7892 (ttm) REVERT: B 298 SER cc_start: 0.8686 (t) cc_final: 0.8248 (p) REVERT: C 6 LEU cc_start: 0.9226 (mt) cc_final: 0.8974 (tt) REVERT: C 94 ASP cc_start: 0.8474 (t0) cc_final: 0.8030 (t0) REVERT: C 167 LEU cc_start: 0.8975 (tp) cc_final: 0.8686 (mt) REVERT: C 277 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: D 32 LEU cc_start: 0.8300 (mt) cc_final: 0.7965 (tp) REVERT: D 130 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.5424 (ptt) REVERT: D 194 GLU cc_start: 0.8485 (tp30) cc_final: 0.8093 (mm-30) REVERT: D 201 ARG cc_start: 0.8557 (tpt-90) cc_final: 0.8244 (tpp80) REVERT: E 57 LYS cc_start: 0.9014 (mttt) cc_final: 0.8786 (mppt) REVERT: E 59 CYS cc_start: 0.4694 (m) cc_final: 0.3903 (t) REVERT: E 67 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8279 (mm) REVERT: E 86 ASN cc_start: 0.8407 (t0) cc_final: 0.8132 (t0) outliers start: 59 outliers final: 26 residues processed: 326 average time/residue: 0.7360 time to fit residues: 258.4872 Evaluate side-chains 314 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 204 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 160 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 145 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN D 231 GLN E 24 HIS E 287 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.105780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.073742 restraints weight = 30760.110| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.30 r_work: 0.2767 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14385 Z= 0.179 Angle : 0.781 15.532 19554 Z= 0.358 Chirality : 0.042 0.270 2267 Planarity : 0.006 0.071 2524 Dihedral : 8.204 146.074 1998 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.44 % Allowed : 23.53 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.20), residues: 1780 helix: 1.65 (0.16), residues: 1095 sheet: 0.18 (0.43), residues: 129 loop : 0.29 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 208 TYR 0.015 0.002 TYR E 47 PHE 0.011 0.001 PHE C 120 TRP 0.026 0.002 TRP A 150 HIS 0.006 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (14369) covalent geometry : angle 0.74420 / 0.36 (19530) hydrogen bonds : bond 0.04106 / 2.71 ( 792) hydrogen bonds : angle 3.95224 / 2.84 ( 2316) metal coordination : bond 0.00618 / 0.40 ( 16) metal coordination : angle 6.78634 / 4.55 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 292 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5239 (tmm) cc_final: 0.4040 (tpt) REVERT: A 71 MET cc_start: 0.6276 (tpt) cc_final: 0.5812 (tpt) REVERT: A 82 LEU cc_start: 0.9169 (pt) cc_final: 0.8795 (tm) REVERT: A 171 CYS cc_start: 0.8907 (t) cc_final: 0.8531 (m) REVERT: A 334 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7754 (ttmm) REVERT: B 60 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8515 (tttt) REVERT: B 110 ASN cc_start: 0.7681 (t0) cc_final: 0.7397 (t160) REVERT: B 148 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8111 (tm-30) REVERT: B 149 HIS cc_start: 0.8370 (m90) cc_final: 0.8161 (m90) REVERT: B 151 LYS cc_start: 0.8380 (mmmt) cc_final: 0.7989 (mmtt) REVERT: B 222 ASP cc_start: 0.8886 (t0) cc_final: 0.8682 (t0) REVERT: B 298 SER cc_start: 0.8660 (t) cc_final: 0.8271 (p) REVERT: C 6 LEU cc_start: 0.9277 (mt) cc_final: 0.8999 (tt) REVERT: C 94 ASP cc_start: 0.8441 (t0) cc_final: 0.8005 (t0) REVERT: C 105 ARG cc_start: 0.7992 (ptt180) cc_final: 0.7731 (ptt180) REVERT: C 167 LEU cc_start: 0.9004 (tp) cc_final: 0.8712 (mt) REVERT: C 176 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8459 (mtpp) REVERT: C 274 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8238 (ttp-110) REVERT: C 277 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7314 (tm-30) REVERT: D 32 LEU cc_start: 0.8345 (mt) cc_final: 0.8021 (tp) REVERT: D 130 MET cc_start: 0.5732 (OUTLIER) cc_final: 0.5391 (ptt) REVERT: D 194 GLU cc_start: 0.8502 (tp30) cc_final: 0.8172 (tp30) REVERT: E 57 LYS cc_start: 0.9029 (mttt) cc_final: 0.8819 (mppt) REVERT: E 59 CYS cc_start: 0.4758 (m) cc_final: 0.4015 (t) REVERT: E 67 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8245 (mm) REVERT: E 86 ASN cc_start: 0.8435 (t0) cc_final: 0.8175 (t0) outliers start: 51 outliers final: 26 residues processed: 318 average time/residue: 0.7828 time to fit residues: 267.7758 Evaluate side-chains 312 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 204 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 20.0000 chunk 156 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 259 ASN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 GLN E 24 HIS E 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.105252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.073302 restraints weight = 30771.572| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.30 r_work: 0.2755 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14385 Z= 0.184 Angle : 0.795 16.631 19554 Z= 0.365 Chirality : 0.043 0.286 2267 Planarity : 0.006 0.083 2524 Dihedral : 8.215 146.687 1998 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.44 % Allowed : 24.14 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.20), residues: 1780 helix: 1.58 (0.16), residues: 1103 sheet: 0.23 (0.41), residues: 141 loop : 0.32 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 80 TYR 0.015 0.002 TYR C 113 PHE 0.019 0.002 PHE A 127 TRP 0.038 0.002 TRP A 150 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (14369) covalent geometry : angle 0.75918 / 0.36 (19530) hydrogen bonds : bond 0.04143 / 2.74 ( 792) hydrogen bonds : angle 3.96623 / 2.84 ( 2316) metal coordination : bond 0.00647 / 0.40 ( 16) metal coordination : angle 6.81961 / 4.52 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 295 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5275 (tmm) cc_final: 0.4061 (tpt) REVERT: A 71 MET cc_start: 0.6333 (tpt) cc_final: 0.5852 (tpt) REVERT: A 82 LEU cc_start: 0.9211 (pt) cc_final: 0.8901 (tm) REVERT: A 334 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7799 (mtmm) REVERT: B 60 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8517 (tttt) REVERT: B 110 ASN cc_start: 0.7840 (t0) cc_final: 0.7529 (t160) REVERT: B 148 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8119 (tm-30) REVERT: B 149 HIS cc_start: 0.8373 (m90) cc_final: 0.8114 (m90) REVERT: B 151 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8121 (mmmt) REVERT: B 298 SER cc_start: 0.8656 (t) cc_final: 0.8285 (p) REVERT: C 6 LEU cc_start: 0.9255 (mt) cc_final: 0.8988 (tt) REVERT: C 94 ASP cc_start: 0.8421 (t0) cc_final: 0.7969 (t0) REVERT: C 105 ARG cc_start: 0.7989 (ptt180) cc_final: 0.7620 (ptt180) REVERT: C 176 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8452 (mtpp) REVERT: C 274 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8253 (ttp-110) REVERT: C 277 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: D 32 LEU cc_start: 0.8424 (mt) cc_final: 0.8023 (tt) REVERT: D 130 MET cc_start: 0.5758 (OUTLIER) cc_final: 0.5457 (ptt) REVERT: D 194 GLU cc_start: 0.8521 (tp30) cc_final: 0.8189 (tp30) REVERT: E 59 CYS cc_start: 0.4819 (m) cc_final: 0.4082 (t) REVERT: E 67 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8246 (mm) REVERT: E 86 ASN cc_start: 0.8396 (t0) cc_final: 0.8144 (t0) outliers start: 51 outliers final: 24 residues processed: 323 average time/residue: 0.7819 time to fit residues: 272.1481 Evaluate side-chains 315 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 285 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 204 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 148 optimal weight: 0.9980 chunk 174 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 146 optimal weight: 0.0470 chunk 69 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 175 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 259 ASN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 GLN D 326 GLN E 24 HIS E 287 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.106542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.074452 restraints weight = 30966.696| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.41 r_work: 0.2785 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14385 Z= 0.147 Angle : 0.811 14.520 19554 Z= 0.375 Chirality : 0.042 0.304 2267 Planarity : 0.006 0.088 2524 Dihedral : 8.131 146.952 1998 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.83 % Allowed : 25.08 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.20), residues: 1780 helix: 1.64 (0.16), residues: 1101 sheet: 0.25 (0.42), residues: 141 loop : 0.36 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 80 TYR 0.016 0.001 TYR E 47 PHE 0.007 0.001 PHE B 136 TRP 0.047 0.002 TRP A 150 HIS 0.006 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (14369) covalent geometry : angle 0.77568 / 0.37 (19530) hydrogen bonds : bond 0.03770 / 2.47 ( 792) hydrogen bonds : angle 3.95314 / 2.83 ( 2316) metal coordination : bond 0.00561 / 0.35 ( 16) metal coordination : angle 6.77186 / 4.45 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 294 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5187 (tmm) cc_final: 0.3966 (tpt) REVERT: A 30 LEU cc_start: 0.8547 (mm) cc_final: 0.8334 (mp) REVERT: A 71 MET cc_start: 0.5971 (tpt) cc_final: 0.5522 (tpt) REVERT: A 81 LEU cc_start: 0.8694 (tm) cc_final: 0.8453 (tm) REVERT: A 82 LEU cc_start: 0.9180 (pt) cc_final: 0.8882 (tm) REVERT: B 60 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8499 (tttt) REVERT: B 110 ASN cc_start: 0.7794 (t0) cc_final: 0.7506 (t160) REVERT: B 148 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8066 (tm-30) REVERT: B 149 HIS cc_start: 0.8352 (m90) cc_final: 0.8093 (m90) REVERT: B 151 LYS cc_start: 0.8343 (mmmt) cc_final: 0.8081 (mmmt) REVERT: B 222 ASP cc_start: 0.8813 (t0) cc_final: 0.8608 (t0) REVERT: B 298 SER cc_start: 0.8704 (t) cc_final: 0.8310 (p) REVERT: C 6 LEU cc_start: 0.9267 (mt) cc_final: 0.8980 (tt) REVERT: C 94 ASP cc_start: 0.8436 (t0) cc_final: 0.7942 (t0) REVERT: C 105 ARG cc_start: 0.8002 (ptt180) cc_final: 0.7723 (ptt180) REVERT: C 176 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8420 (mtpp) REVERT: C 277 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: D 32 LEU cc_start: 0.8486 (mt) cc_final: 0.8102 (tt) REVERT: D 130 MET cc_start: 0.5924 (OUTLIER) cc_final: 0.5614 (ptt) REVERT: D 194 GLU cc_start: 0.8465 (tp30) cc_final: 0.8142 (tp30) REVERT: E 57 LYS cc_start: 0.8627 (mppt) cc_final: 0.8421 (mppt) REVERT: E 59 CYS cc_start: 0.4994 (m) cc_final: 0.4262 (t) REVERT: E 86 ASN cc_start: 0.8448 (t0) cc_final: 0.8166 (t0) outliers start: 42 outliers final: 25 residues processed: 315 average time/residue: 0.7591 time to fit residues: 257.0306 Evaluate side-chains 315 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 287 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 32 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 125 optimal weight: 0.3980 chunk 146 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 182 GLN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 GLN D 326 GLN E 24 HIS E 287 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.103031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.071937 restraints weight = 31275.805| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.18 r_work: 0.2788 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14385 Z= 0.159 Angle : 0.833 14.565 19554 Z= 0.388 Chirality : 0.042 0.312 2267 Planarity : 0.006 0.076 2524 Dihedral : 8.102 146.550 1998 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.23 % Allowed : 26.16 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.20), residues: 1780 helix: 1.57 (0.16), residues: 1106 sheet: 0.16 (0.41), residues: 144 loop : 0.36 (0.30), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 80 TYR 0.015 0.001 TYR E 47 PHE 0.026 0.002 PHE D 120 TRP 0.046 0.002 TRP A 150 HIS 0.007 0.001 HIS C 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (14369) covalent geometry : angle 0.79737 / 0.39 (19530) hydrogen bonds : bond 0.03889 / 2.55 ( 792) hydrogen bonds : angle 3.98343 / 2.85 ( 2316) metal coordination : bond 0.00598 / 0.35 ( 16) metal coordination : angle 6.88193 / 4.49 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 293 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5562 (tmm) cc_final: 0.4410 (tpt) REVERT: A 29 LEU cc_start: 0.8011 (tp) cc_final: 0.7770 (tm) REVERT: A 71 MET cc_start: 0.6176 (tpt) cc_final: 0.5684 (tpt) REVERT: A 81 LEU cc_start: 0.8793 (tm) cc_final: 0.8523 (tm) REVERT: A 82 LEU cc_start: 0.9336 (pt) cc_final: 0.9010 (tm) REVERT: B 60 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8500 (tttt) REVERT: B 110 ASN cc_start: 0.7808 (t0) cc_final: 0.7549 (t160) REVERT: B 148 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8015 (tm-30) REVERT: B 149 HIS cc_start: 0.8330 (m90) cc_final: 0.8066 (m90) REVERT: B 151 LYS cc_start: 0.8302 (mmmt) cc_final: 0.8035 (mmmt) REVERT: B 298 SER cc_start: 0.8686 (t) cc_final: 0.8279 (p) REVERT: C 6 LEU cc_start: 0.9285 (mt) cc_final: 0.9017 (tt) REVERT: C 94 ASP cc_start: 0.8367 (t0) cc_final: 0.7880 (t0) REVERT: C 105 ARG cc_start: 0.7926 (ptt180) cc_final: 0.7720 (ptt180) REVERT: C 176 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8401 (mtpp) REVERT: C 277 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: D 21 GLN cc_start: 0.8666 (pm20) cc_final: 0.7856 (pp30) REVERT: D 32 LEU cc_start: 0.8483 (mt) cc_final: 0.8112 (tt) REVERT: D 127 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7170 (mm-30) REVERT: D 194 GLU cc_start: 0.8427 (tp30) cc_final: 0.8078 (mm-30) REVERT: E 57 LYS cc_start: 0.8591 (mppt) cc_final: 0.8370 (mppt) REVERT: E 59 CYS cc_start: 0.4825 (m) cc_final: 0.4076 (t) REVERT: E 86 ASN cc_start: 0.8424 (t0) cc_final: 0.8150 (t0) outliers start: 33 outliers final: 25 residues processed: 312 average time/residue: 0.7340 time to fit residues: 246.7063 Evaluate side-chains 312 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 285 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 168 optimal weight: 1.9990 chunk 86 optimal weight: 0.0070 chunk 132 optimal weight: 0.0870 chunk 77 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 63 optimal weight: 0.0570 chunk 129 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 0.0870 overall best weight: 0.1872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 GLN D 326 GLN E 24 HIS E 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.074585 restraints weight = 31100.679| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.14 r_work: 0.2852 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14385 Z= 0.135 Angle : 0.974 42.059 19554 Z= 0.444 Chirality : 0.041 0.260 2267 Planarity : 0.006 0.069 2524 Dihedral : 7.999 146.424 1998 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.75 % Allowed : 26.37 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.21), residues: 1780 helix: 1.57 (0.16), residues: 1116 sheet: 0.19 (0.42), residues: 142 loop : 0.34 (0.30), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 80 TYR 0.017 0.001 TYR E 47 PHE 0.017 0.001 PHE D 120 TRP 0.052 0.002 TRP A 150 HIS 0.010 0.001 HIS C 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14369) covalent geometry : angle 0.94758 / 0.44 (19530) hydrogen bonds : bond 0.03490 / 2.25 ( 792) hydrogen bonds : angle 4.01629 / 2.85 ( 2316) metal coordination : bond 0.00536 / 0.32 ( 16) metal coordination : angle 6.52947 / 4.32 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6777.60 seconds wall clock time: 115 minutes 44.96 seconds (6944.96 seconds total)