Starting phenix.real_space_refine on Fri Jun 5 13:27:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyd_71015/06_2026/9oyd_71015.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyd_71015/06_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 { model { file = "/net/cci-nas-00/data/ceres_data/9oyd_71015/06_2026/9oyd_71015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyd_71015/06_2026/9oyd_71015.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oyd_71015/06_2026/9oyd_71015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyd_71015/06_2026/9oyd_71015.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.12, 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: 1.63 Conformation dependent library (CDL) restraints added in 960.7 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: 2.98 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: 4.41 Time building geometry restraints manager: 2.26 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=" N ASP F 121 " pdb=" CA ASP F 121 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.45e+00 bond pdb=" N LEU F 119 " pdb=" CA LEU F 119 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.31e-02 5.83e+03 6.36e+00 bond pdb=" N ASN F 118 " pdb=" CA ASN F 118 " ideal model delta sigma weight residual 1.460 1.490 -0.031 1.28e-02 6.10e+03 5.75e+00 bond pdb=" N TRP F 122 " pdb=" CA TRP F 122 " ideal model delta sigma weight residual 1.456 1.476 -0.020 1.23e-02 6.61e+03 2.60e+00 bond pdb=" N ASP F 120 " pdb=" CA ASP F 120 " ideal model delta sigma weight residual 1.467 1.491 -0.024 1.65e-02 3.67e+03 2.04e+00 ... (remaining 21109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 27743 1.37 - 2.74: 882 2.74 - 4.11: 160 4.11 - 5.48: 42 5.48 - 6.86: 8 Bond angle restraints: 28835 Sorted by residual: angle pdb=" C ASP F 120 " pdb=" CA ASP F 120 " pdb=" CB ASP F 120 " ideal model delta sigma weight residual 116.63 112.27 4.36 1.16e+00 7.43e-01 1.42e+01 angle pdb=" CA ASP A 56 " pdb=" C ASP A 56 " pdb=" N PRO A 57 " ideal model delta sigma weight residual 117.68 120.13 -2.45 7.10e-01 1.98e+00 1.19e+01 angle pdb=" CA LEU F 119 " pdb=" C LEU F 119 " pdb=" O LEU F 119 " ideal model delta sigma weight residual 121.81 118.06 3.75 1.18e+00 7.18e-01 1.01e+01 angle pdb=" C ALA G 113 " pdb=" N ALA G 114 " pdb=" CA ALA G 114 " ideal model delta sigma weight residual 121.54 127.15 -5.61 1.91e+00 2.74e-01 8.63e+00 angle pdb=" CA ASP F 120 " pdb=" CB ASP F 120 " pdb=" CG ASP F 120 " ideal model delta sigma weight residual 112.60 115.53 -2.93 1.00e+00 1.00e+00 8.61e+00 ... (remaining 28830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.34: 12098 27.34 - 54.68: 581 54.68 - 82.02: 88 82.02 - 109.36: 13 109.36 - 136.69: 3 Dihedral angle restraints: 12783 sinusoidal: 5457 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=" O1A AGS C 702 " pdb=" O3A AGS C 702 " pdb=" PA AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sinusoidal sigma weight residual -67.73 68.96 -136.69 1 3.00e+01 1.11e-03 1.84e+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 ... (remaining 12780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1895 0.029 - 0.058: 987 0.058 - 0.087: 272 0.087 - 0.116: 149 0.116 - 0.145: 25 Chirality restraints: 3328 Sorted by residual: chirality pdb=" CG LEU B 282 " pdb=" CB LEU B 282 " pdb=" CD1 LEU B 282 " pdb=" CD2 LEU B 282 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE C 93 " pdb=" N ILE C 93 " pdb=" C ILE C 93 " pdb=" CB ILE C 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 3325 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: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 25.470 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 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 : 0.004 0.052 21130 Z= 0.182 Angle : 0.634 10.751 28859 Z= 0.321 Chirality : 0.040 0.145 3328 Planarity : 0.005 0.055 3606 Dihedral : 15.688 136.695 8029 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 0.00422 / 0.18 (21114) covalent geometry : angle 0.60770 / 0.32 (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 : 0.769 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: 0.9541 time to fit residues: 410.3705 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 : 0.794 ------------------------------------------------------------------------------- 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: 2.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 307 ASN G 186 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.050329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2294 r_free = 0.2294 target = 0.041678 restraints weight = 38796.879| |-----------------------------------------------------------------------------| r_work (start): 0.2293 rms_B_bonded: 1.09 r_work: 0.2204 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2114 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21130 Z= 0.135 Angle : 0.582 10.506 28859 Z= 0.289 Chirality : 0.038 0.143 3328 Planarity : 0.005 0.047 3606 Dihedral : 13.841 137.745 3238 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.41 % Allowed : 8.09 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.17), residues: 2513 helix: 1.71 (0.15), residues: 1320 sheet: 1.47 (0.24), residues: 441 loop : 0.15 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 56 TYR 0.020 0.001 TYR F 284 PHE 0.015 0.001 PHE F 319 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 0.00306 / 0.14 (21114) covalent geometry : angle 0.55840 / 0.29 (28835) hydrogen bonds : bond 0.04333 / 2.88 ( 1166) hydrogen bonds : angle 3.99260 / 2.85 ( 3270) metal coordination : bond 0.00774 / 0.39 ( 16) metal coordination : angle 5.72470 / 3.84 ( 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 363 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 312 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8114 (mtpp) REVERT: A 225 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8368 (mmpt) REVERT: B 46 THR cc_start: 0.9035 (p) cc_final: 0.8760 (t) REVERT: B 285 MET cc_start: 0.8851 (mtp) cc_final: 0.8342 (ttm) REVERT: C 347 MET cc_start: 0.8615 (mtp) cc_final: 0.8324 (mtp) REVERT: D 201 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7013 (ttt-90) REVERT: D 306 MET cc_start: 0.8944 (mmt) cc_final: 0.8433 (mmt) REVERT: E 296 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8723 (mm) REVERT: F 165 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7579 (tm-30) REVERT: F 186 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8751 (pm20) REVERT: F 205 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8467 (mtm110) REVERT: G 230 PHE cc_start: 0.8219 (m-80) cc_final: 0.8002 (m-80) outliers start: 51 outliers final: 18 residues processed: 337 average time/residue: 0.8850 time to fit residues: 325.4569 Evaluate side-chains 325 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 301 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 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 G residue 26 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 146 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: 0.8980 chunk 175 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 209 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 241 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 172 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.049945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2280 r_free = 0.2280 target = 0.041196 restraints weight = 38636.303| |-----------------------------------------------------------------------------| r_work (start): 0.2279 rms_B_bonded: 1.11 r_work: 0.2188 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2098 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1150 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= 0.142 Angle : 0.573 10.045 28859 Z= 0.284 Chirality : 0.038 0.142 3328 Planarity : 0.005 0.049 3606 Dihedral : 13.806 137.245 3238 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.46 % Allowed : 9.89 % Favored : 87.65 % 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: 1.89 (0.17), residues: 2513 helix: 1.85 (0.15), residues: 1316 sheet: 1.47 (0.24), residues: 443 loop : 0.14 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 246 TYR 0.018 0.001 TYR F 284 PHE 0.009 0.001 PHE G 230 TRP 0.014 0.001 TRP D 10 HIS 0.005 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (21114) covalent geometry : angle 0.54989 / 0.28 (28835) hydrogen bonds : bond 0.04187 / 2.77 ( 1166) hydrogen bonds : angle 3.84299 / 2.74 ( 3270) metal coordination : bond 0.00736 / 0.37 ( 16) metal coordination : angle 5.55245 / 3.73 ( 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 360 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 308 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8673 (tttm) REVERT: A 196 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8122 (mtpp) REVERT: A 225 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8355 (mmpt) REVERT: B 46 THR cc_start: 0.9068 (p) cc_final: 0.8815 (t) REVERT: B 285 MET cc_start: 0.8846 (mtp) cc_final: 0.8265 (ttm) REVERT: C 216 ASP cc_start: 0.8655 (m-30) cc_final: 0.8449 (m-30) REVERT: C 277 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: D 201 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7037 (ttt-90) REVERT: D 306 MET cc_start: 0.8998 (mmt) cc_final: 0.8654 (mmt) REVERT: E 264 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: E 296 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8709 (mm) REVERT: F 165 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7585 (tm-30) REVERT: G 149 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: G 186 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8286 (pm20) outliers start: 52 outliers final: 21 residues processed: 334 average time/residue: 0.9294 time to fit residues: 338.7834 Evaluate side-chains 321 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 291 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 264 GLN Chi-restraints excluded: chain E residue 296 ILE 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 26 THR 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 186 GLN 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: 2.9990 chunk 102 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 188 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS ** E 287 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 = 0.2483 r_free = 0.2483 target = 0.048726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2246 r_free = 0.2246 target = 0.039989 restraints weight = 38647.909| |-----------------------------------------------------------------------------| r_work (start): 0.2245 rms_B_bonded: 1.10 r_work: 0.2153 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2062 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 21130 Z= 0.175 Angle : 0.605 10.550 28859 Z= 0.299 Chirality : 0.039 0.144 3328 Planarity : 0.005 0.053 3606 Dihedral : 13.835 136.499 3238 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.89 % Allowed : 11.64 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.17), residues: 2513 helix: 1.80 (0.15), residues: 1316 sheet: 1.56 (0.24), residues: 426 loop : -0.01 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 205 TYR 0.012 0.001 TYR F 284 PHE 0.011 0.002 PHE G 3 TRP 0.014 0.001 TRP D 10 HIS 0.007 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (21114) covalent geometry : angle 0.58125 / 0.30 (28835) hydrogen bonds : bond 0.04449 / 2.93 ( 1166) hydrogen bonds : angle 3.86148 / 2.76 ( 3270) metal coordination : bond 0.00766 / 0.40 ( 16) metal coordination : angle 5.81897 / 3.95 ( 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 363 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 302 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 116 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8708 (tttm) REVERT: A 196 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8127 (mtpp) REVERT: A 225 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8348 (mmpt) REVERT: A 318 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8050 (tm-30) REVERT: B 285 MET cc_start: 0.8829 (mtp) cc_final: 0.8283 (ttm) REVERT: C 262 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8405 (mm-30) REVERT: C 347 MET cc_start: 0.8667 (mtp) cc_final: 0.8356 (mtp) REVERT: D 188 GLU cc_start: 0.8502 (tt0) cc_final: 0.8272 (tt0) REVERT: D 201 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7026 (ttt-90) REVERT: D 244 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8179 (mt) REVERT: D 306 MET cc_start: 0.9032 (mmt) cc_final: 0.8809 (mmt) REVERT: E 264 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: E 287 GLN cc_start: 0.8768 (tt0) cc_final: 0.8564 (tt0) REVERT: E 296 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8731 (mm) REVERT: F 165 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7619 (tm-30) REVERT: F 291 LYS cc_start: 0.8808 (ptmt) cc_final: 0.8596 (ptmt) REVERT: G 100 ARG cc_start: 0.8788 (ptm160) cc_final: 0.8458 (mtp85) REVERT: G 149 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8073 (mt0) REVERT: G 250 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8632 (ttmm) outliers start: 61 outliers final: 31 residues processed: 330 average time/residue: 0.9175 time to fit residues: 331.0725 Evaluate side-chains 336 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 294 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 111 VAL Chi-restraints excluded: chain B residue 112 GLN 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 262 GLU 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 201 ARG Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 244 LEU 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 121 ASP 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 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 G residue 276 GLU 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: 0.0030 chunk 86 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS B 23 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 E 287 GLN ** 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 = 0.2459 r_free = 0.2459 target = 0.047824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2222 r_free = 0.2222 target = 0.039138 restraints weight = 38475.130| |-----------------------------------------------------------------------------| r_work (start): 0.2220 rms_B_bonded: 1.10 r_work: 0.2128 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2036 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 21130 Z= 0.207 Angle : 0.641 11.138 28859 Z= 0.317 Chirality : 0.041 0.160 3328 Planarity : 0.005 0.056 3606 Dihedral : 13.940 135.781 3238 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.22 % Allowed : 12.26 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.17), residues: 2513 helix: 1.69 (0.15), residues: 1317 sheet: 1.55 (0.24), residues: 428 loop : -0.09 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 246 TYR 0.018 0.002 TYR G 284 PHE 0.012 0.002 PHE F 3 TRP 0.015 0.002 TRP D 10 HIS 0.008 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (21114) covalent geometry : angle 0.61726 / 0.32 (28835) hydrogen bonds : bond 0.04765 / 3.13 ( 1166) hydrogen bonds : angle 3.92520 / 2.80 ( 3270) metal coordination : bond 0.00813 / 0.42 ( 16) metal coordination : angle 6.05575 / 4.11 ( 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 365 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 297 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8739 (tttm) REVERT: A 196 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8125 (mtpp) REVERT: A 225 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8346 (mmpt) REVERT: A 318 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: B 46 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8819 (t) REVERT: B 136 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7774 (t80) REVERT: B 285 MET cc_start: 0.8826 (mtp) cc_final: 0.8298 (ttm) REVERT: D 188 GLU cc_start: 0.8501 (tt0) cc_final: 0.8285 (mt-10) REVERT: D 201 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7059 (ttt-90) REVERT: D 330 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: E 264 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: E 296 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8734 (mm) REVERT: F 165 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7607 (tm-30) REVERT: F 291 LYS cc_start: 0.8830 (ptmt) cc_final: 0.8602 (ptmt) REVERT: F 316 GLU cc_start: 0.7179 (tp30) cc_final: 0.6942 (tp30) REVERT: G 48 ASP cc_start: 0.8245 (t0) cc_final: 0.7992 (t0) REVERT: G 100 ARG cc_start: 0.8786 (ptm160) cc_final: 0.8474 (mtp85) REVERT: G 136 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8690 (tttp) REVERT: G 149 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8096 (mt0) REVERT: G 250 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8637 (ttmm) outliers start: 68 outliers final: 30 residues processed: 331 average time/residue: 0.9026 time to fit residues: 325.9740 Evaluate side-chains 328 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 285 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 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 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 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 149 GLN Chi-restraints excluded: chain G residue 172 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 175 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS C 269 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS E 287 GLN G 16 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 = 0.2475 r_free = 0.2475 target = 0.048440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2239 r_free = 0.2239 target = 0.039755 restraints weight = 38381.021| |-----------------------------------------------------------------------------| r_work (start): 0.2237 rms_B_bonded: 1.10 r_work: 0.2145 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2054 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 21130 Z= 0.165 Angle : 0.602 10.898 28859 Z= 0.297 Chirality : 0.039 0.154 3328 Planarity : 0.005 0.055 3606 Dihedral : 13.932 136.687 3238 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.89 % Allowed : 13.63 % Favored : 83.48 % 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: 1.73 (0.17), residues: 2513 helix: 1.78 (0.15), residues: 1315 sheet: 1.49 (0.24), residues: 421 loop : -0.07 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 282 TYR 0.017 0.001 TYR F 284 PHE 0.012 0.001 PHE G 3 TRP 0.016 0.001 TRP D 10 HIS 0.005 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (21114) covalent geometry : angle 0.57846 / 0.30 (28835) hydrogen bonds : bond 0.04306 / 2.83 ( 1166) hydrogen bonds : angle 3.84633 / 2.74 ( 3270) metal coordination : bond 0.00746 / 0.39 ( 16) metal coordination : angle 5.75180 / 3.87 ( 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 350 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 289 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8704 (tttm) REVERT: A 196 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8108 (mtpp) REVERT: A 225 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8357 (mmpt) REVERT: A 318 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: B 285 MET cc_start: 0.8826 (mtp) cc_final: 0.8257 (ttm) REVERT: C 260 ASN cc_start: 0.8683 (t0) cc_final: 0.8408 (t0) REVERT: C 318 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8002 (ptt-90) REVERT: D 154 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8959 (mt) REVERT: D 188 GLU cc_start: 0.8494 (tt0) cc_final: 0.8293 (mt-10) REVERT: D 201 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7038 (ttt-90) REVERT: E 264 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: E 296 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8738 (mm) REVERT: F 165 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7606 (tm-30) REVERT: F 304 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7805 (mm-30) REVERT: G 48 ASP cc_start: 0.8192 (t0) cc_final: 0.7864 (t0) REVERT: G 100 ARG cc_start: 0.8775 (ptm160) cc_final: 0.8472 (mtp85) REVERT: G 149 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8073 (mt0) REVERT: G 206 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8462 (ttm) REVERT: G 250 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8635 (ttmm) outliers start: 61 outliers final: 31 residues processed: 319 average time/residue: 0.9037 time to fit residues: 314.9913 Evaluate side-chains 326 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 283 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 101 VAL Chi-restraints excluded: chain B residue 111 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 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 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 296 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 315 MET 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 4 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 111 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 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: 2.9990 chunk 19 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 228 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 333 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.047415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2211 r_free = 0.2211 target = 0.038763 restraints weight = 38712.167| |-----------------------------------------------------------------------------| r_work (start): 0.2209 rms_B_bonded: 1.10 r_work: 0.2116 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2024 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 21130 Z= 0.212 Angle : 0.656 11.227 28859 Z= 0.324 Chirality : 0.041 0.153 3328 Planarity : 0.005 0.056 3606 Dihedral : 13.981 136.195 3238 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.03 % Allowed : 14.15 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.17), residues: 2513 helix: 1.68 (0.14), residues: 1311 sheet: 1.43 (0.24), residues: 431 loop : -0.12 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 246 TYR 0.028 0.002 TYR F 284 PHE 0.013 0.002 PHE G 3 TRP 0.015 0.002 TRP D 10 HIS 0.006 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 (21114) covalent geometry : angle 0.63223 / 0.32 (28835) hydrogen bonds : bond 0.04812 / 3.16 ( 1166) hydrogen bonds : angle 3.94146 / 2.81 ( 3270) metal coordination : bond 0.00819 / 0.42 ( 16) metal coordination : angle 6.06827 / 4.12 ( 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 350 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 286 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8107 (mtpp) REVERT: A 225 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8341 (mmpt) REVERT: A 313 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8641 (mptm) REVERT: A 318 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: B 46 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8850 (t) REVERT: B 136 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8156 (t80) REVERT: B 285 MET cc_start: 0.8821 (mtp) cc_final: 0.8288 (ttm) REVERT: C 347 MET cc_start: 0.8533 (mtp) cc_final: 0.8237 (mtp) REVERT: D 154 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8990 (mt) REVERT: D 201 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7099 (ttt-90) REVERT: D 306 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8789 (mtt) REVERT: D 330 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: E 264 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: E 296 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8739 (mm) REVERT: F 165 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7612 (tm-30) REVERT: G 1 MET cc_start: 0.8817 (ttp) cc_final: 0.8488 (ttp) REVERT: G 48 ASP cc_start: 0.8234 (t0) cc_final: 0.7928 (t0) REVERT: G 100 ARG cc_start: 0.8767 (ptm160) cc_final: 0.8463 (mtp85) REVERT: G 136 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8681 (tttp) REVERT: G 149 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8095 (mt0) REVERT: G 206 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8479 (ttm) REVERT: G 250 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8629 (ttmm) outliers start: 64 outliers final: 34 residues processed: 319 average time/residue: 0.8871 time to fit residues: 309.4074 Evaluate side-chains 325 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 275 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 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 252 LEU Chi-restraints excluded: chain C residue 277 GLU 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 306 MET 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 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 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 4 THR 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 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 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: 0.0070 chunk 180 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 246 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 174 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS C 269 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS G 16 GLN G 186 GLN ** G 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.048565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2241 r_free = 0.2241 target = 0.039854 restraints weight = 38487.658| |-----------------------------------------------------------------------------| r_work (start): 0.2241 rms_B_bonded: 1.10 r_work: 0.2149 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2058 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21130 Z= 0.153 Angle : 0.594 10.870 28859 Z= 0.294 Chirality : 0.038 0.159 3328 Planarity : 0.005 0.057 3606 Dihedral : 13.940 137.515 3238 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.60 % Allowed : 15.00 % 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: 1.79 (0.17), residues: 2513 helix: 1.83 (0.15), residues: 1309 sheet: 1.44 (0.24), residues: 427 loop : 0.00 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 246 TYR 0.026 0.001 TYR F 284 PHE 0.015 0.001 PHE G 3 TRP 0.017 0.001 TRP D 10 HIS 0.005 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (21114) covalent geometry : angle 0.57190 / 0.29 (28835) hydrogen bonds : bond 0.04129 / 2.73 ( 1166) hydrogen bonds : angle 3.83057 / 2.73 ( 3270) metal coordination : bond 0.00728 / 0.37 ( 16) metal coordination : angle 5.62902 / 3.79 ( 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 341 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 286 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8734 (tttm) REVERT: A 196 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8095 (mtpp) REVERT: A 211 HIS cc_start: 0.8478 (t70) cc_final: 0.7701 (m90) REVERT: A 225 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8304 (mmpt) REVERT: B 136 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8143 (t80) REVERT: B 285 MET cc_start: 0.8827 (mtp) cc_final: 0.8239 (ttm) REVERT: C 318 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7966 (ptt-90) REVERT: C 347 MET cc_start: 0.8536 (mtp) cc_final: 0.8225 (mtp) REVERT: D 154 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8947 (mt) REVERT: D 330 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: E 264 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: E 296 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8742 (mm) REVERT: F 73 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7993 (ttp-170) REVERT: F 165 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7628 (tm-30) REVERT: G 48 ASP cc_start: 0.8173 (t0) cc_final: 0.7900 (t0) REVERT: G 100 ARG cc_start: 0.8754 (ptm160) cc_final: 0.8451 (mtp85) REVERT: G 136 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8674 (tttp) REVERT: G 149 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8063 (mt0) REVERT: G 250 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8636 (ttmm) outliers start: 55 outliers final: 30 residues processed: 315 average time/residue: 0.9226 time to fit residues: 317.0872 Evaluate side-chains 326 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 283 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 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 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 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 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 4 THR 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 149 GLN Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 227 VAL 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: 0.6980 chunk 246 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 176 optimal weight: 0.4980 chunk 222 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.048845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2249 r_free = 0.2249 target = 0.040111 restraints weight = 38524.002| |-----------------------------------------------------------------------------| r_work (start): 0.2248 rms_B_bonded: 1.11 r_work: 0.2156 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2065 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1509 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= 0.148 Angle : 0.590 11.420 28859 Z= 0.292 Chirality : 0.038 0.152 3328 Planarity : 0.005 0.061 3606 Dihedral : 13.878 137.940 3238 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.74 % Allowed : 15.05 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.17), residues: 2513 helix: 1.84 (0.15), residues: 1316 sheet: 1.52 (0.25), residues: 417 loop : 0.00 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 269 TYR 0.016 0.001 TYR G 284 PHE 0.014 0.001 PHE G 3 TRP 0.016 0.001 TRP D 10 HIS 0.005 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (21114) covalent geometry : angle 0.56839 / 0.29 (28835) hydrogen bonds : bond 0.04065 / 2.68 ( 1166) hydrogen bonds : angle 3.79648 / 2.70 ( 3270) metal coordination : bond 0.00725 / 0.37 ( 16) metal coordination : angle 5.50980 / 3.71 ( 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 343 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 285 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8748 (tttm) REVERT: A 196 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8093 (mtpp) REVERT: A 211 HIS cc_start: 0.8470 (t70) cc_final: 0.7697 (m90) REVERT: A 225 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8346 (mmpt) REVERT: B 285 MET cc_start: 0.8824 (mtp) cc_final: 0.8240 (ttm) REVERT: C 260 ASN cc_start: 0.8658 (t0) cc_final: 0.8398 (t0) REVERT: C 274 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6811 (ttp80) REVERT: C 318 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7938 (ptt-90) REVERT: C 347 MET cc_start: 0.8557 (mtp) cc_final: 0.8246 (mtp) REVERT: D 154 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8961 (mt) REVERT: D 330 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: E 264 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: E 296 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8732 (mm) REVERT: F 73 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7989 (ttp-170) REVERT: F 165 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7635 (tm-30) REVERT: G 48 ASP cc_start: 0.8168 (t0) cc_final: 0.7924 (t0) REVERT: G 100 ARG cc_start: 0.8746 (ptm160) cc_final: 0.8457 (mtp85) REVERT: G 136 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8667 (tttp) REVERT: G 149 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8055 (mt0) REVERT: G 250 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8636 (ttmm) outliers start: 58 outliers final: 28 residues processed: 315 average time/residue: 0.8906 time to fit residues: 305.8790 Evaluate side-chains 319 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 278 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 101 VAL Chi-restraints excluded: chain B residue 111 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 274 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 330 GLN Chi-restraints excluded: chain E residue 57 LYS 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 317 ILE 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 110 THR 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 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: 1.9990 chunk 165 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 24 optimal weight: 0.0570 chunk 224 optimal weight: 0.6980 chunk 135 optimal weight: 0.6980 chunk 239 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.049694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2272 r_free = 0.2272 target = 0.040931 restraints weight = 38713.930| |-----------------------------------------------------------------------------| r_work (start): 0.2271 rms_B_bonded: 1.11 r_work: 0.2180 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2090 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21130 Z= 0.127 Angle : 0.572 11.238 28859 Z= 0.283 Chirality : 0.037 0.151 3328 Planarity : 0.005 0.055 3606 Dihedral : 13.825 138.057 3238 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.37 % Allowed : 15.57 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.17), residues: 2513 helix: 1.93 (0.15), residues: 1316 sheet: 1.38 (0.24), residues: 442 loop : 0.13 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 246 TYR 0.019 0.001 TYR G 284 PHE 0.013 0.001 PHE G 230 TRP 0.017 0.001 TRP D 10 HIS 0.004 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (21114) covalent geometry : angle 0.55233 / 0.28 (28835) hydrogen bonds : bond 0.03759 / 2.49 ( 1166) hydrogen bonds : angle 3.73047 / 2.65 ( 3270) metal coordination : bond 0.00704 / 0.37 ( 16) metal coordination : angle 5.24053 / 3.51 ( 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 334 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 284 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 116 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8734 (tttm) REVERT: A 196 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8074 (mtpp) REVERT: A 211 HIS cc_start: 0.8486 (t70) cc_final: 0.7706 (m90) REVERT: A 225 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8344 (mmpt) REVERT: B 46 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8868 (t) REVERT: B 285 MET cc_start: 0.8832 (mtp) cc_final: 0.8237 (ttm) REVERT: C 260 ASN cc_start: 0.8632 (t0) cc_final: 0.8409 (t0) REVERT: C 274 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6812 (ttp80) REVERT: C 277 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: C 318 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7920 (ptt-90) REVERT: C 347 MET cc_start: 0.8561 (mtp) cc_final: 0.8247 (mtp) REVERT: D 80 ARG cc_start: 0.8217 (mtm110) cc_final: 0.7874 (mtt90) REVERT: D 154 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8936 (mt) REVERT: D 330 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: E 264 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: E 296 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8723 (mm) REVERT: F 73 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7985 (ttp-170) REVERT: F 165 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7648 (tm-30) REVERT: G 100 ARG cc_start: 0.8722 (ptm160) cc_final: 0.8447 (mtp85) REVERT: G 136 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8660 (tttp) REVERT: G 149 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: G 186 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8421 (pm20) REVERT: G 250 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8633 (ttmm) outliers start: 50 outliers final: 25 residues processed: 310 average time/residue: 0.9001 time to fit residues: 304.6015 Evaluate side-chains 322 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 116 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 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 365 LEU Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 274 ARG 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 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 186 GLN Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 136 LYS 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 220 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 113 optimal weight: 0.3980 chunk 160 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS C 269 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.049213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.040456 restraints weight = 38681.841| |-----------------------------------------------------------------------------| 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: 2.57 restraints_weight: 0.2500 r_work (final): 0.2076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21130 Z= 0.147 Angle : 0.596 11.116 28859 Z= 0.296 Chirality : 0.038 0.152 3328 Planarity : 0.005 0.060 3606 Dihedral : 13.809 137.494 3238 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.41 % Allowed : 15.85 % Favored : 81.73 % 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: 1.89 (0.17), residues: 2513 helix: 1.90 (0.15), residues: 1316 sheet: 1.37 (0.24), residues: 442 loop : 0.11 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 246 TYR 0.010 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 F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (21114) covalent geometry : angle 0.57647 / 0.29 (28835) hydrogen bonds : bond 0.03981 / 2.62 ( 1166) hydrogen bonds : angle 3.75067 / 2.67 ( 3270) metal coordination : bond 0.00724 / 0.37 ( 16) metal coordination : angle 5.33672 / 3.60 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7962.07 seconds wall clock time: 136 minutes 1.24 seconds (8161.24 seconds total)