Starting phenix.real_space_refine on Fri Aug 7 10:48:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyd_71015/08_2026/9oyd_71015.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyd_71015/08_2026/9oyd_71015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oyd_71015/08_2026/9oyd_71015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyd_71015/08_2026/9oyd_71015.map" model { file = "/net/cci-nas-00/data/ceres_data/9oyd_71015/08_2026/9oyd_71015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyd_71015/08_2026/9oyd_71015.cif" } resolution = 2.73 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= 0.017 sd= 0.721 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 49 5.49 5 Mg 3 5.21 5 S 111 5.16 5 C 12855 2.51 5 N 3705 2.21 5 O 3934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20661 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2726 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "B" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2840 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 16, 'TRANS': 348} Chain: "C" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2865 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "D" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2799 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "E" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2602 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "F" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2835 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 20, 'TRANS': 344} Chain: "G" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2844 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 345} Chain: "H" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 409 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "I" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 230 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3209 SG CYS B 64 29.404 84.033 38.116 1.00 45.59 S ATOM 3269 SG CYS B 73 25.879 83.432 38.370 1.00 55.09 S ATOM 3286 SG CYS B 76 28.220 80.273 37.635 1.00 51.13 S ATOM 3308 SG CYS B 79 28.278 81.918 40.973 1.00 45.34 S ATOM 6049 SG CYS C 64 9.928 58.615 71.672 1.00 42.62 S ATOM 6109 SG CYS C 73 8.391 56.207 73.762 1.00 47.75 S ATOM 6126 SG CYS C 76 11.031 54.817 71.018 1.00 45.95 S ATOM 6148 SG CYS C 79 12.196 56.693 73.918 1.00 44.60 S ATOM 8914 SG CYS D 64 34.829 33.031 101.639 1.00 39.18 S ATOM 8974 SG CYS D 73 36.931 30.652 103.629 1.00 44.14 S ATOM 8991 SG CYS D 76 37.749 30.818 100.002 1.00 39.79 S ATOM 9013 SG CYS D 79 38.605 33.708 101.843 1.00 42.17 S ATOM 11637 SG CYS E 50 81.462 34.922 101.969 1.00 43.48 S ATOM 11706 SG CYS E 59 84.748 33.563 100.965 1.00 42.68 S ATOM 11726 SG CYS E 62 82.156 33.570 98.325 1.00 44.74 S ATOM 11747 SG CYS E 65 83.417 36.875 99.372 1.00 42.65 S Time building chain proxies: 5.16, per 1000 atoms: 0.25 Number of scatterers: 20661 At special positions: 0 Unit cell: (120.888, 123.372, 151.524, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 111 16.00 P 49 15.00 Mg 3 11.99 O 3934 8.00 N 3705 7.00 C 12855 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: 1.73 Conformation dependent library (CDL) restraints added in 908.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 79 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 64 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 76 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 79 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 64 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 76 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 79 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 73 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 76 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 64 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 62 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 65 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 59 " Number of angles added : 24 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4754 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 15 sheets defined 56.1% alpha, 15.2% beta 19 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 8 through 16 removed outlier: 3.632A pdb=" N GLN A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 44 Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 90 through 104 removed outlier: 3.597A pdb=" N GLY A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.506A 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 264 removed outlier: 3.732A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 294 through 315 Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.627A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.568A pdb=" N VAL B 18 " --> pdb=" O PHE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 128 through 131 Processing helix chain 'B' and resid 132 through 145 removed outlier: 4.092A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.513A pdb=" N LEU B 162 " --> pdb=" O PRO B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 169 removed outlier: 3.575A pdb=" N LEU B 167 " --> pdb=" O VAL B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 195 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.865A pdb=" N GLU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 277 through 298 Processing helix chain 'B' and resid 299 through 302 removed outlier: 3.723A pdb=" N LEU B 302 " --> pdb=" O PRO B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.915A pdb=" N ALA B 307 " --> pdb=" O ASN B 304 " (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 5 through 10 Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.513A pdb=" N VAL C 18 " --> pdb=" O PHE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 35 Processing helix chain 'C' and resid 50 through 64 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 100 through 110 removed outlier: 4.309A pdb=" N ASN C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 132 through 145 removed outlier: 4.661A pdb=" N LYS C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 163 through 170 removed outlier: 3.577A pdb=" N ARG C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS C 170 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 194 Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.905A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.597A pdb=" N ALA C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 277 through 298 Processing helix chain 'C' and resid 299 through 302 removed outlier: 4.024A pdb=" N LEU C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 299 through 302' Processing helix chain 'C' and resid 303 through 307 removed outlier: 3.551A pdb=" N ALA C 307 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 321 through 339 Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 14 through 18 Processing helix chain 'D' and resid 21 through 35 Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 132 through 145 removed outlier: 4.729A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.892A 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: 3.562A pdb=" N ARG D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 195 Processing helix chain 'D' and resid 199 through 211 removed outlier: 3.886A pdb=" N GLU D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 245 through 259 Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 277 through 298 Processing helix chain 'D' and resid 299 through 302 removed outlier: 4.059A 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: 3.602A pdb=" N MET D 306 " --> pdb=" O GLY D 303 " (cutoff:3.500A) removed outlier: 3.945A 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: 4.664A pdb=" N ASP E 10 " --> pdb=" O TRP E 6 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER E 17 " --> pdb=" O LYS E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 49 Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 89 through 101 removed outlier: 3.546A pdb=" N LYS E 99 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 121 through 134 removed outlier: 3.564A pdb=" N LEU E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N THR E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 152 through 158 removed outlier: 3.721A pdb=" N ARG E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 178 removed outlier: 3.765A pdb=" N ARG E 178 " --> pdb=" O THR E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 197 through 206 Processing helix chain 'E' and resid 208 through 227 Proline residue: E 225 - end of helix Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 240 through 260 Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 282 through 303 Processing helix chain 'E' and resid 307 through 323 Processing helix chain 'F' and resid 7 through 18 removed outlier: 4.272A pdb=" N LYS F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) Proline residue: F 13 - end of helix Processing helix chain 'F' and resid 27 through 30 Processing helix chain 'F' and resid 72 through 82 Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.686A pdb=" N THR F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N PHE F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 157 removed outlier: 3.652A pdb=" N GLY F 157 " --> pdb=" O TYR F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 207 Processing helix chain 'F' and resid 243 through 248 removed outlier: 4.026A pdb=" N VAL F 247 " --> pdb=" O ASP F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.740A pdb=" N LEU F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 332 Processing helix chain 'G' and resid 7 through 18 removed outlier: 4.490A pdb=" N LYS G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) Proline residue: G 13 - end of helix Processing helix chain 'G' and resid 27 through 32 removed outlier: 3.768A pdb=" N GLY G 31 " --> pdb=" O PRO G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 82 removed outlier: 3.656A pdb=" N LEU G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.606A pdb=" N THR G 142 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE G 144 " --> pdb=" O GLU G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 197 through 207 Processing helix chain 'G' and resid 243 through 248 Processing helix chain 'G' and resid 260 through 271 Processing helix chain 'G' and resid 272 through 274 No H-bonds generated for 'chain 'G' and resid 272 through 274' Processing helix chain 'G' and resid 321 through 332 removed outlier: 3.522A pdb=" N LYS G 332 " --> pdb=" O LEU G 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 13 Processing helix chain 'J' and resid 21 through 25 removed outlier: 3.528A pdb=" N LEU J 25 " --> pdb=" O PRO J 22 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 6.245A pdb=" N ILE A 2 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR A 138 " --> pdb=" O ILE A 2 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU A 4 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE A 47 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N THR A 79 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU A 49 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU A 81 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N HIS A 51 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU A 83 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE A 53 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.293A pdb=" N GLU A 161 " --> pdb=" O LEU A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.188A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TYR B 41 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N THR B 156 " --> pdb=" O TYR B 41 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N PHE B 43 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N PHE B 173 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B 42 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 197 through 198 removed outlier: 6.720A pdb=" N ALA B 197 " --> pdb=" O VAL B 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 94 removed outlier: 6.254A pdb=" N LYS C 121 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU C 153 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA C 155 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE C 125 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 90 through 94 removed outlier: 6.331A pdb=" N ILE D 91 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP D 126 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE D 93 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LYS D 121 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU D 153 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TYR D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA D 155 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE D 125 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA D 40 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N PHE D 173 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU D 42 " --> pdb=" O PHE D 173 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 76 through 79 removed outlier: 6.114A pdb=" N LEU E 27 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N THR E 145 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE E 29 " --> pdb=" O THR E 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 2 through 6 removed outlier: 3.512A pdb=" N SER F 101 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASN G 295 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY G 280 " --> pdb=" O ASN G 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.378A pdb=" N ASN F 32 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N THR F 47 " --> pdb=" O ASN F 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 309 through 310 removed outlier: 3.722A pdb=" N ALA F 258 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASP F 351 " --> pdb=" O ALA F 357 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA F 357 " --> pdb=" O ASP F 351 " (cutoff:3.500A) removed outlier: 15.798A pdb=" N SER F 181 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 16.001A pdb=" N THR F 172 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 15.074A pdb=" N VAL F 170 " --> pdb=" O PRO F 183 " (cutoff:3.500A) removed outlier: 13.977A pdb=" N GLY F 185 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 14.244A pdb=" N ARG F 168 " --> pdb=" O GLY F 185 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N SER F 187 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLU F 166 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLY F 164 " --> pdb=" O PRO F 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 303 through 307 removed outlier: 3.756A pdb=" N MET F 315 " --> pdb=" O VAL F 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 2 through 6 Processing sheet with id=AB5, first strand: chain 'G' and resid 111 through 112 removed outlier: 3.534A pdb=" N GLY G 66 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 254 through 259 removed outlier: 4.478A pdb=" N ASP G 351 " --> pdb=" O ALA G 357 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA G 357 " --> pdb=" O ASP G 351 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU G 165 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N GLN G 186 " --> pdb=" O GLU G 163 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N GLU G 163 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N LEU G 188 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N GLU G 161 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 13.545A pdb=" N SER G 190 " --> pdb=" O LEU G 159 " (cutoff:3.500A) removed outlier: 13.961A pdb=" N LEU G 159 " --> pdb=" O SER G 190 " (cutoff:3.500A) removed outlier: 13.338A pdb=" N SER G 192 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 12.951A pdb=" N GLY G 157 " --> pdb=" O SER G 192 " (cutoff:3.500A) 1115 hydrogen bonds defined for protein. 3168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7104 1.36 - 1.51: 5783 1.51 - 1.66: 8043 1.66 - 1.80: 158 1.80 - 1.95: 26 Bond restraints: 21114 Sorted by residual: bond pdb=" O3B AGS D 702 " pdb=" PB AGS D 702 " ideal model delta sigma weight residual 1.673 1.590 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" O3B AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sigma weight residual 1.673 1.590 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" O3B AGS B 702 " pdb=" PB AGS B 702 " ideal model delta sigma weight residual 1.673 1.590 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O3A AGS D 702 " pdb=" PA AGS D 702 " ideal model delta sigma weight residual 1.664 1.584 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" O3A AGS C 702 " pdb=" PA AGS C 702 " ideal model delta sigma weight residual 1.664 1.586 0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 21109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 28220 1.98 - 3.95: 531 3.95 - 5.93: 63 5.93 - 7.91: 12 7.91 - 9.88: 9 Bond angle restraints: 28835 Sorted by residual: angle pdb=" N3 DT H 33 " pdb=" C4 DT H 33 " pdb=" O4 DT H 33 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT I 14 " pdb=" C4 DT I 14 " pdb=" O4 DT I 14 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT I 8 " pdb=" C4 DT I 8 " pdb=" O4 DT I 8 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT I 16 " pdb=" C4 DT I 16 " pdb=" O4 DT I 16 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT H 27 " pdb=" C4 DT H 27 " pdb=" O4 DT H 27 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 ... (remaining 28830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 11457 17.88 - 35.76: 990 35.76 - 53.64: 280 53.64 - 71.52: 86 71.52 - 89.40: 24 Dihedral angle restraints: 12837 sinusoidal: 5511 harmonic: 7326 Sorted by residual: dihedral pdb=" CA SER G 107 " pdb=" C SER G 107 " pdb=" N LEU G 108 " pdb=" CA LEU G 108 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA VAL B 19 " pdb=" C VAL B 19 " pdb=" N GLY B 20 " pdb=" CA GLY B 20 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA VAL C 19 " pdb=" C VAL C 19 " pdb=" N GLY C 20 " pdb=" CA GLY C 20 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 12834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2853 0.059 - 0.118: 440 0.118 - 0.177: 26 0.177 - 0.236: 0 0.236 - 0.296: 3 Chirality restraints: 3322 Sorted by residual: chirality pdb=" C3' AGS D 702 " pdb=" C2' AGS D 702 " pdb=" C4' AGS D 702 " pdb=" O3' AGS D 702 " both_signs ideal model delta sigma weight residual False -2.37 -2.67 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C3' AGS C 702 " pdb=" C2' AGS C 702 " pdb=" C4' AGS C 702 " pdb=" O3' AGS C 702 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C3' AGS B 702 " pdb=" C2' AGS B 702 " pdb=" C4' AGS B 702 " pdb=" O3' AGS B 702 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 3319 not shown) Planarity restraints: 3606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 296 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO F 297 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO F 297 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 297 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 122 " 0.022 2.00e-02 2.50e+03 1.22e-02 3.69e+00 pdb=" CG TRP F 122 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP F 122 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP F 122 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP F 122 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP F 122 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 122 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 122 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 122 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 122 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 70 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO F 71 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 71 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 71 " 0.025 5.00e-02 4.00e+02 ... (remaining 3603 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 9 2.49 - 3.09: 13889 3.09 - 3.69: 31313 3.69 - 4.30: 46777 4.30 - 4.90: 78110 Nonbonded interactions: 170098 Sorted by model distance: nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 703 " model vdw 1.887 2.170 nonbonded pdb=" O2G AGS B 702 " pdb="MG MG B 703 " model vdw 1.942 2.170 nonbonded pdb=" OG1 THR D 52 " pdb="MG MG D 703 " model vdw 1.989 2.170 nonbonded pdb=" OG1 THR B 52 " pdb="MG MG B 703 " model vdw 1.998 2.170 nonbonded pdb=" O2G AGS D 702 " pdb="MG MG D 703 " model vdw 2.094 2.170 ... (remaining 170093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 361 or resid 701 through 703)) selection = (chain 'C' and (resid 2 through 361 or resid 701 through 703)) selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 365) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 24.290 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 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 0.083 21130 Z= 0.254 Angle : 0.690 10.751 28859 Z= 0.363 Chirality : 0.043 0.296 3322 Planarity : 0.005 0.055 3606 Dihedral : 15.551 89.403 8083 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.05 % Allowed : 0.62 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.17), residues: 2513 helix: 1.45 (0.15), residues: 1303 sheet: 1.67 (0.24), residues: 424 loop : 0.03 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 47 TYR 0.013 0.002 TYR D 3 PHE 0.013 0.002 PHE F 319 TRP 0.030 0.002 TRP F 122 HIS 0.008 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.25 (21114) covalent geometry : angle 0.66568 / 0.36 (28835) hydrogen bonds : bond 0.13796 / 8.96 ( 1166) hydrogen bonds : angle 4.97994 / 3.56 ( 3270) metal coordination : bond 0.00906 / 0.45 ( 16) metal coordination : angle 6.26745 / 4.25 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 395 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 MET cc_start: 0.8863 (mmm) cc_final: 0.8637 (mmp) REVERT: B 285 MET cc_start: 0.8839 (mtp) cc_final: 0.8309 (ttm) REVERT: D 148 GLU cc_start: 0.8338 (tp30) cc_final: 0.8133 (tp30) REVERT: F 165 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7538 (tm-30) REVERT: F 282 ARG cc_start: 0.8402 (mtp-110) cc_final: 0.8152 (mtp-110) outliers start: 1 outliers final: 0 residues processed: 396 average time/residue: 0.9508 time to fit residues: 410.8613 Evaluate side-chains 307 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.0270 chunk 247 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 GLN A 167 ASN A 183 GLN A 333 HIS B 13 GLN ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 186 GLN D 13 GLN E 54 GLN E 56 HIS ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.050151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2286 r_free = 0.2286 target = 0.041443 restraints weight = 38199.243| |-----------------------------------------------------------------------------| r_work (start): 0.2286 rms_B_bonded: 1.11 r_work: 0.2195 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2105 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21130 Z= 0.139 Angle : 0.595 10.521 28859 Z= 0.298 Chirality : 0.039 0.146 3322 Planarity : 0.005 0.052 3606 Dihedral : 13.441 59.791 3292 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.32 % Allowed : 8.05 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.17), residues: 2513 helix: 1.70 (0.15), residues: 1320 sheet: 1.49 (0.24), residues: 440 loop : 0.13 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 240 TYR 0.018 0.001 TYR F 284 PHE 0.015 0.001 PHE F 319 TRP 0.015 0.001 TRP D 10 HIS 0.006 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (21114) covalent geometry : angle 0.57129 / 0.30 (28835) hydrogen bonds : bond 0.04640 / 3.07 ( 1166) hydrogen bonds : angle 4.07793 / 2.91 ( 3270) metal coordination : bond 0.00731 / 0.37 ( 16) metal coordination : angle 5.78281 / 3.89 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 312 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8172 (mtpp) REVERT: A 225 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8367 (mmpt) REVERT: B 46 THR cc_start: 0.9039 (p) cc_final: 0.8741 (t) REVERT: B 285 MET cc_start: 0.8836 (mtp) cc_final: 0.8310 (ttm) REVERT: C 347 MET cc_start: 0.8615 (mtp) cc_final: 0.8381 (mtp) REVERT: D 201 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.6984 (ttt-90) REVERT: D 306 MET cc_start: 0.8973 (mmt) cc_final: 0.8367 (mmt) REVERT: E 296 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8685 (mm) REVERT: F 165 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7582 (tm-30) REVERT: F 186 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8779 (pm20) REVERT: F 205 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8441 (mtm110) REVERT: F 316 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7184 (tp30) REVERT: G 48 ASP cc_start: 0.8121 (t0) cc_final: 0.7916 (t0) outliers start: 49 outliers final: 20 residues processed: 336 average time/residue: 0.8488 time to fit residues: 312.2536 Evaluate side-chains 327 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 300 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 223 GLN Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 205 ARG Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 146 MET Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 99 optimal weight: 0.5980 chunk 209 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN D 269 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS G 186 GLN G 295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.048816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2251 r_free = 0.2251 target = 0.040127 restraints weight = 38671.971| |-----------------------------------------------------------------------------| r_work (start): 0.2250 rms_B_bonded: 1.11 r_work: 0.2159 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2068 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 21130 Z= 0.178 Angle : 0.622 10.693 28859 Z= 0.309 Chirality : 0.040 0.148 3322 Planarity : 0.005 0.058 3606 Dihedral : 13.471 59.922 3292 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.79 % Allowed : 9.70 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.17), residues: 2513 helix: 1.73 (0.15), residues: 1314 sheet: 1.47 (0.24), residues: 444 loop : 0.04 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 246 TYR 0.021 0.002 TYR G 284 PHE 0.020 0.002 PHE G 230 TRP 0.015 0.002 TRP D 10 HIS 0.007 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (21114) covalent geometry : angle 0.59790 / 0.31 (28835) hydrogen bonds : bond 0.04749 / 3.12 ( 1166) hydrogen bonds : angle 3.96304 / 2.83 ( 3270) metal coordination : bond 0.00800 / 0.41 ( 16) metal coordination : angle 5.97346 / 4.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 300 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8148 (mtpp) REVERT: A 225 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8355 (mmpt) REVERT: B 46 THR cc_start: 0.9079 (p) cc_final: 0.8800 (t) REVERT: B 285 MET cc_start: 0.8835 (mtp) cc_final: 0.8362 (ttm) REVERT: C 161 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8857 (mttm) REVERT: C 277 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: D 201 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7052 (ttt-90) REVERT: D 306 MET cc_start: 0.9068 (mmt) cc_final: 0.8655 (mmt) REVERT: E 264 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.7807 (tm-30) REVERT: E 296 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8718 (mm) REVERT: F 165 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7601 (tm-30) REVERT: F 316 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7257 (tp30) REVERT: G 149 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8061 (mt0) REVERT: G 250 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8620 (ttmm) outliers start: 59 outliers final: 26 residues processed: 329 average time/residue: 0.8380 time to fit residues: 301.8067 Evaluate side-chains 320 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 284 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 136 LYS Chi-restraints excluded: chain G residue 146 MET Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 276 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 84 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN C 269 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS G 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.049126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.040396 restraints weight = 38746.864| |-----------------------------------------------------------------------------| r_work (start): 0.2257 rms_B_bonded: 1.11 r_work: 0.2166 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2076 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 21130 Z= 0.152 Angle : 0.590 10.659 28859 Z= 0.293 Chirality : 0.039 0.145 3322 Planarity : 0.005 0.058 3606 Dihedral : 13.451 59.966 3292 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.70 % Allowed : 11.50 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.17), residues: 2513 helix: 1.81 (0.15), residues: 1315 sheet: 1.54 (0.24), residues: 426 loop : -0.03 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 205 TYR 0.018 0.001 TYR F 284 PHE 0.032 0.002 PHE G 230 TRP 0.015 0.001 TRP D 10 HIS 0.005 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (21114) covalent geometry : angle 0.56675 / 0.29 (28835) hydrogen bonds : bond 0.04302 / 2.83 ( 1166) hydrogen bonds : angle 3.86508 / 2.76 ( 3270) metal coordination : bond 0.00744 / 0.38 ( 16) metal coordination : angle 5.70989 / 3.86 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 297 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8702 (tttm) REVERT: A 196 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8121 (mtpp) REVERT: A 225 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8349 (mmpt) REVERT: B 46 THR cc_start: 0.9085 (p) cc_final: 0.8818 (t) REVERT: B 285 MET cc_start: 0.8835 (mtp) cc_final: 0.8267 (ttm) REVERT: C 161 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8886 (mttm) REVERT: C 277 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: D 201 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7030 (ttt-90) REVERT: D 306 MET cc_start: 0.9055 (mmt) cc_final: 0.8738 (mmt) REVERT: E 264 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: E 296 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8724 (mm) REVERT: F 165 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7618 (tm-30) REVERT: F 316 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7221 (tp30) REVERT: G 149 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: G 250 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8637 (ttmm) outliers start: 57 outliers final: 26 residues processed: 321 average time/residue: 0.8689 time to fit residues: 306.1933 Evaluate side-chains 325 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 288 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 136 LYS Chi-restraints excluded: chain G residue 146 MET Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 168 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 35 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN E 56 HIS E 287 GLN F 186 GLN G 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.048564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2242 r_free = 0.2242 target = 0.039843 restraints weight = 38525.075| |-----------------------------------------------------------------------------| r_work (start): 0.2242 rms_B_bonded: 1.10 r_work: 0.2150 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2059 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 21130 Z= 0.171 Angle : 0.607 10.705 28859 Z= 0.301 Chirality : 0.039 0.145 3322 Planarity : 0.005 0.058 3606 Dihedral : 13.459 59.900 3292 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.12 % Allowed : 12.83 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.17), residues: 2513 helix: 1.77 (0.15), residues: 1315 sheet: 1.52 (0.24), residues: 426 loop : -0.06 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 205 TYR 0.019 0.001 TYR F 284 PHE 0.023 0.002 PHE G 230 TRP 0.014 0.001 TRP D 10 HIS 0.006 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (21114) covalent geometry : angle 0.58376 / 0.30 (28835) hydrogen bonds : bond 0.04460 / 2.94 ( 1166) hydrogen bonds : angle 3.87477 / 2.77 ( 3270) metal coordination : bond 0.00763 / 0.40 ( 16) metal coordination : angle 5.81021 / 3.94 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 290 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8131 (mtpp) REVERT: A 225 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8354 (mmpt) REVERT: A 313 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8578 (mttm) REVERT: A 318 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8035 (tm-30) REVERT: B 109 ASP cc_start: 0.8838 (m-30) cc_final: 0.8629 (m-30) REVERT: B 285 MET cc_start: 0.8822 (mtp) cc_final: 0.8269 (ttm) REVERT: C 161 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8847 (mttm) REVERT: C 277 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: D 154 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8956 (mt) REVERT: D 201 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7025 (ttt-90) REVERT: D 244 LEU cc_start: 0.8842 (mp) cc_final: 0.8541 (mp) REVERT: D 306 MET cc_start: 0.9076 (mmt) cc_final: 0.8843 (mmt) REVERT: E 52 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8865 (pt0) REVERT: E 264 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: E 296 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8732 (mm) REVERT: F 165 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7621 (tm-30) REVERT: F 316 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7200 (tp30) REVERT: G 149 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8084 (mt0) REVERT: G 186 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8559 (pm20) REVERT: G 206 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8595 (mtp) outliers start: 66 outliers final: 29 residues processed: 321 average time/residue: 0.8316 time to fit residues: 293.4375 Evaluate side-chains 327 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 283 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 285 ARG Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 136 LYS Chi-restraints excluded: chain G residue 146 MET Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 276 GLU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 333 HIS B 23 HIS C 269 ASN E 56 HIS ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.048832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2249 r_free = 0.2249 target = 0.040091 restraints weight = 38419.744| |-----------------------------------------------------------------------------| r_work (start): 0.2249 rms_B_bonded: 1.10 r_work: 0.2158 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2067 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 21130 Z= 0.152 Angle : 0.589 10.653 28859 Z= 0.292 Chirality : 0.039 0.148 3322 Planarity : 0.005 0.060 3606 Dihedral : 13.441 59.979 3292 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.08 % Allowed : 13.16 % Favored : 83.77 % 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: 1.82 (0.17), residues: 2513 helix: 1.84 (0.15), residues: 1315 sheet: 1.50 (0.24), residues: 427 loop : -0.00 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 246 TYR 0.018 0.001 TYR G 284 PHE 0.010 0.001 PHE G 230 TRP 0.015 0.001 TRP D 10 HIS 0.005 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (21114) covalent geometry : angle 0.56615 / 0.29 (28835) hydrogen bonds : bond 0.04213 / 2.77 ( 1166) hydrogen bonds : angle 3.82246 / 2.73 ( 3270) metal coordination : bond 0.00726 / 0.38 ( 16) metal coordination : angle 5.61252 / 3.79 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 287 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8728 (tttm) REVERT: A 196 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8120 (mtpp) REVERT: A 225 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8369 (mmpt) REVERT: A 313 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8561 (mttm) REVERT: A 318 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: B 285 MET cc_start: 0.8824 (mtp) cc_final: 0.8258 (ttm) REVERT: C 161 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8842 (mttm) REVERT: C 277 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: C 318 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8047 (ptt-90) REVERT: D 154 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8946 (mt) REVERT: D 244 LEU cc_start: 0.8840 (mp) cc_final: 0.8566 (mp) REVERT: D 306 MET cc_start: 0.9070 (mmt) cc_final: 0.8869 (mmt) REVERT: D 330 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: E 264 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: E 296 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8731 (mm) REVERT: F 73 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8007 (ttp-170) REVERT: F 165 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7594 (tm-30) REVERT: F 269 ARG cc_start: 0.8776 (mtm110) cc_final: 0.8150 (mtm110) REVERT: G 250 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8646 (ttmm) outliers start: 65 outliers final: 28 residues processed: 319 average time/residue: 0.8168 time to fit residues: 286.7794 Evaluate side-chains 324 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 282 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 146 MET Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 276 GLU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 111 optimal weight: 1.9990 chunk 250 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.047762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2220 r_free = 0.2220 target = 0.039065 restraints weight = 38689.598| |-----------------------------------------------------------------------------| r_work (start): 0.2219 rms_B_bonded: 1.10 r_work: 0.2126 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2034 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 21130 Z= 0.200 Angle : 0.638 11.034 28859 Z= 0.317 Chirality : 0.041 0.169 3322 Planarity : 0.005 0.059 3606 Dihedral : 13.512 59.730 3292 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.17 % Allowed : 13.87 % Favored : 82.96 % 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: 1.67 (0.17), residues: 2513 helix: 1.71 (0.15), residues: 1315 sheet: 1.52 (0.24), residues: 428 loop : -0.09 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 246 TYR 0.013 0.002 TYR D 3 PHE 0.018 0.002 PHE B 136 TRP 0.014 0.002 TRP D 10 HIS 0.007 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (21114) covalent geometry : angle 0.61516 / 0.32 (28835) hydrogen bonds : bond 0.04701 / 3.09 ( 1166) hydrogen bonds : angle 3.90941 / 2.79 ( 3270) metal coordination : bond 0.00790 / 0.41 ( 16) metal coordination : angle 5.95285 / 4.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 288 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8753 (tttm) REVERT: A 196 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8125 (mtpp) REVERT: A 225 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8341 (mmpt) REVERT: A 313 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8513 (mttm) REVERT: A 318 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: B 46 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8844 (t) REVERT: B 285 MET cc_start: 0.8821 (mtp) cc_final: 0.8292 (ttm) REVERT: C 161 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8794 (mttm) REVERT: C 318 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8040 (ptt-90) REVERT: D 154 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8972 (mt) REVERT: D 201 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7007 (ttt-90) REVERT: D 244 LEU cc_start: 0.8841 (mp) cc_final: 0.8502 (mt) REVERT: D 306 MET cc_start: 0.9111 (mmt) cc_final: 0.8892 (mmt) REVERT: D 330 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: E 264 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: E 296 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8737 (mm) REVERT: F 165 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7615 (tm-30) REVERT: F 269 ARG cc_start: 0.8763 (mtm110) cc_final: 0.8467 (mtm110) REVERT: G 136 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8694 (tttp) REVERT: G 250 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8646 (ttmm) outliers start: 67 outliers final: 34 residues processed: 324 average time/residue: 0.8665 time to fit residues: 308.1869 Evaluate side-chains 330 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 281 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 285 ARG Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 136 LYS Chi-restraints excluded: chain G residue 146 MET Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 227 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 180 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 246 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 174 optimal weight: 0.0980 chunk 55 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS C 269 ASN E 56 HIS G 16 GLN G 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.048833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2249 r_free = 0.2249 target = 0.040110 restraints weight = 38532.618| |-----------------------------------------------------------------------------| r_work (start): 0.2249 rms_B_bonded: 1.10 r_work: 0.2158 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2068 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21130 Z= 0.139 Angle : 0.589 10.936 28859 Z= 0.292 Chirality : 0.038 0.155 3322 Planarity : 0.005 0.073 3606 Dihedral : 13.461 59.631 3292 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.74 % Allowed : 14.48 % Favored : 82.77 % 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: 1.81 (0.17), residues: 2513 helix: 1.84 (0.15), residues: 1316 sheet: 1.46 (0.24), residues: 429 loop : -0.00 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 274 TYR 0.016 0.001 TYR F 284 PHE 0.016 0.001 PHE G 230 TRP 0.016 0.001 TRP D 10 HIS 0.005 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (21114) covalent geometry : angle 0.56692 / 0.29 (28835) hydrogen bonds : bond 0.04077 / 2.69 ( 1166) hydrogen bonds : angle 3.81080 / 2.71 ( 3270) metal coordination : bond 0.00708 / 0.36 ( 16) metal coordination : angle 5.50648 / 3.71 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 287 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8729 (tttm) REVERT: A 196 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8109 (mtpp) REVERT: A 225 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8348 (mmpt) REVERT: A 318 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: B 46 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8862 (t) REVERT: B 285 MET cc_start: 0.8823 (mtp) cc_final: 0.8247 (ttm) REVERT: C 260 ASN cc_start: 0.8643 (t0) cc_final: 0.8424 (t0) REVERT: C 318 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7999 (ptt-90) REVERT: D 154 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8944 (mt) REVERT: D 201 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7015 (ttt-90) REVERT: D 244 LEU cc_start: 0.8815 (mp) cc_final: 0.8483 (mt) REVERT: D 306 MET cc_start: 0.9088 (mmt) cc_final: 0.8872 (mtt) REVERT: D 330 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: E 264 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: E 296 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8733 (mm) REVERT: F 73 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8005 (ttp-170) REVERT: F 165 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7603 (tm-30) REVERT: F 269 ARG cc_start: 0.8736 (mtm110) cc_final: 0.8501 (ptm-80) REVERT: G 48 ASP cc_start: 0.8191 (t0) cc_final: 0.7922 (t0) REVERT: G 149 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: G 186 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8595 (pm20) REVERT: G 206 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8475 (ttm) REVERT: G 250 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8634 (ttmm) outliers start: 58 outliers final: 31 residues processed: 313 average time/residue: 0.8394 time to fit residues: 288.4028 Evaluate side-chains 328 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 281 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 146 MET Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 276 GLU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 225 optimal weight: 0.9980 chunk 246 optimal weight: 4.9990 chunk 250 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 chunk 143 optimal weight: 0.5980 chunk 238 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 176 optimal weight: 0.8980 chunk 222 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS C 269 ASN E 56 HIS G 186 GLN ** G 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.049146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.040425 restraints weight = 38582.020| |-----------------------------------------------------------------------------| r_work (start): 0.2257 rms_B_bonded: 1.10 r_work: 0.2166 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2076 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21130 Z= 0.136 Angle : 0.586 11.206 28859 Z= 0.291 Chirality : 0.038 0.157 3322 Planarity : 0.005 0.065 3606 Dihedral : 13.428 59.997 3292 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.46 % Allowed : 15.14 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.17), residues: 2513 helix: 1.88 (0.15), residues: 1316 sheet: 1.45 (0.24), residues: 428 loop : 0.03 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 246 TYR 0.019 0.001 TYR F 284 PHE 0.018 0.001 PHE G 230 TRP 0.016 0.001 TRP D 10 HIS 0.005 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (21114) covalent geometry : angle 0.56514 / 0.29 (28835) hydrogen bonds : bond 0.04000 / 2.64 ( 1166) hydrogen bonds : angle 3.77926 / 2.69 ( 3270) metal coordination : bond 0.00702 / 0.36 ( 16) metal coordination : angle 5.38592 / 3.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 282 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8731 (tttm) REVERT: A 196 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8096 (mtpp) REVERT: A 225 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8341 (mmpt) REVERT: A 318 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: B 46 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8863 (t) REVERT: B 285 MET cc_start: 0.8825 (mtp) cc_final: 0.8242 (ttm) REVERT: C 260 ASN cc_start: 0.8626 (t0) cc_final: 0.8419 (t0) REVERT: C 318 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7980 (ptt-90) REVERT: C 347 MET cc_start: 0.8575 (mtp) cc_final: 0.8248 (mtp) REVERT: D 154 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8954 (mt) REVERT: D 201 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7016 (ttt-90) REVERT: D 244 LEU cc_start: 0.8799 (mp) cc_final: 0.8483 (mt) REVERT: D 306 MET cc_start: 0.9074 (mmt) cc_final: 0.8855 (mtt) REVERT: D 330 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: E 264 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.7815 (tm-30) REVERT: E 296 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8728 (mm) REVERT: F 73 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7985 (ttp-170) REVERT: F 165 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7604 (tm-30) REVERT: F 269 ARG cc_start: 0.8704 (mtm110) cc_final: 0.8480 (ptm-80) REVERT: G 48 ASP cc_start: 0.8164 (t0) cc_final: 0.7856 (t0) REVERT: G 149 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8008 (mt0) REVERT: G 250 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8635 (ttmm) outliers start: 52 outliers final: 28 residues processed: 305 average time/residue: 0.8801 time to fit residues: 294.5342 Evaluate side-chains 319 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 277 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 146 MET Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 276 GLU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 104 optimal weight: 0.9980 chunk 165 optimal weight: 0.4980 chunk 103 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 24 optimal weight: 0.0050 chunk 224 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 239 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS C 269 ASN E 56 HIS G 16 GLN G 91 GLN G 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.049470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2267 r_free = 0.2267 target = 0.040732 restraints weight = 38726.427| |-----------------------------------------------------------------------------| r_work (start): 0.2266 rms_B_bonded: 1.11 r_work: 0.2176 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2086 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21130 Z= 0.129 Angle : 0.581 10.986 28859 Z= 0.288 Chirality : 0.038 0.174 3322 Planarity : 0.005 0.067 3606 Dihedral : 13.399 59.928 3292 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.41 % Allowed : 15.19 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.17), residues: 2513 helix: 1.91 (0.15), residues: 1316 sheet: 1.45 (0.24), residues: 426 loop : 0.07 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 246 TYR 0.021 0.001 TYR F 284 PHE 0.013 0.001 PHE G 3 TRP 0.016 0.001 TRP D 10 HIS 0.005 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (21114) covalent geometry : angle 0.56119 / 0.29 (28835) hydrogen bonds : bond 0.03873 / 2.55 ( 1166) hydrogen bonds : angle 3.74505 / 2.67 ( 3270) metal coordination : bond 0.00697 / 0.36 ( 16) metal coordination : angle 5.25589 / 3.55 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 286 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8738 (tttm) REVERT: A 196 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8091 (mtpp) REVERT: A 211 HIS cc_start: 0.8477 (t70) cc_final: 0.7700 (m90) REVERT: A 225 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8342 (mmpt) REVERT: A 318 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: B 46 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8868 (t) REVERT: B 285 MET cc_start: 0.8827 (mtp) cc_final: 0.8245 (ttm) REVERT: C 260 ASN cc_start: 0.8611 (t0) cc_final: 0.8398 (t0) REVERT: C 318 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7994 (ptt-90) REVERT: C 347 MET cc_start: 0.8526 (mtp) cc_final: 0.8201 (mtp) REVERT: D 154 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8940 (mt) REVERT: D 201 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7054 (ttt-90) REVERT: D 244 LEU cc_start: 0.8787 (mp) cc_final: 0.8469 (mt) REVERT: E 264 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: E 296 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8725 (mm) REVERT: F 73 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7985 (ttp-170) REVERT: F 165 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7585 (tm-30) REVERT: F 269 ARG cc_start: 0.8704 (mtm110) cc_final: 0.8301 (ptm-80) REVERT: G 48 ASP cc_start: 0.8131 (t0) cc_final: 0.7873 (t0) REVERT: G 149 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8012 (mt0) REVERT: G 206 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8462 (ttm) REVERT: G 250 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8634 (ttmm) outliers start: 51 outliers final: 26 residues processed: 308 average time/residue: 0.8413 time to fit residues: 285.2182 Evaluate side-chains 321 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 281 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 146 MET Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 276 GLU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 220 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 174 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 113 optimal weight: 0.0470 chunk 160 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS C 269 ASN G 16 GLN G 91 GLN G 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.049456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2269 r_free = 0.2269 target = 0.040797 restraints weight = 38743.912| |-----------------------------------------------------------------------------| r_work (start): 0.2268 rms_B_bonded: 1.08 r_work: 0.2178 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2089 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21130 Z= 0.134 Angle : 0.586 10.837 28859 Z= 0.290 Chirality : 0.038 0.187 3322 Planarity : 0.005 0.062 3606 Dihedral : 13.385 59.774 3292 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.32 % Allowed : 15.76 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.17), residues: 2513 helix: 1.91 (0.15), residues: 1316 sheet: 1.44 (0.24), residues: 426 loop : 0.08 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 246 TYR 0.018 0.001 TYR F 284 PHE 0.013 0.001 PHE G 3 TRP 0.015 0.001 TRP D 10 HIS 0.005 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (21114) covalent geometry : angle 0.56604 / 0.29 (28835) hydrogen bonds : bond 0.03892 / 2.56 ( 1166) hydrogen bonds : angle 3.73567 / 2.66 ( 3270) metal coordination : bond 0.00701 / 0.36 ( 16) metal coordination : angle 5.24223 / 3.55 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7370.23 seconds wall clock time: 126 minutes 2.46 seconds (7562.46 seconds total)