Starting phenix.real_space_refine on Sat Jul 4 11:48:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f8s_28935/07_2026/8f8s_28935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f8s_28935/07_2026/8f8s_28935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f8s_28935/07_2026/8f8s_28935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f8s_28935/07_2026/8f8s_28935.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8f8s_28935/07_2026/8f8s_28935.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f8s_28935/07_2026/8f8s_28935.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f8s_28935/07_2026/8f8s_28935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f8s_28935/07_2026/8f8s_28935.map" } resolution = 2.84 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= 0.001 sd= 0.018 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: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 7 5.21 5 S 143 5.16 5 C 12848 2.51 5 N 3434 2.21 5 O 3925 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20371 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2811 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2819 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.50, per 1000 atoms: 0.22 Number of scatterers: 20371 At special positions: 0 Unit cell: (84.24, 104.76, 241.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 143 16.00 P 14 15.00 Mg 7 11.99 O 3925 8.00 N 3434 7.00 C 12848 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: 1.20 Conformation dependent library (CDL) restraints added in 657.4 milliseconds 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4778 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 40 sheets defined 49.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.673A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.507A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.520A pdb=" N ASP A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.648A pdb=" N ARG A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.834A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.776A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.512A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.053A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 353 removed outlier: 3.616A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 353' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.065A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.506A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.895A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.576A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.501A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.998A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 217 removed outlier: 3.602A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.635A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.753A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.542A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.525A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.249A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.624A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 359 through 365 removed outlier: 3.638A pdb=" N ASP B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.086A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.836A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.064A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.839A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.758A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.702A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.189A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.912A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.039A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.532A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.696A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.555A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.538A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.628A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.018A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.709A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.606A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.323A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.976A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.511A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.989A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.718A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.521A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.621A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.212A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 92 Processing helix chain 'G' and resid 112 through 126 removed outlier: 4.032A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 202 through 217 removed outlier: 3.651A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.674A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 262 Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 286 through 288 No H-bonds generated for 'chain 'G' and resid 286 through 288' Processing helix chain 'G' and resid 289 through 295 Processing helix chain 'G' and resid 302 through 306 removed outlier: 4.079A pdb=" N TYR G 306 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 349 Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 368 through 374 removed outlier: 4.135A pdb=" N ARG G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.496A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.989A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.749A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 250 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.573A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 103 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.090A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.885A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.082A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.443A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.627A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB8, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.599A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC2, first strand: chain 'D' and resid 176 through 178 removed outlier: 6.522A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 176 through 178 Processing sheet with id=AC4, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC5, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.012A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC8, first strand: chain 'E' and resid 176 through 178 removed outlier: 6.462A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 176 through 178 removed outlier: 3.798A pdb=" N GLN G 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD2, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.584A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD4, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD5, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD6, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.636A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD8, first strand: chain 'G' and resid 29 through 32 removed outlier: 3.961A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN G 12 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE1, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AE2, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AE3, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.634A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 238 through 241 1015 hydrogen bonds defined for protein. 2619 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6603 1.34 - 1.46: 3207 1.46 - 1.57: 10733 1.57 - 1.69: 21 1.69 - 1.81: 251 Bond restraints: 20815 Sorted by residual: bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.94e+00 bond pdb=" CE1 HIC G 73 " pdb=" NE2 HIC G 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.71e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.44e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.38e+00 ... (remaining 20810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 27372 1.39 - 2.78: 614 2.78 - 4.17: 189 4.17 - 5.56: 50 5.56 - 6.95: 29 Bond angle restraints: 28254 Sorted by residual: angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 116.24 -5.74 1.70e+00 3.46e-01 1.14e+01 angle pdb=" N HIC F 73 " pdb=" CA HIC F 73 " pdb=" CB HIC F 73 " ideal model delta sigma weight residual 110.50 115.82 -5.32 1.70e+00 3.46e-01 9.79e+00 angle pdb=" N HIC E 73 " pdb=" CA HIC E 73 " pdb=" CB HIC E 73 " ideal model delta sigma weight residual 110.50 115.78 -5.28 1.70e+00 3.46e-01 9.64e+00 angle pdb=" C ILE B 71 " pdb=" N GLU B 72 " pdb=" CA GLU B 72 " ideal model delta sigma weight residual 121.70 127.12 -5.42 1.80e+00 3.09e-01 9.05e+00 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 115.55 -5.05 1.70e+00 3.46e-01 8.84e+00 ... (remaining 28249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 12206 33.77 - 67.54: 294 67.54 - 101.31: 11 101.31 - 135.08: 7 135.08 - 168.85: 2 Dihedral angle restraints: 12520 sinusoidal: 5060 harmonic: 7460 Sorted by residual: dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.86 -168.85 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 87.96 -147.96 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 65.95 -125.95 1 2.00e+01 2.50e-03 3.81e+01 ... (remaining 12517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1590 0.029 - 0.057: 945 0.057 - 0.086: 342 0.086 - 0.114: 216 0.114 - 0.143: 48 Chirality restraints: 3141 Sorted by residual: chirality pdb=" CA ILE G 165 " pdb=" N ILE G 165 " pdb=" C ILE G 165 " pdb=" CB ILE G 165 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE F 165 " pdb=" N ILE F 165 " pdb=" C ILE F 165 " pdb=" CB ILE F 165 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE C 165 " pdb=" N ILE C 165 " pdb=" C ILE C 165 " pdb=" CB ILE C 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 3138 not shown) Planarity restraints: 3609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 321 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO D 322 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 322 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 322 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 321 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO E 322 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 322 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 322 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 321 " 0.041 5.00e-02 4.00e+02 6.33e-02 6.40e+00 pdb=" N PRO F 322 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 322 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 322 " 0.035 5.00e-02 4.00e+02 ... (remaining 3606 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 139 2.58 - 3.16: 15570 3.16 - 3.74: 31433 3.74 - 4.32: 45129 4.32 - 4.90: 75663 Nonbonded interactions: 167934 Sorted by model distance: nonbonded pdb=" O3B ADP F 401 " pdb="MG MG F 402 " model vdw 2.002 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 2.039 2.170 nonbonded pdb=" O3B ADP G 401 " pdb="MG MG G 402 " model vdw 2.042 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.146 2.170 nonbonded pdb=" O GLY D 156 " pdb=" OG1 THR D 303 " model vdw 2.232 3.040 ... (remaining 167929 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 'A' selection = (chain 'B' and (resid 5 through 40 or resid 52 through 402)) selection = (chain 'C' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) selection = (chain 'D' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) selection = (chain 'E' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) selection = (chain 'F' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) selection = (chain 'G' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) } 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=0.00 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: 5.840 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.610 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 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 0.057 20815 Z= 0.167 Angle : 0.613 6.945 28254 Z= 0.306 Chirality : 0.046 0.143 3141 Planarity : 0.005 0.064 3609 Dihedral : 14.041 168.855 7742 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.94 % Allowed : 7.85 % Favored : 89.22 % 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: -0.35 (0.17), residues: 2540 helix: -0.79 (0.15), residues: 1065 sheet: 0.58 (0.24), residues: 473 loop : 0.29 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 256 TYR 0.012 0.001 TYR F 143 PHE 0.013 0.001 PHE D 255 TRP 0.011 0.002 TRP E 79 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (20815) covalent geometry : angle 0.61320 / 0.31 (28254) hydrogen bonds : bond 0.20664 / 13.84 ( 991) hydrogen bonds : angle 6.93904 / 4.89 ( 2619) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 621 time to evaluate : 0.820 Fit side-chains REVERT: A 61 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7920 (pttp) REVERT: A 71 ILE cc_start: 0.8137 (mm) cc_final: 0.7868 (mt) REVERT: A 82 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7613 (tpp) REVERT: A 94 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7575 (tm) REVERT: A 99 GLU cc_start: 0.7474 (mp0) cc_final: 0.7256 (mp0) REVERT: A 116 ARG cc_start: 0.7376 (ttp80) cc_final: 0.6710 (ttp80) REVERT: A 122 ILE cc_start: 0.8450 (mm) cc_final: 0.8236 (mp) REVERT: A 214 GLU cc_start: 0.7899 (tt0) cc_final: 0.7663 (mt-10) REVERT: A 215 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7772 (ttmm) REVERT: A 224 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7239 (tp30) REVERT: A 299 MET cc_start: 0.8651 (mtp) cc_final: 0.8323 (mtp) REVERT: A 316 GLU cc_start: 0.8736 (tp30) cc_final: 0.8497 (tp30) REVERT: A 355 MET cc_start: 0.7153 (mpp) cc_final: 0.6918 (mpp) REVERT: B 61 LYS cc_start: 0.8081 (mmtp) cc_final: 0.7833 (mmtp) REVERT: B 83 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: B 116 ARG cc_start: 0.7849 (ptm160) cc_final: 0.7556 (ptm160) REVERT: B 117 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7350 (mm-30) REVERT: B 118 LYS cc_start: 0.7876 (tptt) cc_final: 0.7620 (tptt) REVERT: B 184 ASP cc_start: 0.8086 (m-30) cc_final: 0.7873 (m-30) REVERT: B 205 GLU cc_start: 0.7378 (mp0) cc_final: 0.7145 (mp0) REVERT: B 207 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 248 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8092 (pt) REVERT: B 291 LYS cc_start: 0.8581 (tttp) cc_final: 0.8321 (tttm) REVERT: C 72 GLU cc_start: 0.7694 (tt0) cc_final: 0.7430 (tp30) REVERT: C 98 PRO cc_start: 0.8808 (Cg_exo) cc_final: 0.8560 (Cg_endo) REVERT: C 99 GLU cc_start: 0.7518 (pm20) cc_final: 0.7273 (pm20) REVERT: C 118 LYS cc_start: 0.8423 (mtpp) cc_final: 0.8168 (mttm) REVERT: C 227 MET cc_start: 0.8814 (mmm) cc_final: 0.8607 (mmm) REVERT: C 334 GLU cc_start: 0.7734 (pm20) cc_final: 0.7434 (pm20) REVERT: D 44 MET cc_start: 0.7811 (tpp) cc_final: 0.7550 (tpp) REVERT: D 90 PHE cc_start: 0.8594 (m-80) cc_final: 0.8360 (m-80) REVERT: D 117 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7793 (mt-10) REVERT: D 227 MET cc_start: 0.8516 (mmm) cc_final: 0.8313 (mmp) REVERT: D 284 LYS cc_start: 0.8571 (mttp) cc_final: 0.8328 (mtpm) REVERT: E 99 GLU cc_start: 0.7566 (pm20) cc_final: 0.7298 (pp20) REVERT: E 121 GLN cc_start: 0.8395 (tt0) cc_final: 0.8146 (tt0) REVERT: E 147 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8716 (ptp-170) REVERT: E 288 ASP cc_start: 0.7758 (m-30) cc_final: 0.7499 (m-30) REVERT: E 313 MET cc_start: 0.8488 (mmm) cc_final: 0.8219 (tpt) REVERT: E 337 TYR cc_start: 0.8774 (m-10) cc_final: 0.8568 (m-80) REVERT: F 68 LYS cc_start: 0.8708 (mmtp) cc_final: 0.8453 (mmtp) REVERT: F 96 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8554 (m) REVERT: F 99 GLU cc_start: 0.7742 (mp0) cc_final: 0.7410 (mp0) REVERT: F 167 GLU cc_start: 0.8039 (mp0) cc_final: 0.7820 (mp0) REVERT: F 210 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7999 (ttm110) REVERT: F 222 ASP cc_start: 0.7979 (t0) cc_final: 0.7745 (t0) REVERT: F 354 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7244 (mm-40) REVERT: F 355 MET cc_start: 0.8216 (mtp) cc_final: 0.8002 (mtm) REVERT: F 364 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7248 (mm-30) REVERT: F 373 LYS cc_start: 0.8625 (tttp) cc_final: 0.8250 (mtpt) REVERT: G 117 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7737 (tp30) REVERT: G 147 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7907 (ptm160) REVERT: G 270 GLU cc_start: 0.6394 (mp0) cc_final: 0.5622 (mp0) REVERT: G 283 MET cc_start: 0.8209 (mmt) cc_final: 0.7760 (mmt) REVERT: G 311 ASP cc_start: 0.7838 (p0) cc_final: 0.7584 (p0) outliers start: 64 outliers final: 21 residues processed: 654 average time/residue: 0.6584 time to fit residues: 477.8525 Evaluate side-chains 620 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 589 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 147 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 354 GLN B 88 HIS B 111 ASN B 115 ASN B 297 ASN B 360 GLN C 12 ASN C 137 GLN C 246 GLN C 371 HIS D 137 GLN D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN E 353 GLN F 59 GLN F 137 GLN F 246 GLN F 297 ASN G 12 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.091215 restraints weight = 29853.864| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.63 r_work: 0.3003 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20815 Z= 0.214 Angle : 0.659 8.021 28254 Z= 0.324 Chirality : 0.048 0.224 3141 Planarity : 0.005 0.057 3609 Dihedral : 10.764 168.073 2967 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.36 % Allowed : 15.47 % Favored : 80.17 % 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: -0.10 (0.17), residues: 2540 helix: -0.28 (0.16), residues: 1101 sheet: 0.53 (0.24), residues: 470 loop : 0.15 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 254 TYR 0.016 0.002 TYR A 198 PHE 0.017 0.002 PHE A 223 TRP 0.014 0.002 TRP E 79 HIS 0.004 0.001 HIS F 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 (20815) covalent geometry : angle 0.65888 / 0.32 (28254) hydrogen bonds : bond 0.04556 / 3.05 ( 991) hydrogen bonds : angle 5.08158 / 3.61 ( 2619) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 593 time to evaluate : 0.791 Fit side-chains REVERT: A 61 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7982 (pttp) REVERT: A 81 ASP cc_start: 0.7755 (p0) cc_final: 0.7224 (p0) REVERT: A 82 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7592 (tpp) REVERT: A 99 GLU cc_start: 0.7791 (mp0) cc_final: 0.7435 (mp0) REVERT: A 157 ASP cc_start: 0.7216 (t0) cc_final: 0.6995 (t0) REVERT: A 167 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8025 (tp30) REVERT: A 214 GLU cc_start: 0.7809 (tt0) cc_final: 0.7562 (mt-10) REVERT: A 299 MET cc_start: 0.8501 (mtp) cc_final: 0.8146 (mtp) REVERT: A 316 GLU cc_start: 0.8641 (tp30) cc_final: 0.8421 (tp30) REVERT: B 21 PHE cc_start: 0.8691 (m-80) cc_final: 0.8320 (m-80) REVERT: B 61 LYS cc_start: 0.8206 (mmtp) cc_final: 0.7973 (mmtp) REVERT: B 117 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7145 (mm-30) REVERT: B 118 LYS cc_start: 0.8046 (tptt) cc_final: 0.7734 (tptt) REVERT: B 132 MET cc_start: 0.7974 (ttp) cc_final: 0.7749 (ttp) REVERT: B 205 GLU cc_start: 0.7252 (mp0) cc_final: 0.6917 (mp0) REVERT: B 215 LYS cc_start: 0.8526 (mttp) cc_final: 0.8161 (mttp) REVERT: C 44 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7469 (mpp) REVERT: C 72 GLU cc_start: 0.8019 (tt0) cc_final: 0.7710 (tp30) REVERT: C 98 PRO cc_start: 0.8750 (Cg_exo) cc_final: 0.8548 (Cg_endo) REVERT: C 99 GLU cc_start: 0.7591 (pm20) cc_final: 0.7304 (pm20) REVERT: C 118 LYS cc_start: 0.8382 (mtpp) cc_final: 0.8144 (mttm) REVERT: C 224 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8025 (mm-30) REVERT: C 334 GLU cc_start: 0.7810 (pm20) cc_final: 0.7513 (pm20) REVERT: D 44 MET cc_start: 0.8072 (tpp) cc_final: 0.7658 (tpp) REVERT: D 90 PHE cc_start: 0.8561 (m-80) cc_final: 0.8346 (m-80) REVERT: D 132 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8172 (ppp) REVERT: D 180 LEU cc_start: 0.8850 (tp) cc_final: 0.8649 (tt) REVERT: D 211 ASP cc_start: 0.8197 (t0) cc_final: 0.7962 (t0) REVERT: D 227 MET cc_start: 0.8559 (mmm) cc_final: 0.8350 (mmp) REVERT: D 284 LYS cc_start: 0.8728 (mttp) cc_final: 0.8479 (mtpm) REVERT: E 99 GLU cc_start: 0.7764 (pm20) cc_final: 0.7433 (pp20) REVERT: E 147 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8708 (ptp-170) REVERT: E 288 ASP cc_start: 0.7764 (m-30) cc_final: 0.7471 (m-30) REVERT: E 313 MET cc_start: 0.8461 (mmm) cc_final: 0.8194 (mmm) REVERT: F 68 LYS cc_start: 0.8748 (mmtp) cc_final: 0.8525 (mmtp) REVERT: F 96 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8586 (m) REVERT: F 99 GLU cc_start: 0.7773 (mp0) cc_final: 0.7360 (mp0) REVERT: F 210 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8221 (ttm110) REVERT: F 354 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7425 (mm-40) REVERT: F 355 MET cc_start: 0.8393 (mtp) cc_final: 0.8173 (mtm) REVERT: G 125 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: G 147 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8312 (ptm160) REVERT: G 222 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7433 (p0) REVERT: G 270 GLU cc_start: 0.6409 (mp0) cc_final: 0.5747 (mp0) REVERT: G 283 MET cc_start: 0.8352 (mmt) cc_final: 0.8025 (mmt) REVERT: G 355 MET cc_start: 0.8403 (mmm) cc_final: 0.8198 (mmm) outliers start: 95 outliers final: 43 residues processed: 636 average time/residue: 0.6539 time to fit residues: 461.1247 Evaluate side-chains 630 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 577 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 147 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 120 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 221 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 199 optimal weight: 0.0670 chunk 161 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 208 optimal weight: 0.3980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 78 ASN A 101 HIS A 111 ASN A 115 ASN A 354 GLN B 111 ASN B 297 ASN C 115 ASN C 137 GLN C 246 GLN D 12 ASN D 137 GLN D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN F 59 GLN F 137 GLN F 246 GLN F 353 GLN G 12 ASN G 92 ASN G 115 ASN G 297 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.108444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.093156 restraints weight = 29926.666| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.62 r_work: 0.3004 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20815 Z= 0.150 Angle : 0.612 7.383 28254 Z= 0.297 Chirality : 0.046 0.188 3141 Planarity : 0.004 0.056 3609 Dihedral : 10.188 170.233 2951 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.31 % Allowed : 17.53 % Favored : 78.16 % 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: 0.18 (0.17), residues: 2540 helix: 0.03 (0.16), residues: 1112 sheet: 0.48 (0.24), residues: 471 loop : 0.33 (0.22), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 372 TYR 0.015 0.001 TYR A 198 PHE 0.012 0.001 PHE B 31 TRP 0.013 0.002 TRP D 79 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (20815) covalent geometry : angle 0.61214 / 0.30 (28254) hydrogen bonds : bond 0.03845 / 2.57 ( 991) hydrogen bonds : angle 4.78864 / 3.39 ( 2619) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 592 time to evaluate : 0.811 Fit side-chains REVERT: A 61 LYS cc_start: 0.8330 (pttp) cc_final: 0.7959 (pttp) REVERT: A 81 ASP cc_start: 0.7662 (p0) cc_final: 0.7380 (p0) REVERT: A 99 GLU cc_start: 0.7765 (mp0) cc_final: 0.7355 (mp0) REVERT: A 115 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7957 (t0) REVERT: A 157 ASP cc_start: 0.7211 (t0) cc_final: 0.6964 (t0) REVERT: A 167 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8003 (tp30) REVERT: A 214 GLU cc_start: 0.7834 (tt0) cc_final: 0.7585 (mt-10) REVERT: A 215 LYS cc_start: 0.8268 (ttmm) cc_final: 0.8024 (ttmm) REVERT: A 254 ARG cc_start: 0.8308 (mtp85) cc_final: 0.7986 (mtp180) REVERT: A 316 GLU cc_start: 0.8643 (tp30) cc_final: 0.8386 (tp30) REVERT: A 355 MET cc_start: 0.7512 (mpp) cc_final: 0.7298 (mpp) REVERT: B 11 ASP cc_start: 0.8730 (t0) cc_final: 0.8299 (t70) REVERT: B 21 PHE cc_start: 0.8684 (m-80) cc_final: 0.8370 (m-80) REVERT: B 61 LYS cc_start: 0.8239 (mmtp) cc_final: 0.7990 (mmtp) REVERT: B 89 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8448 (t) REVERT: B 99 GLU cc_start: 0.7789 (pm20) cc_final: 0.7546 (pm20) REVERT: B 117 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7129 (mm-30) REVERT: B 118 LYS cc_start: 0.8000 (tptt) cc_final: 0.7710 (tptt) REVERT: B 205 GLU cc_start: 0.7455 (mp0) cc_final: 0.7077 (mp0) REVERT: C 44 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7393 (mpp) REVERT: C 72 GLU cc_start: 0.7983 (tt0) cc_final: 0.7676 (tp30) REVERT: C 98 PRO cc_start: 0.8725 (Cg_exo) cc_final: 0.8503 (Cg_endo) REVERT: C 99 GLU cc_start: 0.7604 (pm20) cc_final: 0.7278 (pm20) REVERT: C 113 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8135 (mtmm) REVERT: C 118 LYS cc_start: 0.8368 (mtpp) cc_final: 0.8161 (mttm) REVERT: C 297 ASN cc_start: 0.8453 (m110) cc_final: 0.8167 (m110) REVERT: C 334 GLU cc_start: 0.7841 (pm20) cc_final: 0.7521 (pm20) REVERT: D 44 MET cc_start: 0.8068 (tpp) cc_final: 0.7844 (tpp) REVERT: D 132 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7874 (ppp) REVERT: D 211 ASP cc_start: 0.8184 (t0) cc_final: 0.7936 (t0) REVERT: D 284 LYS cc_start: 0.8692 (mttp) cc_final: 0.8438 (mtpm) REVERT: E 99 GLU cc_start: 0.7743 (pm20) cc_final: 0.7473 (pp20) REVERT: E 147 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8607 (ptp-170) REVERT: E 288 ASP cc_start: 0.7744 (m-30) cc_final: 0.7436 (m-30) REVERT: E 313 MET cc_start: 0.8449 (mmm) cc_final: 0.8235 (mmm) REVERT: F 68 LYS cc_start: 0.8748 (mmtp) cc_final: 0.8500 (mmtp) REVERT: F 96 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8583 (m) REVERT: F 99 GLU cc_start: 0.7790 (mp0) cc_final: 0.7325 (mp0) REVERT: F 210 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8184 (ttm110) REVERT: F 314 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: F 327 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8352 (mp) REVERT: F 354 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7442 (mm-40) REVERT: F 355 MET cc_start: 0.8406 (mtp) cc_final: 0.8173 (mtm) REVERT: G 125 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7678 (mm-30) REVERT: G 147 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8292 (ptm160) REVERT: G 270 GLU cc_start: 0.6384 (mp0) cc_final: 0.5705 (mp0) outliers start: 94 outliers final: 44 residues processed: 634 average time/residue: 0.6917 time to fit residues: 486.4509 Evaluate side-chains 637 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 581 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 147 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 326 LYS Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 150 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 222 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 195 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 111 ASN B 111 ASN B 297 ASN C 12 ASN C 128 ASN C 137 GLN C 162 ASN D 115 ASN D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN F 59 GLN F 137 GLN F 246 GLN F 353 GLN G 12 ASN G 92 ASN G 115 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.104697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.089245 restraints weight = 29972.756| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.61 r_work: 0.3007 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20815 Z= 0.183 Angle : 0.632 9.982 28254 Z= 0.307 Chirality : 0.047 0.171 3141 Planarity : 0.005 0.055 3609 Dihedral : 10.142 174.687 2941 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.41 % Allowed : 17.90 % Favored : 77.70 % 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: 0.32 (0.17), residues: 2540 helix: 0.24 (0.16), residues: 1088 sheet: 0.57 (0.24), residues: 459 loop : 0.24 (0.21), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 372 TYR 0.013 0.001 TYR A 198 PHE 0.012 0.001 PHE B 31 TRP 0.013 0.002 TRP D 79 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (20815) covalent geometry : angle 0.63159 / 0.31 (28254) hydrogen bonds : bond 0.03895 / 2.59 ( 991) hydrogen bonds : angle 4.71847 / 3.33 ( 2619) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 594 time to evaluate : 0.647 Fit side-chains REVERT: A 18 LYS cc_start: 0.8300 (mptt) cc_final: 0.8098 (mptt) REVERT: A 61 LYS cc_start: 0.8329 (pttp) cc_final: 0.7950 (pttp) REVERT: A 99 GLU cc_start: 0.7776 (mp0) cc_final: 0.7367 (mp0) REVERT: A 115 ASN cc_start: 0.8206 (t0) cc_final: 0.7897 (t0) REVERT: A 154 ASP cc_start: 0.7810 (t70) cc_final: 0.7569 (t70) REVERT: A 157 ASP cc_start: 0.7240 (t0) cc_final: 0.7009 (t0) REVERT: A 167 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7890 (mm-30) REVERT: A 215 LYS cc_start: 0.8249 (ttmm) cc_final: 0.8031 (ttmm) REVERT: A 254 ARG cc_start: 0.8291 (mtp85) cc_final: 0.7977 (mtp180) REVERT: A 299 MET cc_start: 0.8384 (mtp) cc_final: 0.8122 (mtm) REVERT: A 316 GLU cc_start: 0.8632 (tp30) cc_final: 0.8216 (tp30) REVERT: A 355 MET cc_start: 0.7554 (mpp) cc_final: 0.7339 (mpp) REVERT: B 21 PHE cc_start: 0.8662 (m-80) cc_final: 0.8366 (m-80) REVERT: B 61 LYS cc_start: 0.8190 (mmtp) cc_final: 0.7963 (mmtp) REVERT: B 99 GLU cc_start: 0.7799 (pm20) cc_final: 0.7560 (pm20) REVERT: B 117 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7128 (mm-30) REVERT: B 118 LYS cc_start: 0.8070 (tptt) cc_final: 0.7774 (tptt) REVERT: B 205 GLU cc_start: 0.7469 (mp0) cc_final: 0.7078 (mp0) REVERT: B 207 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7853 (mm-30) REVERT: C 44 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7439 (mpp) REVERT: C 72 GLU cc_start: 0.8006 (tt0) cc_final: 0.7697 (tp30) REVERT: C 98 PRO cc_start: 0.8737 (Cg_exo) cc_final: 0.8490 (Cg_endo) REVERT: C 99 GLU cc_start: 0.7593 (pm20) cc_final: 0.7274 (pm20) REVERT: C 113 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8160 (mtmm) REVERT: C 118 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8187 (mttm) REVERT: C 297 ASN cc_start: 0.8464 (m110) cc_final: 0.8192 (m110) REVERT: C 334 GLU cc_start: 0.7858 (pm20) cc_final: 0.7531 (pm20) REVERT: D 132 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7917 (ppp) REVERT: D 211 ASP cc_start: 0.8178 (t0) cc_final: 0.7926 (t0) REVERT: D 284 LYS cc_start: 0.8710 (mttp) cc_final: 0.8441 (mtpm) REVERT: E 99 GLU cc_start: 0.7750 (pm20) cc_final: 0.7481 (pp20) REVERT: E 288 ASP cc_start: 0.7744 (m-30) cc_final: 0.7432 (m-30) REVERT: F 68 LYS cc_start: 0.8749 (mmtp) cc_final: 0.8534 (mmtp) REVERT: F 96 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8577 (m) REVERT: F 99 GLU cc_start: 0.7789 (mp0) cc_final: 0.7392 (mp0) REVERT: F 113 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7830 (mmtp) REVERT: F 210 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8194 (ttm110) REVERT: F 241 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: F 314 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: F 327 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8366 (mp) REVERT: F 354 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7423 (mm-40) REVERT: F 355 MET cc_start: 0.8386 (mtp) cc_final: 0.8152 (mtm) REVERT: G 116 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7554 (ttm-80) REVERT: G 125 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: G 147 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8396 (ptm160) REVERT: G 270 GLU cc_start: 0.6435 (mp0) cc_final: 0.5835 (mp0) outliers start: 96 outliers final: 45 residues processed: 637 average time/residue: 0.7048 time to fit residues: 497.6230 Evaluate side-chains 649 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 592 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 326 LYS Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 82 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 212 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 184 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 139 optimal weight: 0.2980 chunk 91 optimal weight: 0.9980 chunk 241 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 111 ASN B 111 ASN B 173 HIS B 297 ASN C 101 HIS C 137 GLN C 162 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN F 59 GLN F 246 GLN G 12 ASN G 92 ASN G 115 ASN G 162 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.105158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.089724 restraints weight = 29709.726| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.60 r_work: 0.3008 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20815 Z= 0.163 Angle : 0.620 7.949 28254 Z= 0.300 Chirality : 0.046 0.172 3141 Planarity : 0.005 0.058 3609 Dihedral : 9.946 179.573 2937 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.41 % Allowed : 18.77 % Favored : 76.82 % 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: 0.40 (0.17), residues: 2540 helix: 0.31 (0.16), residues: 1095 sheet: 0.53 (0.24), residues: 468 loop : 0.33 (0.21), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 206 TYR 0.012 0.001 TYR A 198 PHE 0.012 0.001 PHE F 31 TRP 0.012 0.002 TRP B 356 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (20815) covalent geometry : angle 0.62028 / 0.30 (28254) hydrogen bonds : bond 0.03660 / 2.43 ( 991) hydrogen bonds : angle 4.62787 / 3.26 ( 2619) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 600 time to evaluate : 0.715 Fit side-chains REVERT: A 18 LYS cc_start: 0.8277 (mptt) cc_final: 0.8040 (mptt) REVERT: A 61 LYS cc_start: 0.8316 (pttp) cc_final: 0.7938 (pttp) REVERT: A 99 GLU cc_start: 0.7816 (mp0) cc_final: 0.7369 (mp0) REVERT: A 154 ASP cc_start: 0.7845 (t70) cc_final: 0.7612 (t70) REVERT: A 157 ASP cc_start: 0.7238 (t0) cc_final: 0.6964 (t0) REVERT: A 167 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8062 (tp30) REVERT: A 215 LYS cc_start: 0.8254 (ttmm) cc_final: 0.8053 (ttmm) REVERT: A 225 ASN cc_start: 0.8257 (t0) cc_final: 0.7771 (t0) REVERT: A 254 ARG cc_start: 0.8292 (mtp85) cc_final: 0.7996 (mtp180) REVERT: A 299 MET cc_start: 0.8388 (mtp) cc_final: 0.8133 (mtm) REVERT: A 316 GLU cc_start: 0.8612 (tp30) cc_final: 0.8375 (tp30) REVERT: A 355 MET cc_start: 0.7609 (mpp) cc_final: 0.7342 (mpp) REVERT: A 361 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7038 (mt-10) REVERT: B 21 PHE cc_start: 0.8664 (m-80) cc_final: 0.8352 (m-80) REVERT: B 61 LYS cc_start: 0.8234 (mmtp) cc_final: 0.7958 (mmtp) REVERT: B 89 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8269 (t) REVERT: B 99 GLU cc_start: 0.7792 (pm20) cc_final: 0.7551 (pm20) REVERT: B 117 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7113 (mm-30) REVERT: B 118 LYS cc_start: 0.8033 (tptt) cc_final: 0.7750 (tptt) REVERT: B 205 GLU cc_start: 0.7506 (mp0) cc_final: 0.7100 (mp0) REVERT: B 207 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7827 (mm-30) REVERT: C 44 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7427 (mpp) REVERT: C 72 GLU cc_start: 0.8000 (tt0) cc_final: 0.7689 (tp30) REVERT: C 98 PRO cc_start: 0.8767 (Cg_exo) cc_final: 0.8519 (Cg_endo) REVERT: C 99 GLU cc_start: 0.7575 (pm20) cc_final: 0.7275 (pm20) REVERT: C 113 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8169 (mtmm) REVERT: C 118 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8161 (mttm) REVERT: C 297 ASN cc_start: 0.8453 (m110) cc_final: 0.8170 (m110) REVERT: C 334 GLU cc_start: 0.7851 (pm20) cc_final: 0.7517 (pm20) REVERT: D 51 ASP cc_start: 0.7904 (p0) cc_final: 0.7703 (p0) REVERT: D 107 GLU cc_start: 0.7569 (tp30) cc_final: 0.7305 (mm-30) REVERT: D 132 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7850 (ppp) REVERT: D 211 ASP cc_start: 0.8198 (t0) cc_final: 0.7990 (t0) REVERT: D 284 LYS cc_start: 0.8702 (mttp) cc_final: 0.8438 (mtpm) REVERT: E 59 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8332 (tp40) REVERT: E 99 GLU cc_start: 0.7728 (pm20) cc_final: 0.7481 (pp20) REVERT: E 205 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7506 (mt-10) REVERT: E 288 ASP cc_start: 0.7744 (m-30) cc_final: 0.7430 (m-30) REVERT: F 68 LYS cc_start: 0.8748 (mmtp) cc_final: 0.8530 (mmtp) REVERT: F 96 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8580 (m) REVERT: F 99 GLU cc_start: 0.7790 (mp0) cc_final: 0.7318 (mp0) REVERT: F 113 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7829 (mmtp) REVERT: F 210 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8180 (ttm110) REVERT: F 241 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: F 314 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: F 327 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8344 (mp) REVERT: G 116 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7567 (ttm-80) REVERT: G 125 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7712 (mm-30) REVERT: G 147 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8293 (ptm160) REVERT: G 270 GLU cc_start: 0.6388 (mp0) cc_final: 0.5775 (mp0) outliers start: 96 outliers final: 50 residues processed: 646 average time/residue: 0.6614 time to fit residues: 474.3959 Evaluate side-chains 647 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 583 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 313 MET Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 326 LYS Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 chunk 44 optimal weight: 0.7980 chunk 201 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 111 ASN A 115 ASN B 12 ASN B 111 ASN B 297 ASN C 137 GLN C 162 ASN D 225 ASN E 78 ASN E 115 ASN E 225 ASN E 353 GLN F 59 GLN F 137 GLN F 161 HIS F 246 GLN G 12 ASN G 92 ASN G 115 ASN G 162 ASN G 297 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.105034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.089658 restraints weight = 29673.575| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.59 r_work: 0.3007 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20815 Z= 0.168 Angle : 0.630 8.143 28254 Z= 0.304 Chirality : 0.047 0.164 3141 Planarity : 0.005 0.060 3609 Dihedral : 9.825 173.647 2934 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.50 % Allowed : 19.78 % Favored : 75.72 % 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: 0.45 (0.17), residues: 2540 helix: 0.34 (0.16), residues: 1095 sheet: 0.59 (0.24), residues: 466 loop : 0.35 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 372 TYR 0.013 0.001 TYR D 166 PHE 0.012 0.001 PHE F 31 TRP 0.012 0.002 TRP D 79 HIS 0.005 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (20815) covalent geometry : angle 0.62977 / 0.30 (28254) hydrogen bonds : bond 0.03657 / 2.43 ( 991) hydrogen bonds : angle 4.60557 / 3.24 ( 2619) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 587 time to evaluate : 0.808 Fit side-chains REVERT: A 18 LYS cc_start: 0.8228 (mptt) cc_final: 0.7968 (mptt) REVERT: A 61 LYS cc_start: 0.8310 (pttp) cc_final: 0.7893 (pttp) REVERT: A 82 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7306 (tpp) REVERT: A 99 GLU cc_start: 0.7826 (mp0) cc_final: 0.7376 (mp0) REVERT: A 154 ASP cc_start: 0.7847 (t70) cc_final: 0.7619 (t70) REVERT: A 157 ASP cc_start: 0.7244 (t0) cc_final: 0.6972 (t0) REVERT: A 167 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8087 (mm-30) REVERT: A 225 ASN cc_start: 0.8251 (t0) cc_final: 0.7767 (t0) REVERT: A 254 ARG cc_start: 0.8298 (mtp85) cc_final: 0.8002 (mtp180) REVERT: A 265 SER cc_start: 0.8741 (m) cc_final: 0.8388 (t) REVERT: A 299 MET cc_start: 0.8380 (mtp) cc_final: 0.8126 (mtm) REVERT: A 316 GLU cc_start: 0.8617 (tp30) cc_final: 0.8361 (tp30) REVERT: A 355 MET cc_start: 0.7622 (mpp) cc_final: 0.7341 (mpp) REVERT: A 361 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6826 (mt-10) REVERT: A 364 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.6050 (pt0) REVERT: B 21 PHE cc_start: 0.8649 (m-80) cc_final: 0.8361 (m-80) REVERT: B 61 LYS cc_start: 0.8223 (mmtp) cc_final: 0.7949 (mmtp) REVERT: B 89 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8229 (t) REVERT: B 99 GLU cc_start: 0.7801 (pm20) cc_final: 0.7568 (pm20) REVERT: B 117 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7096 (mm-30) REVERT: B 118 LYS cc_start: 0.8038 (tptt) cc_final: 0.7764 (tptt) REVERT: B 205 GLU cc_start: 0.7552 (mp0) cc_final: 0.7092 (mp0) REVERT: B 207 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7834 (mm-30) REVERT: B 211 ASP cc_start: 0.8061 (t0) cc_final: 0.7772 (t0) REVERT: B 291 LYS cc_start: 0.8572 (tttm) cc_final: 0.8337 (tttm) REVERT: C 44 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7436 (mpp) REVERT: C 72 GLU cc_start: 0.8000 (tt0) cc_final: 0.7693 (tp30) REVERT: C 98 PRO cc_start: 0.8769 (Cg_exo) cc_final: 0.8517 (Cg_endo) REVERT: C 99 GLU cc_start: 0.7580 (pm20) cc_final: 0.7293 (pm20) REVERT: C 113 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8150 (mtmm) REVERT: C 118 LYS cc_start: 0.8386 (mtpp) cc_final: 0.8157 (mttm) REVERT: C 297 ASN cc_start: 0.8445 (m110) cc_final: 0.8161 (m110) REVERT: C 334 GLU cc_start: 0.7844 (pm20) cc_final: 0.7511 (pm20) REVERT: D 51 ASP cc_start: 0.7906 (p0) cc_final: 0.7698 (p0) REVERT: D 90 PHE cc_start: 0.8423 (m-80) cc_final: 0.7775 (m-80) REVERT: D 107 GLU cc_start: 0.7580 (tp30) cc_final: 0.7303 (mm-30) REVERT: D 132 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7895 (ppp) REVERT: D 211 ASP cc_start: 0.8191 (t0) cc_final: 0.7976 (t0) REVERT: D 284 LYS cc_start: 0.8715 (mttp) cc_final: 0.8446 (mtpm) REVERT: E 99 GLU cc_start: 0.7723 (pm20) cc_final: 0.7480 (pp20) REVERT: E 205 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7512 (mt-10) REVERT: E 288 ASP cc_start: 0.7759 (m-30) cc_final: 0.7441 (m-30) REVERT: F 99 GLU cc_start: 0.7800 (mp0) cc_final: 0.7427 (mp0) REVERT: F 113 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7823 (mmtp) REVERT: F 210 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8191 (ttm110) REVERT: F 241 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: F 314 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: F 327 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8349 (mp) REVERT: G 116 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7581 (ttm-80) REVERT: G 125 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: G 147 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8381 (ptm160) REVERT: G 270 GLU cc_start: 0.6414 (mp0) cc_final: 0.5629 (mp0) REVERT: G 276 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8176 (mt-10) outliers start: 98 outliers final: 54 residues processed: 632 average time/residue: 0.6745 time to fit residues: 472.4373 Evaluate side-chains 657 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 589 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 200 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 150 optimal weight: 0.0470 chunk 251 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 158 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 111 ASN A 115 ASN B 12 ASN B 111 ASN B 297 ASN C 137 GLN C 162 ASN D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN E 353 GLN F 59 GLN F 137 GLN F 162 ASN F 246 GLN G 12 ASN G 92 ASN G 162 ASN G 297 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.090710 restraints weight = 29588.537| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.59 r_work: 0.3019 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20815 Z= 0.141 Angle : 0.622 8.613 28254 Z= 0.298 Chirality : 0.046 0.160 3141 Planarity : 0.004 0.062 3609 Dihedral : 9.585 167.376 2934 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.36 % Allowed : 20.24 % Favored : 75.40 % 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: 0.53 (0.17), residues: 2540 helix: 0.35 (0.16), residues: 1109 sheet: 0.60 (0.24), residues: 471 loop : 0.50 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 206 TYR 0.011 0.001 TYR E 143 PHE 0.012 0.001 PHE F 255 TRP 0.012 0.001 TRP D 79 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (20815) covalent geometry : angle 0.62219 / 0.30 (28254) hydrogen bonds : bond 0.03426 / 2.28 ( 991) hydrogen bonds : angle 4.53680 / 3.19 ( 2619) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 588 time to evaluate : 0.743 Fit side-chains REVERT: A 18 LYS cc_start: 0.8189 (mptt) cc_final: 0.7913 (mptt) REVERT: A 61 LYS cc_start: 0.8302 (pttp) cc_final: 0.7884 (pttp) REVERT: A 82 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7233 (tpp) REVERT: A 99 GLU cc_start: 0.7838 (mp0) cc_final: 0.7402 (mp0) REVERT: A 154 ASP cc_start: 0.7823 (t70) cc_final: 0.7562 (t0) REVERT: A 157 ASP cc_start: 0.7229 (t0) cc_final: 0.6950 (t0) REVERT: A 225 ASN cc_start: 0.8257 (t0) cc_final: 0.7770 (t0) REVERT: A 254 ARG cc_start: 0.8296 (mtp85) cc_final: 0.8005 (mtp180) REVERT: A 265 SER cc_start: 0.8743 (m) cc_final: 0.8402 (t) REVERT: A 299 MET cc_start: 0.8371 (mtp) cc_final: 0.8121 (mtm) REVERT: A 316 GLU cc_start: 0.8613 (tp30) cc_final: 0.8394 (tp30) REVERT: A 355 MET cc_start: 0.7635 (mpp) cc_final: 0.7320 (mpp) REVERT: A 361 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6780 (mt-10) REVERT: A 364 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.6079 (pt0) REVERT: B 21 PHE cc_start: 0.8645 (m-80) cc_final: 0.8331 (m-80) REVERT: B 61 LYS cc_start: 0.8227 (mmtp) cc_final: 0.7949 (mmtp) REVERT: B 89 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8228 (t) REVERT: B 99 GLU cc_start: 0.7777 (pm20) cc_final: 0.7544 (pm20) REVERT: B 117 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7081 (mm-30) REVERT: B 118 LYS cc_start: 0.8041 (tptt) cc_final: 0.7751 (tptt) REVERT: B 205 GLU cc_start: 0.7539 (mp0) cc_final: 0.7081 (mp0) REVERT: B 207 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7831 (mm-30) REVERT: B 211 ASP cc_start: 0.8053 (t0) cc_final: 0.7771 (t0) REVERT: C 44 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7418 (mpp) REVERT: C 72 GLU cc_start: 0.7963 (tt0) cc_final: 0.7652 (tp30) REVERT: C 98 PRO cc_start: 0.8762 (Cg_exo) cc_final: 0.8510 (Cg_endo) REVERT: C 99 GLU cc_start: 0.7569 (pm20) cc_final: 0.7251 (pm20) REVERT: C 113 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8125 (mtmm) REVERT: C 118 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8144 (mttm) REVERT: C 297 ASN cc_start: 0.8457 (m110) cc_final: 0.8180 (m110) REVERT: C 334 GLU cc_start: 0.7831 (pm20) cc_final: 0.7489 (pm20) REVERT: D 51 ASP cc_start: 0.7898 (p0) cc_final: 0.7693 (p0) REVERT: D 90 PHE cc_start: 0.8430 (m-80) cc_final: 0.7750 (m-80) REVERT: D 132 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7842 (ppp) REVERT: D 211 ASP cc_start: 0.8168 (t0) cc_final: 0.7963 (t0) REVERT: D 284 LYS cc_start: 0.8689 (mttp) cc_final: 0.8427 (mtpm) REVERT: D 305 MET cc_start: 0.8900 (mmp) cc_final: 0.8621 (mmm) REVERT: E 99 GLU cc_start: 0.7706 (pm20) cc_final: 0.7473 (pp20) REVERT: E 205 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7512 (mt-10) REVERT: E 288 ASP cc_start: 0.7666 (m-30) cc_final: 0.7339 (m-30) REVERT: F 99 GLU cc_start: 0.7793 (mp0) cc_final: 0.7387 (mp0) REVERT: F 113 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7829 (mmtp) REVERT: F 210 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8183 (ttm110) REVERT: F 241 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: F 314 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: F 327 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8353 (mp) REVERT: G 9 VAL cc_start: 0.8372 (t) cc_final: 0.8088 (m) REVERT: G 116 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7570 (ttm-80) REVERT: G 125 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7678 (mm-30) REVERT: G 147 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8389 (ptm160) REVERT: G 270 GLU cc_start: 0.6392 (mp0) cc_final: 0.5595 (mp0) REVERT: G 276 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8166 (mt-10) outliers start: 95 outliers final: 54 residues processed: 631 average time/residue: 0.6511 time to fit residues: 455.5663 Evaluate side-chains 648 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 580 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.0020 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 111 ASN A 115 ASN B 111 ASN B 297 ASN C 137 GLN C 162 ASN C 353 GLN D 371 HIS E 59 GLN E 78 ASN E 115 ASN E 225 ASN E 353 GLN F 59 GLN F 137 GLN F 162 ASN F 246 GLN G 12 ASN G 92 ASN G 115 ASN G 162 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.089335 restraints weight = 29832.616| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.60 r_work: 0.3008 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20815 Z= 0.186 Angle : 0.654 10.730 28254 Z= 0.315 Chirality : 0.048 0.212 3141 Planarity : 0.005 0.064 3609 Dihedral : 9.534 156.739 2933 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.18 % Allowed : 20.65 % Favored : 75.17 % 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: 0.47 (0.17), residues: 2540 helix: 0.29 (0.16), residues: 1110 sheet: 0.60 (0.24), residues: 466 loop : 0.47 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 372 TYR 0.023 0.001 TYR A 198 PHE 0.012 0.001 PHE F 31 TRP 0.012 0.002 TRP D 79 HIS 0.005 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (20815) covalent geometry : angle 0.65428 / 0.31 (28254) hydrogen bonds : bond 0.03724 / 2.47 ( 991) hydrogen bonds : angle 4.58468 / 3.22 ( 2619) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 573 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8153 (mptt) cc_final: 0.7845 (mptt) REVERT: A 61 LYS cc_start: 0.8311 (pttp) cc_final: 0.7907 (pttp) REVERT: A 82 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7232 (tpp) REVERT: A 99 GLU cc_start: 0.7846 (mp0) cc_final: 0.7406 (mp0) REVERT: A 154 ASP cc_start: 0.7845 (t70) cc_final: 0.7613 (t70) REVERT: A 157 ASP cc_start: 0.7232 (t0) cc_final: 0.6931 (t0) REVERT: A 254 ARG cc_start: 0.8316 (mtp85) cc_final: 0.8014 (mtp180) REVERT: A 265 SER cc_start: 0.8743 (m) cc_final: 0.8405 (t) REVERT: A 299 MET cc_start: 0.8382 (mtp) cc_final: 0.8142 (mtm) REVERT: A 355 MET cc_start: 0.7611 (mpp) cc_final: 0.7307 (mpp) REVERT: B 21 PHE cc_start: 0.8650 (m-80) cc_final: 0.8335 (m-80) REVERT: B 61 LYS cc_start: 0.8219 (mmtp) cc_final: 0.7935 (mmtp) REVERT: B 89 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8267 (t) REVERT: B 99 GLU cc_start: 0.7805 (pm20) cc_final: 0.7553 (pm20) REVERT: B 117 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7072 (mm-30) REVERT: B 118 LYS cc_start: 0.8091 (tptt) cc_final: 0.7801 (tptt) REVERT: B 205 GLU cc_start: 0.7538 (mp0) cc_final: 0.7080 (mp0) REVERT: B 207 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7856 (mm-30) REVERT: B 291 LYS cc_start: 0.8583 (tttm) cc_final: 0.8337 (tttm) REVERT: C 44 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7437 (mpp) REVERT: C 72 GLU cc_start: 0.8000 (tt0) cc_final: 0.7693 (tp30) REVERT: C 98 PRO cc_start: 0.8780 (Cg_exo) cc_final: 0.8514 (Cg_endo) REVERT: C 99 GLU cc_start: 0.7560 (pm20) cc_final: 0.7254 (pm20) REVERT: C 113 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8157 (mtmm) REVERT: C 118 LYS cc_start: 0.8391 (mtpp) cc_final: 0.8163 (mttm) REVERT: C 297 ASN cc_start: 0.8442 (m110) cc_final: 0.8159 (m110) REVERT: C 334 GLU cc_start: 0.7844 (pm20) cc_final: 0.7504 (pm20) REVERT: D 51 ASP cc_start: 0.7919 (p0) cc_final: 0.7714 (p0) REVERT: D 90 PHE cc_start: 0.8452 (m-80) cc_final: 0.7847 (m-80) REVERT: D 107 GLU cc_start: 0.7604 (tp30) cc_final: 0.7339 (mm-30) REVERT: D 132 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7844 (ppp) REVERT: D 211 ASP cc_start: 0.8169 (t0) cc_final: 0.7960 (t0) REVERT: D 284 LYS cc_start: 0.8713 (mttp) cc_final: 0.8444 (mtpm) REVERT: D 305 MET cc_start: 0.8953 (mmp) cc_final: 0.8683 (mmm) REVERT: E 59 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8324 (tp40) REVERT: E 99 GLU cc_start: 0.7712 (pm20) cc_final: 0.7481 (pp20) REVERT: E 205 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7480 (mt-10) REVERT: E 288 ASP cc_start: 0.7667 (m-30) cc_final: 0.7339 (m-30) REVERT: F 99 GLU cc_start: 0.7797 (mp0) cc_final: 0.7429 (mp0) REVERT: F 113 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7827 (mmtp) REVERT: F 210 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8204 (ttm110) REVERT: F 241 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: F 314 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: F 327 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8345 (mp) REVERT: G 9 VAL cc_start: 0.8379 (t) cc_final: 0.8084 (m) REVERT: G 116 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7582 (ttm-80) REVERT: G 125 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: G 147 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8360 (ptm160) REVERT: G 270 GLU cc_start: 0.6413 (mp0) cc_final: 0.5760 (mp0) REVERT: G 276 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8185 (mt-10) outliers start: 91 outliers final: 61 residues processed: 612 average time/residue: 0.6497 time to fit residues: 441.8886 Evaluate side-chains 653 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 578 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 313 MET Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 326 LYS Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 72 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 chunk 184 optimal weight: 0.0370 chunk 227 optimal weight: 0.7980 chunk 128 optimal weight: 0.3980 chunk 239 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 111 ASN A 115 ASN B 111 ASN B 297 ASN C 137 GLN C 162 ASN C 353 GLN E 59 GLN E 78 ASN E 115 ASN E 225 ASN F 59 GLN F 137 GLN F 162 ASN F 246 GLN G 12 ASN G 162 ASN G 297 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.108133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.092805 restraints weight = 29652.456| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.63 r_work: 0.3001 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20815 Z= 0.143 Angle : 0.641 10.191 28254 Z= 0.307 Chirality : 0.046 0.177 3141 Planarity : 0.005 0.067 3609 Dihedral : 9.222 146.433 2927 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.90 % Allowed : 21.16 % Favored : 74.94 % 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: 0.57 (0.17), residues: 2540 helix: 0.36 (0.16), residues: 1109 sheet: 0.59 (0.24), residues: 477 loop : 0.56 (0.22), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 206 TYR 0.020 0.001 TYR A 198 PHE 0.012 0.001 PHE F 255 TRP 0.012 0.001 TRP D 79 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (20815) covalent geometry : angle 0.64089 / 0.31 (28254) hydrogen bonds : bond 0.03423 / 2.27 ( 991) hydrogen bonds : angle 4.51271 / 3.17 ( 2619) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 574 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8305 (pttp) cc_final: 0.7905 (pttp) REVERT: A 82 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7272 (tpp) REVERT: A 99 GLU cc_start: 0.7880 (mp0) cc_final: 0.7411 (mp0) REVERT: A 154 ASP cc_start: 0.7840 (t70) cc_final: 0.7592 (t0) REVERT: A 157 ASP cc_start: 0.7237 (t0) cc_final: 0.6939 (t0) REVERT: A 254 ARG cc_start: 0.8310 (mtp85) cc_final: 0.8016 (mtp180) REVERT: A 265 SER cc_start: 0.8760 (m) cc_final: 0.8405 (t) REVERT: A 299 MET cc_start: 0.8385 (mtp) cc_final: 0.8147 (mtm) REVERT: A 355 MET cc_start: 0.7633 (mpp) cc_final: 0.7317 (mpp) REVERT: B 21 PHE cc_start: 0.8648 (m-80) cc_final: 0.8288 (m-80) REVERT: B 61 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7944 (mmtp) REVERT: B 89 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8236 (t) REVERT: B 99 GLU cc_start: 0.7800 (pm20) cc_final: 0.7540 (pm20) REVERT: B 117 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7065 (mm-30) REVERT: B 118 LYS cc_start: 0.8074 (tptt) cc_final: 0.7782 (tptt) REVERT: B 205 GLU cc_start: 0.7562 (mp0) cc_final: 0.7091 (mp0) REVERT: B 207 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7892 (mm-30) REVERT: C 44 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7459 (mpp) REVERT: C 72 GLU cc_start: 0.7987 (tt0) cc_final: 0.7678 (tp30) REVERT: C 98 PRO cc_start: 0.8770 (Cg_exo) cc_final: 0.8513 (Cg_endo) REVERT: C 99 GLU cc_start: 0.7586 (pm20) cc_final: 0.7273 (pm20) REVERT: C 113 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8139 (mtmm) REVERT: C 118 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8145 (mttm) REVERT: C 297 ASN cc_start: 0.8470 (m110) cc_final: 0.8194 (m110) REVERT: C 334 GLU cc_start: 0.7853 (pm20) cc_final: 0.7580 (pm20) REVERT: D 51 ASP cc_start: 0.7933 (p0) cc_final: 0.7723 (p0) REVERT: D 90 PHE cc_start: 0.8437 (m-80) cc_final: 0.7754 (m-80) REVERT: D 132 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7837 (ppp) REVERT: D 211 ASP cc_start: 0.8180 (t0) cc_final: 0.7963 (t0) REVERT: D 284 LYS cc_start: 0.8701 (mttp) cc_final: 0.8434 (mtpm) REVERT: D 305 MET cc_start: 0.8927 (mmp) cc_final: 0.8634 (mmm) REVERT: E 99 GLU cc_start: 0.7706 (pm20) cc_final: 0.7473 (pp20) REVERT: E 205 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7500 (mt-10) REVERT: E 288 ASP cc_start: 0.7687 (m-30) cc_final: 0.7350 (m-30) REVERT: F 99 GLU cc_start: 0.7773 (mp0) cc_final: 0.7403 (mp0) REVERT: F 113 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7825 (mmtp) REVERT: F 210 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8191 (ttm110) REVERT: F 241 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: F 314 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: F 327 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8353 (mp) REVERT: G 9 VAL cc_start: 0.8373 (t) cc_final: 0.8068 (m) REVERT: G 125 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7706 (mm-30) REVERT: G 147 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8294 (ptm160) REVERT: G 270 GLU cc_start: 0.6342 (mp0) cc_final: 0.5636 (mp0) REVERT: G 276 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8184 (mt-10) outliers start: 85 outliers final: 57 residues processed: 612 average time/residue: 0.6529 time to fit residues: 443.5186 Evaluate side-chains 649 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 580 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 313 MET Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 235 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 155 optimal weight: 0.4980 chunk 221 optimal weight: 0.0980 chunk 89 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 111 ASN A 115 ASN B 111 ASN B 297 ASN C 137 GLN C 162 ASN C 353 GLN D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN E 353 GLN F 59 GLN F 137 GLN F 162 ASN F 246 GLN G 12 ASN G 162 ASN G 297 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.092741 restraints weight = 29738.705| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.61 r_work: 0.3017 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20815 Z= 0.145 Angle : 0.648 11.610 28254 Z= 0.309 Chirality : 0.046 0.184 3141 Planarity : 0.005 0.068 3609 Dihedral : 9.076 132.805 2927 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.81 % Allowed : 21.29 % Favored : 74.90 % 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: 0.60 (0.17), residues: 2540 helix: 0.38 (0.16), residues: 1109 sheet: 0.63 (0.24), residues: 472 loop : 0.57 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 206 TYR 0.019 0.001 TYR A 198 PHE 0.012 0.001 PHE F 255 TRP 0.012 0.002 TRP D 79 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (20815) covalent geometry : angle 0.64814 / 0.31 (28254) hydrogen bonds : bond 0.03408 / 2.25 ( 991) hydrogen bonds : angle 4.49061 / 3.15 ( 2619) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 586 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8306 (pttp) cc_final: 0.7901 (pttp) REVERT: A 82 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7260 (tpp) REVERT: A 99 GLU cc_start: 0.7881 (mp0) cc_final: 0.7429 (mp0) REVERT: A 124 PHE cc_start: 0.8104 (m-10) cc_final: 0.7815 (m-80) REVERT: A 154 ASP cc_start: 0.7832 (t70) cc_final: 0.7587 (t0) REVERT: A 157 ASP cc_start: 0.7266 (t0) cc_final: 0.6975 (t0) REVERT: A 213 LYS cc_start: 0.7333 (tmtt) cc_final: 0.7105 (ttpt) REVERT: A 223 PHE cc_start: 0.7959 (t80) cc_final: 0.7429 (t80) REVERT: A 265 SER cc_start: 0.8760 (m) cc_final: 0.8419 (t) REVERT: A 299 MET cc_start: 0.8385 (mtp) cc_final: 0.8147 (mtm) REVERT: A 355 MET cc_start: 0.7638 (mpp) cc_final: 0.7304 (mpp) REVERT: B 21 PHE cc_start: 0.8648 (m-80) cc_final: 0.8370 (m-80) REVERT: B 28 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.8170 (ttm170) REVERT: B 61 LYS cc_start: 0.8214 (mmtp) cc_final: 0.7929 (mmtp) REVERT: B 89 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8199 (t) REVERT: B 99 GLU cc_start: 0.7801 (pm20) cc_final: 0.7540 (pm20) REVERT: B 117 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7042 (mm-30) REVERT: B 118 LYS cc_start: 0.8007 (tptt) cc_final: 0.7721 (tptt) REVERT: B 205 GLU cc_start: 0.7520 (mp0) cc_final: 0.7053 (mp0) REVERT: B 207 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7915 (mm-30) REVERT: B 241 GLU cc_start: 0.7428 (tp30) cc_final: 0.6854 (tp30) REVERT: B 291 LYS cc_start: 0.8549 (tttm) cc_final: 0.8340 (tttm) REVERT: B 316 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8112 (mm-30) REVERT: C 44 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7448 (mpp) REVERT: C 72 GLU cc_start: 0.7984 (tt0) cc_final: 0.7676 (tp30) REVERT: C 98 PRO cc_start: 0.8763 (Cg_exo) cc_final: 0.8513 (Cg_endo) REVERT: C 99 GLU cc_start: 0.7578 (pm20) cc_final: 0.7270 (pm20) REVERT: C 113 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8135 (mtmm) REVERT: C 118 LYS cc_start: 0.8388 (mtpp) cc_final: 0.8159 (mttm) REVERT: C 153 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8441 (tp) REVERT: C 297 ASN cc_start: 0.8444 (m110) cc_final: 0.8186 (m110) REVERT: C 334 GLU cc_start: 0.7829 (pm20) cc_final: 0.7562 (pm20) REVERT: D 51 ASP cc_start: 0.7923 (p0) cc_final: 0.7717 (p0) REVERT: D 90 PHE cc_start: 0.8449 (m-80) cc_final: 0.7723 (m-80) REVERT: D 132 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7907 (ppp) REVERT: D 211 ASP cc_start: 0.8167 (t0) cc_final: 0.7955 (t0) REVERT: D 284 LYS cc_start: 0.8699 (mttp) cc_final: 0.8436 (mtpm) REVERT: D 305 MET cc_start: 0.8909 (mmp) cc_final: 0.8625 (mmm) REVERT: E 47 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.5651 (ppp) REVERT: E 99 GLU cc_start: 0.7708 (pm20) cc_final: 0.7474 (pp20) REVERT: E 202 THR cc_start: 0.8578 (p) cc_final: 0.8191 (p) REVERT: E 288 ASP cc_start: 0.7667 (m-30) cc_final: 0.7336 (m-30) REVERT: F 99 GLU cc_start: 0.7768 (mp0) cc_final: 0.7412 (mp0) REVERT: F 113 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7824 (mmtp) REVERT: F 210 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8192 (ttm110) REVERT: F 241 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: F 314 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: F 327 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8334 (mp) REVERT: G 9 VAL cc_start: 0.8373 (t) cc_final: 0.8079 (m) REVERT: G 125 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7677 (mm-30) REVERT: G 147 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8291 (ptm160) REVERT: G 270 GLU cc_start: 0.6350 (mp0) cc_final: 0.5769 (OUTLIER) REVERT: G 276 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8187 (mt-10) outliers start: 83 outliers final: 57 residues processed: 625 average time/residue: 0.6579 time to fit residues: 456.0709 Evaluate side-chains 661 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 591 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 313 MET Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 0.2980 chunk 114 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 0.0470 chunk 12 optimal weight: 0.3980 chunk 199 optimal weight: 0.9990 chunk 110 optimal weight: 0.0000 chunk 237 optimal weight: 0.8980 overall best weight: 0.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 111 ASN A 115 ASN B 111 ASN B 162 ASN B 297 ASN C 137 GLN C 162 ASN C 353 GLN E 59 GLN E 115 ASN E 225 ASN F 59 GLN F 137 GLN F 162 ASN F 246 GLN G 12 ASN G 162 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.109778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.094335 restraints weight = 29798.455| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.63 r_work: 0.3041 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20815 Z= 0.102 Angle : 0.633 11.057 28254 Z= 0.298 Chirality : 0.045 0.237 3141 Planarity : 0.004 0.068 3609 Dihedral : 8.701 131.489 2927 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.21 % Allowed : 22.07 % Favored : 74.71 % 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: 0.76 (0.17), residues: 2540 helix: 0.52 (0.16), residues: 1111 sheet: 0.74 (0.24), residues: 474 loop : 0.64 (0.22), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 206 TYR 0.016 0.001 TYR A 240 PHE 0.013 0.001 PHE A 255 TRP 0.015 0.001 TRP G 86 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (20815) covalent geometry : angle 0.63345 / 0.30 (28254) hydrogen bonds : bond 0.02859 / 1.88 ( 991) hydrogen bonds : angle 4.37675 / 3.07 ( 2619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8768.11 seconds wall clock time: 149 minutes 25.16 seconds (8965.16 seconds total)