Starting phenix.real_space_refine on Wed Jun 18 00:30:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f8s_28935/06_2025/8f8s_28935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f8s_28935/06_2025/8f8s_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8f8s_28935/06_2025/8f8s_28935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f8s_28935/06_2025/8f8s_28935.map" model { file = "/net/cci-nas-00/data/ceres_data/8f8s_28935/06_2025/8f8s_28935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f8s_28935/06_2025/8f8s_28935.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.05, per 1000 atoms: 0.64 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: 5.04 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 3.04 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: 7.78 Time building geometry restraints manager: 5.66 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 374 or resid 401 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: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 48.510 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.080 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:13.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 4.56 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.002 TRP E 79 HIS 0.005 0.001 HIS C 161 PHE 0.013 0.001 PHE D 255 TYR 0.012 0.001 TYR F 143 ARG 0.006 0.001 ARG F 256 Details of bonding type rmsd hydrogen bonds : bond 0.20664 ( 991) hydrogen bonds : angle 6.93904 ( 2619) covalent geometry : bond 0.00374 (20815) covalent geometry : angle 0.61320 (28254) *********************** 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 : 2.076 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: 0.6917 (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: 0.8608 (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: 0.8246 (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: 1.5869 time to fit residues: 1146.3549 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 : 2.087 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.0370 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 297 ASN G 12 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 = 0.107151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.091706 restraints weight = 29774.768| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.63 r_work: 0.3007 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- 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: 22 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20815 Z= 0.184 Angle : 0.642 8.251 28254 Z= 0.315 Chirality : 0.047 0.218 3141 Planarity : 0.005 0.056 3609 Dihedral : 10.656 165.869 2967 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.13 % Allowed : 15.56 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.17), residues: 2540 helix: -0.22 (0.16), residues: 1100 sheet: 0.54 (0.24), residues: 471 loop : 0.27 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 79 HIS 0.004 0.001 HIS F 161 PHE 0.017 0.001 PHE A 223 TYR 0.016 0.001 TYR A 198 ARG 0.007 0.001 ARG A 254 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 991) hydrogen bonds : angle 5.05363 ( 2619) covalent geometry : bond 0.00436 (20815) covalent geometry : angle 0.64235 (28254) *********************** 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 683 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 593 time to evaluate : 2.352 Fit side-chains REVERT: A 61 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7971 (pttp) REVERT: A 81 ASP cc_start: 0.7750 (p0) cc_final: 0.7191 (p0) REVERT: A 82 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7599 (tpp) REVERT: A 99 GLU cc_start: 0.7782 (mp0) cc_final: 0.7451 (mp0) REVERT: A 157 ASP cc_start: 0.7231 (t0) cc_final: 0.7014 (t0) REVERT: A 167 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7971 (tp30) REVERT: A 214 GLU cc_start: 0.7808 (tt0) cc_final: 0.7555 (mt-10) REVERT: A 215 LYS cc_start: 0.8289 (ttmm) cc_final: 0.8085 (ttmm) REVERT: A 254 ARG cc_start: 0.8317 (mtp85) cc_final: 0.8007 (mtp180) REVERT: A 299 MET cc_start: 0.8517 (mtp) cc_final: 0.8155 (mtp) REVERT: A 316 GLU cc_start: 0.8647 (tp30) cc_final: 0.8424 (tp30) REVERT: B 21 PHE cc_start: 0.8690 (m-80) cc_final: 0.8313 (m-80) REVERT: B 61 LYS cc_start: 0.8193 (mmtp) cc_final: 0.7963 (mmtp) REVERT: B 117 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7149 (mm-30) REVERT: B 118 LYS cc_start: 0.8034 (tptt) cc_final: 0.7723 (tptt) REVERT: B 184 ASP cc_start: 0.7935 (m-30) cc_final: 0.7714 (m-30) REVERT: B 205 GLU cc_start: 0.7228 (mp0) cc_final: 0.6897 (mp0) REVERT: B 215 LYS cc_start: 0.8521 (mttp) cc_final: 0.8178 (mttp) REVERT: C 44 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7411 (mpp) REVERT: C 72 GLU cc_start: 0.8022 (tt0) cc_final: 0.7712 (tp30) REVERT: C 99 GLU cc_start: 0.7604 (pm20) cc_final: 0.7321 (pm20) REVERT: C 118 LYS cc_start: 0.8366 (mtpp) cc_final: 0.8131 (mttm) REVERT: C 224 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8031 (mm-30) REVERT: C 334 GLU cc_start: 0.7827 (pm20) cc_final: 0.7525 (pm20) REVERT: D 44 MET cc_start: 0.8062 (tpp) cc_final: 0.7674 (tpp) REVERT: D 132 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8100 (ppp) REVERT: D 211 ASP cc_start: 0.8189 (t0) cc_final: 0.7954 (t0) REVERT: D 284 LYS cc_start: 0.8702 (mttp) cc_final: 0.8465 (mtpm) REVERT: E 99 GLU cc_start: 0.7758 (pm20) cc_final: 0.7432 (pp20) REVERT: E 147 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8691 (ptp-170) REVERT: E 288 ASP cc_start: 0.7745 (m-30) cc_final: 0.7460 (m-30) REVERT: E 313 MET cc_start: 0.8455 (mmm) cc_final: 0.8190 (tpt) REVERT: F 68 LYS cc_start: 0.8749 (mmtp) cc_final: 0.8526 (mmtp) REVERT: F 96 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8563 (m) REVERT: F 99 GLU cc_start: 0.7773 (mp0) cc_final: 0.7423 (mp0) REVERT: F 210 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8222 (ttm110) REVERT: F 355 MET cc_start: 0.8425 (mtp) cc_final: 0.8215 (mtm) REVERT: G 125 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: G 147 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8305 (ptm160) REVERT: G 222 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7423 (p0) REVERT: G 270 GLU cc_start: 0.6383 (mp0) cc_final: 0.5699 (mp0) REVERT: G 283 MET cc_start: 0.8362 (mmt) cc_final: 0.8039 (mmt) REVERT: G 355 MET cc_start: 0.8415 (mmm) cc_final: 0.8207 (mmm) outliers start: 90 outliers final: 40 residues processed: 635 average time/residue: 1.7062 time to fit residues: 1200.4181 Evaluate side-chains 623 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 573 time to evaluate : 2.230 ------------------------------------------------------------------------------- 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 288 ASP Chi-restraints excluded: chain A residue 339 VAL 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 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 214 optimal weight: 0.0770 chunk 235 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 148 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 223 optimal weight: 0.8980 chunk 155 optimal weight: 0.0980 chunk 21 optimal weight: 0.5980 chunk 198 optimal weight: 0.8980 chunk 67 optimal weight: 0.0170 chunk 144 optimal weight: 0.8980 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 101 HIS A 111 ASN A 115 ASN A 354 GLN B 111 ASN B 121 GLN B 173 HIS B 297 ASN C 12 ASN C 115 ASN C 137 GLN C 246 GLN D 12 ASN D 115 ASN D 137 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN D 297 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN E 246 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.093384 restraints weight = 29583.520| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.63 r_work: 0.3040 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20815 Z= 0.104 Angle : 0.585 7.190 28254 Z= 0.279 Chirality : 0.044 0.170 3141 Planarity : 0.004 0.053 3609 Dihedral : 9.894 161.631 2951 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.81 % Allowed : 17.76 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.17), residues: 2540 helix: 0.13 (0.16), residues: 1113 sheet: 0.70 (0.24), residues: 468 loop : 0.39 (0.22), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 356 HIS 0.004 0.001 HIS C 161 PHE 0.011 0.001 PHE B 31 TYR 0.014 0.001 TYR A 198 ARG 0.008 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 991) hydrogen bonds : angle 4.67284 ( 2619) covalent geometry : bond 0.00236 (20815) covalent geometry : angle 0.58514 (28254) *********************** 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 692 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 609 time to evaluate : 2.820 Fit side-chains REVERT: A 61 LYS cc_start: 0.8318 (pttp) cc_final: 0.7933 (pttp) REVERT: A 81 ASP cc_start: 0.7678 (p0) cc_final: 0.7417 (p0) REVERT: A 82 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7514 (tpp) REVERT: A 99 GLU cc_start: 0.7755 (mp0) cc_final: 0.7377 (mp0) REVERT: A 115 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7943 (t0) REVERT: A 157 ASP cc_start: 0.7209 (t0) cc_final: 0.6942 (t0) REVERT: A 167 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8018 (tp30) REVERT: A 214 GLU cc_start: 0.7817 (tt0) cc_final: 0.7496 (mt-10) REVERT: A 215 LYS cc_start: 0.8267 (ttmm) cc_final: 0.8025 (ttmm) REVERT: A 254 ARG cc_start: 0.8290 (mtp85) cc_final: 0.7986 (mtp180) REVERT: A 299 MET cc_start: 0.8470 (mtp) cc_final: 0.8101 (mtp) REVERT: A 316 GLU cc_start: 0.8638 (tp30) cc_final: 0.8399 (tp30) REVERT: B 6 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7566 (p) REVERT: B 21 PHE cc_start: 0.8674 (m-80) cc_final: 0.8365 (m-80) REVERT: B 30 VAL cc_start: 0.8282 (t) cc_final: 0.8059 (m) REVERT: B 61 LYS cc_start: 0.8211 (mmtp) cc_final: 0.7978 (mmtp) REVERT: B 65 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7859 (pt) REVERT: B 89 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8312 (t) REVERT: B 117 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7126 (mm-30) REVERT: B 118 LYS cc_start: 0.8027 (tptt) cc_final: 0.7715 (tptt) REVERT: B 205 GLU cc_start: 0.7405 (mp0) cc_final: 0.7134 (mp0) REVERT: B 215 LYS cc_start: 0.8531 (mttp) cc_final: 0.8311 (mtmm) REVERT: C 44 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7366 (mpp) REVERT: C 72 GLU cc_start: 0.7981 (tt0) cc_final: 0.7662 (tp30) REVERT: C 99 GLU cc_start: 0.7574 (pm20) cc_final: 0.7275 (pm20) REVERT: C 118 LYS cc_start: 0.8342 (mtpp) cc_final: 0.8129 (mttm) REVERT: C 148 THR cc_start: 0.8530 (m) cc_final: 0.8244 (t) REVERT: C 153 LEU cc_start: 0.8668 (tp) cc_final: 0.8456 (tp) REVERT: C 297 ASN cc_start: 0.8436 (m110) cc_final: 0.8156 (m110) REVERT: C 313 MET cc_start: 0.8563 (mmm) cc_final: 0.8354 (tpp) REVERT: C 334 GLU cc_start: 0.7795 (pm20) cc_final: 0.7479 (pm20) REVERT: D 44 MET cc_start: 0.8026 (tpp) cc_final: 0.7578 (tpp) REVERT: D 90 PHE cc_start: 0.8433 (m-80) cc_final: 0.7717 (m-80) REVERT: D 211 ASP cc_start: 0.8192 (t0) cc_final: 0.7986 (t0) REVERT: D 284 LYS cc_start: 0.8689 (mttp) cc_final: 0.8448 (mtpm) REVERT: E 59 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8290 (tp40) REVERT: E 99 GLU cc_start: 0.7739 (pm20) cc_final: 0.7479 (pp20) REVERT: E 147 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8548 (ptp-170) REVERT: E 288 ASP cc_start: 0.7705 (m-30) cc_final: 0.7401 (m-30) REVERT: E 313 MET cc_start: 0.8426 (mmm) cc_final: 0.8172 (tpt) REVERT: F 68 LYS cc_start: 0.8740 (mmtp) cc_final: 0.8488 (mmtp) REVERT: F 96 VAL cc_start: 0.8857 (p) cc_final: 0.8569 (m) REVERT: F 99 GLU cc_start: 0.7783 (mp0) cc_final: 0.7353 (mp0) REVERT: F 314 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: F 355 MET cc_start: 0.8406 (mtp) cc_final: 0.8182 (mtm) REVERT: G 9 VAL cc_start: 0.8379 (t) cc_final: 0.8112 (m) REVERT: G 147 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8182 (ptm160) REVERT: G 222 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7373 (p0) REVERT: G 270 GLU cc_start: 0.6296 (mp0) cc_final: 0.5723 (mp0) REVERT: G 349 LEU cc_start: 0.8326 (tp) cc_final: 0.8122 (tp) outliers start: 83 outliers final: 36 residues processed: 646 average time/residue: 2.1325 time to fit residues: 1530.4832 Evaluate side-chains 642 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 595 time to evaluate : 3.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET 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 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 64 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 89 THR 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 250 ILE 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 44 MET Chi-restraints excluded: chain C residue 95 ARG 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 149 THR 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 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 F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN 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 222 ASP 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 53 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 106 optimal weight: 0.0000 chunk 254 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN B 111 ASN B 297 ASN C 12 ASN C 101 HIS C 128 ASN C 137 GLN C 162 ASN C 246 GLN D 12 ASN D 137 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN E 78 ASN E 92 ASN E 115 ASN E 162 ASN E 225 ASN E 353 GLN F 59 GLN F 137 GLN F 225 ASN 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.092550 restraints weight = 29886.302| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.65 r_work: 0.3008 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1584 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 : 0.623 8.889 28254 Z= 0.299 Chirality : 0.047 0.165 3141 Planarity : 0.005 0.055 3609 Dihedral : 9.840 169.024 2939 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.50 % Allowed : 18.08 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2540 helix: 0.28 (0.16), residues: 1106 sheet: 0.72 (0.24), residues: 468 loop : 0.42 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 79 HIS 0.004 0.001 HIS C 161 PHE 0.021 0.001 PHE G 31 TYR 0.012 0.001 TYR A 198 ARG 0.009 0.001 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 991) hydrogen bonds : angle 4.62985 ( 2619) covalent geometry : bond 0.00400 (20815) covalent geometry : angle 0.62252 (28254) *********************** 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 688 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 590 time to evaluate : 2.818 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8341 (pttp) cc_final: 0.7953 (pttp) REVERT: A 82 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7606 (tpp) REVERT: A 99 GLU cc_start: 0.7791 (mp0) cc_final: 0.7398 (mp0) REVERT: A 115 ASN cc_start: 0.8179 (t0) cc_final: 0.7897 (t0) REVERT: A 154 ASP cc_start: 0.7818 (t70) cc_final: 0.7561 (t70) REVERT: A 157 ASP cc_start: 0.7219 (t0) cc_final: 0.6966 (t0) REVERT: A 167 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8068 (tp30) REVERT: A 214 GLU cc_start: 0.7813 (tt0) cc_final: 0.7564 (mt-10) REVERT: A 215 LYS cc_start: 0.8257 (ttmm) cc_final: 0.8041 (ttmm) REVERT: A 254 ARG cc_start: 0.8300 (mtp85) cc_final: 0.7992 (mtp180) REVERT: A 316 GLU cc_start: 0.8650 (tp30) cc_final: 0.8379 (tp30) REVERT: B 6 THR cc_start: 0.7775 (m) cc_final: 0.7562 (p) REVERT: B 11 ASP cc_start: 0.8720 (t0) cc_final: 0.8239 (t70) REVERT: B 21 PHE cc_start: 0.8680 (m-80) cc_final: 0.8348 (m-80) REVERT: B 57 GLU cc_start: 0.8152 (tt0) cc_final: 0.7928 (tp30) REVERT: B 61 LYS cc_start: 0.8215 (mmtp) cc_final: 0.7979 (mmtp) REVERT: B 89 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8322 (t) REVERT: B 117 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7119 (mm-30) REVERT: B 118 LYS cc_start: 0.8058 (tptt) cc_final: 0.7759 (tptt) REVERT: B 205 GLU cc_start: 0.7501 (mp0) cc_final: 0.7147 (mp0) REVERT: B 207 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7920 (mm-30) REVERT: B 211 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7510 (t70) REVERT: C 47 MET cc_start: 0.4240 (pmm) cc_final: 0.3005 (ppp) REVERT: C 72 GLU cc_start: 0.8011 (tt0) cc_final: 0.7695 (tp30) REVERT: C 99 GLU cc_start: 0.7574 (pm20) cc_final: 0.7235 (pm20) REVERT: C 113 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8158 (mtmm) REVERT: C 118 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8172 (mttm) REVERT: C 297 ASN cc_start: 0.8438 (m110) cc_final: 0.8159 (m110) REVERT: C 334 GLU cc_start: 0.7846 (pm20) cc_final: 0.7533 (pm20) REVERT: D 44 MET cc_start: 0.8085 (tpp) cc_final: 0.7606 (tpp) REVERT: D 90 PHE cc_start: 0.8469 (m-80) cc_final: 0.7751 (m-80) REVERT: D 99 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7171 (pm20) REVERT: D 132 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.7937 (ppp) REVERT: D 211 ASP cc_start: 0.8154 (t0) cc_final: 0.7919 (t0) REVERT: D 284 LYS cc_start: 0.8688 (mttp) cc_final: 0.8440 (mtpm) REVERT: E 99 GLU cc_start: 0.7765 (pm20) cc_final: 0.7498 (pp20) REVERT: E 147 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8607 (ptp-170) REVERT: E 288 ASP cc_start: 0.7761 (m-30) cc_final: 0.7452 (m-30) REVERT: E 313 MET cc_start: 0.8436 (mmm) cc_final: 0.8228 (mmm) REVERT: F 68 LYS cc_start: 0.8741 (mmtp) cc_final: 0.8505 (mmtp) REVERT: F 96 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8560 (m) REVERT: F 99 GLU cc_start: 0.7797 (mp0) cc_final: 0.7381 (mp0) REVERT: F 113 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7831 (mmtp) REVERT: F 241 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: F 314 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: F 355 MET cc_start: 0.8426 (mtp) cc_final: 0.8208 (mtm) REVERT: G 125 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7666 (mm-30) REVERT: G 147 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8256 (ptm160) REVERT: G 222 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7355 (p0) REVERT: G 270 GLU cc_start: 0.6391 (mp0) cc_final: 0.5820 (mp0) outliers start: 98 outliers final: 46 residues processed: 639 average time/residue: 2.3902 time to fit residues: 1693.3367 Evaluate side-chains 654 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 594 time to evaluate : 3.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 180 LEU 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 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 202 THR Chi-restraints excluded: chain B residue 211 ASP 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 45 VAL 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 18 LYS Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 GLU 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 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 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 222 ASP 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 172 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN B 12 ASN B 111 ASN B 297 ASN C 128 ASN C 137 GLN C 162 ASN C 246 GLN D 12 ASN D 137 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN D 371 HIS 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.106286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.090974 restraints weight = 30074.885| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.62 r_work: 0.2968 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 20815 Z= 0.305 Angle : 0.712 8.295 28254 Z= 0.350 Chirality : 0.052 0.185 3141 Planarity : 0.005 0.056 3609 Dihedral : 10.309 170.574 2936 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.14 % Allowed : 18.31 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2540 helix: 0.15 (0.16), residues: 1087 sheet: 0.68 (0.24), residues: 467 loop : 0.10 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 79 HIS 0.008 0.002 HIS C 101 PHE 0.020 0.002 PHE G 31 TYR 0.013 0.002 TYR B 362 ARG 0.009 0.001 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 991) hydrogen bonds : angle 4.81293 ( 2619) covalent geometry : bond 0.00736 (20815) covalent geometry : angle 0.71236 (28254) *********************** 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 714 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 602 time to evaluate : 2.451 Fit side-chains REVERT: A 61 LYS cc_start: 0.8342 (pttp) cc_final: 0.7922 (pttp) REVERT: A 82 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7587 (tpp) REVERT: A 99 GLU cc_start: 0.7824 (mp0) cc_final: 0.7405 (mp0) REVERT: A 127 PHE cc_start: 0.8360 (m-10) cc_final: 0.8102 (m-10) REVERT: A 154 ASP cc_start: 0.7872 (t70) cc_final: 0.7634 (t70) REVERT: A 157 ASP cc_start: 0.7280 (t0) cc_final: 0.7017 (t0) REVERT: A 167 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8128 (mm-30) REVERT: A 214 GLU cc_start: 0.7803 (tt0) cc_final: 0.7592 (mt-10) REVERT: A 225 ASN cc_start: 0.8292 (t0) cc_final: 0.7797 (t0) REVERT: A 226 GLU cc_start: 0.8275 (tp30) cc_final: 0.8048 (tp30) REVERT: A 299 MET cc_start: 0.8413 (mtp) cc_final: 0.8160 (mtm) REVERT: A 316 GLU cc_start: 0.8639 (tp30) cc_final: 0.8407 (tp30) REVERT: A 361 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6996 (mt-10) REVERT: B 6 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7594 (p) REVERT: B 21 PHE cc_start: 0.8689 (m-80) cc_final: 0.8345 (m-80) REVERT: B 61 LYS cc_start: 0.8262 (mmtp) cc_final: 0.7978 (mmtp) REVERT: B 89 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8394 (t) REVERT: B 117 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7129 (mm-30) REVERT: B 118 LYS cc_start: 0.8043 (tptt) cc_final: 0.7775 (tptt) REVERT: B 205 GLU cc_start: 0.7558 (mp0) cc_final: 0.7220 (mp0) REVERT: B 207 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7909 (mm-30) REVERT: C 72 GLU cc_start: 0.8024 (tt0) cc_final: 0.7732 (tp30) REVERT: C 99 GLU cc_start: 0.7589 (pm20) cc_final: 0.7277 (pm20) REVERT: C 113 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8226 (mtmm) REVERT: C 118 LYS cc_start: 0.8412 (mtpp) cc_final: 0.8199 (mttm) REVERT: C 148 THR cc_start: 0.8773 (m) cc_final: 0.8415 (p) REVERT: C 297 ASN cc_start: 0.8435 (m110) cc_final: 0.8172 (m110) REVERT: C 334 GLU cc_start: 0.7812 (pm20) cc_final: 0.7478 (pm20) REVERT: D 51 ASP cc_start: 0.7943 (p0) cc_final: 0.7733 (p0) REVERT: D 132 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8005 (ppp) REVERT: D 211 ASP cc_start: 0.8213 (t0) cc_final: 0.7979 (t0) REVERT: E 99 GLU cc_start: 0.7794 (pm20) cc_final: 0.7438 (pp20) REVERT: E 147 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8642 (ptp-170) REVERT: E 288 ASP cc_start: 0.7711 (m-30) cc_final: 0.7397 (m-30) REVERT: E 313 MET cc_start: 0.8461 (mmm) cc_final: 0.8240 (mmm) REVERT: F 59 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8216 (tp40) REVERT: F 99 GLU cc_start: 0.7805 (mp0) cc_final: 0.7373 (mp0) REVERT: F 113 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7940 (mmtp) REVERT: F 210 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8248 (ttm110) REVERT: F 241 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: F 314 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: F 355 MET cc_start: 0.8378 (mtp) cc_final: 0.8143 (mtm) REVERT: G 125 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: G 147 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8376 (ptm160) REVERT: G 222 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7350 (p0) REVERT: G 270 GLU cc_start: 0.6520 (mp0) cc_final: 0.5833 (mp0) outliers start: 112 outliers final: 60 residues processed: 650 average time/residue: 1.6603 time to fit residues: 1193.2925 Evaluate side-chains 660 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 586 time to evaluate : 2.440 ------------------------------------------------------------------------------- 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 119 MET Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 6 THR 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 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 212 ILE 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 43 VAL 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 122 ILE 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 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 291 LYS 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 199 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain F residue 59 GLN 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 136 ILE 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 G residue 12 ASN Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 222 ASP 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 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 86 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 213 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 192 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 102 optimal weight: 0.0770 chunk 83 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 41 optimal weight: 0.0170 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN A 115 ASN B 12 ASN B 111 ASN B 297 ASN C 137 GLN D 12 ASN D 162 ASN D 225 ASN E 59 GLN E 78 ASN E 225 ASN E 353 GLN F 59 GLN F 246 GLN F 353 GLN G 12 ASN G 162 ASN G 297 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.089733 restraints weight = 29721.906| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.60 r_work: 0.3010 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 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 = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20815 Z= 0.143 Angle : 0.635 10.239 28254 Z= 0.305 Chirality : 0.046 0.179 3141 Planarity : 0.005 0.060 3609 Dihedral : 9.809 167.168 2933 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.59 % Allowed : 20.19 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.17), residues: 2540 helix: 0.33 (0.16), residues: 1095 sheet: 0.57 (0.24), residues: 467 loop : 0.33 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 79 HIS 0.005 0.001 HIS C 161 PHE 0.018 0.001 PHE G 31 TYR 0.027 0.001 TYR A 198 ARG 0.009 0.001 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 991) hydrogen bonds : angle 4.60033 ( 2619) covalent geometry : bond 0.00339 (20815) covalent geometry : angle 0.63474 (28254) *********************** 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 688 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 588 time to evaluate : 2.887 Fit side-chains REVERT: A 61 LYS cc_start: 0.8295 (pttp) cc_final: 0.7880 (pttp) REVERT: A 82 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7576 (tpp) REVERT: A 99 GLU cc_start: 0.7812 (mp0) cc_final: 0.7330 (mp0) REVERT: A 154 ASP cc_start: 0.7850 (t70) cc_final: 0.7621 (t70) REVERT: A 157 ASP cc_start: 0.7247 (t0) cc_final: 0.6957 (t0) REVERT: A 225 ASN cc_start: 0.8250 (t0) cc_final: 0.7761 (t0) REVERT: A 226 GLU cc_start: 0.8223 (tp30) cc_final: 0.7824 (mm-30) REVERT: A 254 ARG cc_start: 0.8280 (mtp85) cc_final: 0.8003 (mtp180) REVERT: A 299 MET cc_start: 0.8384 (mtp) cc_final: 0.8145 (mtm) REVERT: A 316 GLU cc_start: 0.8637 (tp30) cc_final: 0.8289 (tp30) REVERT: A 361 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6822 (mt-10) REVERT: A 364 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.6020 (pt0) REVERT: B 6 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7558 (p) REVERT: B 21 PHE cc_start: 0.8659 (m-80) cc_final: 0.8309 (m-80) REVERT: B 61 LYS cc_start: 0.8251 (mmtp) cc_final: 0.7958 (mmtp) REVERT: B 89 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8264 (t) REVERT: B 117 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7054 (mm-30) REVERT: B 118 LYS cc_start: 0.8036 (tptt) cc_final: 0.7763 (tptt) REVERT: B 205 GLU cc_start: 0.7520 (mp0) cc_final: 0.7182 (mp0) REVERT: B 207 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7818 (mm-30) REVERT: B 211 ASP cc_start: 0.8062 (t0) cc_final: 0.7768 (t70) REVERT: C 72 GLU cc_start: 0.8016 (tt0) cc_final: 0.7707 (tp30) REVERT: C 99 GLU cc_start: 0.7562 (pm20) cc_final: 0.7231 (pm20) REVERT: C 118 LYS cc_start: 0.8410 (mtpp) cc_final: 0.8177 (mttm) REVERT: C 297 ASN cc_start: 0.8410 (m110) cc_final: 0.8142 (m110) REVERT: C 334 GLU cc_start: 0.7834 (pm20) cc_final: 0.7502 (pm20) REVERT: D 51 ASP cc_start: 0.7935 (p0) cc_final: 0.7720 (p0) REVERT: D 107 GLU cc_start: 0.7580 (tp30) cc_final: 0.7311 (mm-30) REVERT: D 132 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7941 (ppp) REVERT: D 211 ASP cc_start: 0.8177 (t0) cc_final: 0.7925 (t0) REVERT: E 99 GLU cc_start: 0.7727 (pm20) cc_final: 0.7451 (pp20) REVERT: E 205 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7484 (mt-10) REVERT: E 288 ASP cc_start: 0.7739 (m-30) cc_final: 0.7413 (m-30) REVERT: E 313 MET cc_start: 0.8431 (mmm) cc_final: 0.8223 (mmm) REVERT: F 99 GLU cc_start: 0.7805 (mp0) cc_final: 0.7392 (mp0) REVERT: F 113 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7804 (mmtp) REVERT: F 210 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8289 (ttm110) REVERT: F 241 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: F 314 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: F 355 MET cc_start: 0.8371 (mtp) cc_final: 0.8131 (mtm) REVERT: G 125 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: G 147 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8337 (ptm160) REVERT: G 222 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7343 (p0) REVERT: G 270 GLU cc_start: 0.6398 (mp0) cc_final: 0.4838 (tt0) outliers start: 100 outliers final: 49 residues processed: 634 average time/residue: 1.7113 time to fit residues: 1201.0693 Evaluate side-chains 657 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 596 time to evaluate : 2.259 ------------------------------------------------------------------------------- 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 180 LEU 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 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 83 GLU Chi-restraints excluded: chain B residue 89 THR 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 45 VAL Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 122 ILE 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 D residue 18 LYS 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 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 G residue 17 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 222 ASP 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 53 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 chunk 147 optimal weight: 0.5980 chunk 187 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN A 115 ASN B 111 ASN B 297 ASN C 137 GLN D 12 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 G 12 ASN G 162 ASN G 297 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.107493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.092112 restraints weight = 29748.346| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.64 r_work: 0.2987 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 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 = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20815 Z= 0.190 Angle : 0.657 8.471 28254 Z= 0.316 Chirality : 0.048 0.159 3141 Planarity : 0.005 0.061 3609 Dihedral : 9.663 155.849 2929 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.77 % Allowed : 19.96 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2540 helix: 0.34 (0.16), residues: 1095 sheet: 0.58 (0.24), residues: 467 loop : 0.36 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.005 0.001 HIS C 101 PHE 0.016 0.001 PHE G 31 TYR 0.021 0.001 TYR A 198 ARG 0.010 0.001 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 991) hydrogen bonds : angle 4.60766 ( 2619) covalent geometry : bond 0.00458 (20815) covalent geometry : angle 0.65657 (28254) *********************** 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 692 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 588 time to evaluate : 2.361 Fit side-chains REVERT: A 61 LYS cc_start: 0.8317 (pttp) cc_final: 0.7916 (pttp) REVERT: A 82 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7482 (tpp) REVERT: A 99 GLU cc_start: 0.7875 (mp0) cc_final: 0.7340 (mp0) REVERT: A 154 ASP cc_start: 0.7868 (t70) cc_final: 0.7629 (t70) REVERT: A 157 ASP cc_start: 0.7265 (t0) cc_final: 0.6959 (t0) REVERT: A 226 GLU cc_start: 0.8259 (tp30) cc_final: 0.7886 (mm-30) REVERT: A 265 SER cc_start: 0.8736 (m) cc_final: 0.8390 (t) REVERT: A 299 MET cc_start: 0.8392 (mtp) cc_final: 0.8163 (mtm) REVERT: A 316 GLU cc_start: 0.8632 (tp30) cc_final: 0.8284 (tp30) REVERT: A 354 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6842 (pm20) REVERT: A 355 MET cc_start: 0.7312 (mpp) cc_final: 0.6994 (mpp) REVERT: A 361 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6851 (mt-10) REVERT: A 364 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.6074 (pt0) REVERT: B 6 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7590 (p) REVERT: B 11 ASP cc_start: 0.8710 (t0) cc_final: 0.8288 (t70) REVERT: B 21 PHE cc_start: 0.8663 (m-80) cc_final: 0.8308 (m-80) REVERT: B 61 LYS cc_start: 0.8260 (mmtp) cc_final: 0.7974 (mmtp) REVERT: B 89 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8254 (t) REVERT: B 117 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7051 (mm-30) REVERT: B 118 LYS cc_start: 0.8033 (tptt) cc_final: 0.7761 (tptt) REVERT: B 205 GLU cc_start: 0.7548 (mp0) cc_final: 0.7192 (mp0) REVERT: B 207 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7852 (mm-30) REVERT: B 211 ASP cc_start: 0.8092 (t0) cc_final: 0.7795 (t70) REVERT: C 72 GLU cc_start: 0.8011 (tt0) cc_final: 0.7700 (tp30) REVERT: C 99 GLU cc_start: 0.7601 (pm20) cc_final: 0.7256 (pm20) REVERT: C 113 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8179 (mtmm) REVERT: C 118 LYS cc_start: 0.8410 (mtpp) cc_final: 0.8178 (mttm) REVERT: C 297 ASN cc_start: 0.8451 (m110) cc_final: 0.8182 (m110) REVERT: C 334 GLU cc_start: 0.7872 (pm20) cc_final: 0.7526 (pm20) REVERT: D 51 ASP cc_start: 0.7944 (p0) cc_final: 0.7725 (p0) REVERT: D 107 GLU cc_start: 0.7611 (tp30) cc_final: 0.7316 (mm-30) REVERT: D 132 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7928 (ppp) REVERT: D 211 ASP cc_start: 0.8193 (t0) cc_final: 0.7949 (t0) REVERT: D 305 MET cc_start: 0.8894 (mmp) cc_final: 0.8682 (mmm) REVERT: E 99 GLU cc_start: 0.7749 (pm20) cc_final: 0.7457 (pp20) REVERT: E 205 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7501 (mt-10) REVERT: E 288 ASP cc_start: 0.7699 (m-30) cc_final: 0.7372 (m-30) REVERT: F 28 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8071 (ttm-80) REVERT: F 59 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8106 (tp40) REVERT: F 99 GLU cc_start: 0.7828 (mp0) cc_final: 0.7440 (mp0) REVERT: F 113 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7829 (mmtp) REVERT: F 210 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8268 (ttm110) REVERT: F 241 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: F 314 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: G 125 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7685 (mm-30) REVERT: G 147 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8352 (ptm160) REVERT: G 222 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7371 (p0) REVERT: G 270 GLU cc_start: 0.6469 (mp0) cc_final: 0.4888 (tt0) outliers start: 104 outliers final: 60 residues processed: 634 average time/residue: 1.6502 time to fit residues: 1161.3952 Evaluate side-chains 667 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 591 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP 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 180 LEU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 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 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 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 45 VAL Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 122 ILE 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 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 227 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 59 GLN 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 G residue 17 VAL Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 126 THR 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 235 SER Chi-restraints excluded: chain G residue 303 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 199 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 172 optimal weight: 0.5980 chunk 151 optimal weight: 0.9980 chunk 208 optimal weight: 0.0020 chunk 100 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 144 optimal weight: 0.3980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN A 115 ASN B 111 ASN B 297 ASN C 137 GLN D 137 GLN D 162 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 162 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.108599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.093258 restraints weight = 29900.452| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.63 r_work: 0.3007 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20815 Z= 0.129 Angle : 0.635 10.081 28254 Z= 0.301 Chirality : 0.045 0.149 3141 Planarity : 0.005 0.065 3609 Dihedral : 9.377 151.482 2929 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.13 % Allowed : 21.06 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2540 helix: 0.48 (0.16), residues: 1094 sheet: 0.63 (0.24), residues: 471 loop : 0.46 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 356 HIS 0.005 0.001 HIS C 161 PHE 0.016 0.001 PHE G 31 TYR 0.020 0.001 TYR A 198 ARG 0.012 0.001 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 991) hydrogen bonds : angle 4.49545 ( 2619) covalent geometry : bond 0.00306 (20815) covalent geometry : angle 0.63489 (28254) *********************** 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 678 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 588 time to evaluate : 2.232 Fit side-chains REVERT: A 61 LYS cc_start: 0.8304 (pttp) cc_final: 0.7904 (pttp) REVERT: A 82 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7465 (tpp) REVERT: A 99 GLU cc_start: 0.7866 (mp0) cc_final: 0.7331 (mp0) REVERT: A 154 ASP cc_start: 0.7863 (t70) cc_final: 0.7620 (t70) REVERT: A 157 ASP cc_start: 0.7266 (t0) cc_final: 0.6948 (t0) REVERT: A 226 GLU cc_start: 0.8230 (tp30) cc_final: 0.7872 (mm-30) REVERT: A 265 SER cc_start: 0.8738 (m) cc_final: 0.8409 (t) REVERT: A 299 MET cc_start: 0.8383 (mtp) cc_final: 0.8154 (mtm) REVERT: A 316 GLU cc_start: 0.8629 (tp30) cc_final: 0.8297 (tp30) REVERT: A 361 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6986 (mt-10) REVERT: B 6 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7554 (p) REVERT: B 21 PHE cc_start: 0.8653 (m-80) cc_final: 0.8270 (m-80) REVERT: B 61 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7943 (mmtp) REVERT: B 89 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8229 (t) REVERT: B 117 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7050 (mm-30) REVERT: B 118 LYS cc_start: 0.8084 (tptt) cc_final: 0.7800 (tptt) REVERT: B 205 GLU cc_start: 0.7526 (mp0) cc_final: 0.7181 (mp0) REVERT: B 211 ASP cc_start: 0.8067 (t0) cc_final: 0.7771 (t70) REVERT: C 72 GLU cc_start: 0.7997 (tt0) cc_final: 0.7687 (tp30) REVERT: C 99 GLU cc_start: 0.7598 (pm20) cc_final: 0.7271 (pm20) REVERT: C 113 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8122 (mtmm) REVERT: C 118 LYS cc_start: 0.8405 (mtpp) cc_final: 0.8174 (mttm) REVERT: C 297 ASN cc_start: 0.8431 (m110) cc_final: 0.8170 (m110) REVERT: C 334 GLU cc_start: 0.7845 (pm20) cc_final: 0.7573 (pm20) REVERT: D 51 ASP cc_start: 0.7943 (p0) cc_final: 0.7730 (p0) REVERT: D 90 PHE cc_start: 0.8402 (m-80) cc_final: 0.7813 (m-80) REVERT: D 132 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7946 (ppp) REVERT: D 211 ASP cc_start: 0.8179 (t0) cc_final: 0.7968 (t0) REVERT: D 305 MET cc_start: 0.8852 (mmp) cc_final: 0.8649 (mmm) REVERT: E 99 GLU cc_start: 0.7719 (pm20) cc_final: 0.7469 (pp20) REVERT: E 205 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7500 (mt-10) REVERT: E 288 ASP cc_start: 0.7751 (m-30) cc_final: 0.7429 (m-30) REVERT: F 28 ARG cc_start: 0.8342 (ttm170) cc_final: 0.8054 (ttm-80) REVERT: F 99 GLU cc_start: 0.7811 (mp0) cc_final: 0.7444 (mp0) REVERT: F 113 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7835 (mmtp) REVERT: F 210 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8284 (ttm110) REVERT: F 241 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: F 314 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: G 125 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7651 (mm-30) REVERT: G 147 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8372 (ptm160) REVERT: G 222 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7366 (p0) REVERT: G 270 GLU cc_start: 0.6381 (mp0) cc_final: 0.4861 (tt0) outliers start: 90 outliers final: 53 residues processed: 624 average time/residue: 1.6261 time to fit residues: 1119.8633 Evaluate side-chains 657 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 592 time to evaluate : 2.148 ------------------------------------------------------------------------------- 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 180 LEU 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 6 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 64 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 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 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 122 ILE 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 18 LYS 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 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 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 G residue 17 VAL Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 222 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 156 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN B 111 ASN B 297 ASN C 137 GLN C 353 GLN D 225 ASN E 59 GLN E 115 ASN E 225 ASN E 353 GLN F 59 GLN F 137 GLN F 246 GLN G 12 ASN G 162 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.092300 restraints weight = 29747.442| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.62 r_work: 0.2999 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 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 = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20815 Z= 0.189 Angle : 0.678 9.879 28254 Z= 0.324 Chirality : 0.048 0.217 3141 Planarity : 0.005 0.065 3609 Dihedral : 9.368 151.707 2923 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.22 % Allowed : 21.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2540 helix: 0.32 (0.16), residues: 1110 sheet: 0.57 (0.24), residues: 468 loop : 0.47 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.005 0.001 HIS C 101 PHE 0.015 0.001 PHE G 31 TYR 0.021 0.001 TYR A 198 ARG 0.011 0.001 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 991) hydrogen bonds : angle 4.57208 ( 2619) covalent geometry : bond 0.00457 (20815) covalent geometry : angle 0.67822 (28254) *********************** 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 692 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 600 time to evaluate : 2.107 Fit side-chains REVERT: A 61 LYS cc_start: 0.8296 (pttp) cc_final: 0.7873 (pttp) REVERT: A 82 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7482 (tpp) REVERT: A 124 PHE cc_start: 0.8110 (m-10) cc_final: 0.7813 (m-80) REVERT: A 154 ASP cc_start: 0.7856 (t70) cc_final: 0.7621 (t70) REVERT: A 157 ASP cc_start: 0.7276 (t0) cc_final: 0.6970 (t0) REVERT: A 223 PHE cc_start: 0.7983 (t80) cc_final: 0.7665 (t80) REVERT: A 226 GLU cc_start: 0.8241 (tp30) cc_final: 0.7902 (mm-30) REVERT: A 265 SER cc_start: 0.8778 (m) cc_final: 0.8429 (t) REVERT: A 299 MET cc_start: 0.8388 (mtp) cc_final: 0.8160 (mtm) REVERT: A 316 GLU cc_start: 0.8625 (tp30) cc_final: 0.8286 (tp30) REVERT: A 352 PHE cc_start: 0.8118 (t80) cc_final: 0.7705 (t80) REVERT: A 354 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: A 361 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6984 (mt-10) REVERT: B 6 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7568 (p) REVERT: B 21 PHE cc_start: 0.8661 (m-80) cc_final: 0.8333 (m-80) REVERT: B 61 LYS cc_start: 0.8228 (mmtp) cc_final: 0.7943 (mmtp) REVERT: B 89 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8264 (t) REVERT: B 117 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7073 (mm-30) REVERT: B 118 LYS cc_start: 0.8057 (tptt) cc_final: 0.7784 (tptt) REVERT: B 205 GLU cc_start: 0.7516 (mp0) cc_final: 0.7169 (mp0) REVERT: B 211 ASP cc_start: 0.8056 (t0) cc_final: 0.7719 (t70) REVERT: C 72 GLU cc_start: 0.8008 (tt0) cc_final: 0.7697 (tp30) REVERT: C 99 GLU cc_start: 0.7593 (pm20) cc_final: 0.7267 (pm20) REVERT: C 113 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8172 (mtmm) REVERT: C 118 LYS cc_start: 0.8421 (mtpp) cc_final: 0.8188 (mttm) REVERT: C 297 ASN cc_start: 0.8438 (m110) cc_final: 0.8176 (m110) REVERT: C 334 GLU cc_start: 0.7847 (pm20) cc_final: 0.7578 (pm20) REVERT: D 51 ASP cc_start: 0.7948 (p0) cc_final: 0.7735 (p0) REVERT: D 90 PHE cc_start: 0.8428 (m-80) cc_final: 0.7871 (m-80) REVERT: D 107 GLU cc_start: 0.7594 (tp30) cc_final: 0.7319 (mm-30) REVERT: D 132 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7920 (ppp) REVERT: D 211 ASP cc_start: 0.8174 (t0) cc_final: 0.7933 (t0) REVERT: E 47 MET cc_start: 0.6026 (OUTLIER) cc_final: 0.5662 (ppp) REVERT: E 99 GLU cc_start: 0.7703 (pm20) cc_final: 0.7466 (pp20) REVERT: E 205 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7515 (mt-10) REVERT: E 288 ASP cc_start: 0.7675 (m-30) cc_final: 0.7350 (m-30) REVERT: F 28 ARG cc_start: 0.8337 (ttm170) cc_final: 0.8043 (ttm-80) REVERT: F 99 GLU cc_start: 0.7784 (mp0) cc_final: 0.7446 (mp0) REVERT: F 113 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7831 (mmtp) REVERT: F 210 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8287 (ttm110) REVERT: F 241 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: F 314 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: F 327 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8348 (mp) REVERT: G 47 MET cc_start: 0.6426 (pmm) cc_final: 0.6184 (pmm) REVERT: G 125 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7748 (mm-30) REVERT: G 147 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8328 (ptm160) REVERT: G 270 GLU cc_start: 0.6446 (mp0) cc_final: 0.4888 (tt0) outliers start: 92 outliers final: 65 residues processed: 640 average time/residue: 1.6399 time to fit residues: 1158.0550 Evaluate side-chains 681 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 602 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP 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 180 LEU 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 A residue 354 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 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 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 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 122 ILE 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 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 227 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 317 ILE 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 F residue 368 SER Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 126 THR 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 Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 219 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 159 optimal weight: 0.2980 chunk 154 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 221 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN A 115 ASN B 111 ASN B 297 ASN C 137 GLN C 353 GLN D 12 ASN D 137 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN F 59 GLN F 137 GLN F 246 GLN G 12 ASN G 162 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.089995 restraints weight = 29700.493| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.60 r_work: 0.3010 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 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 = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20815 Z= 0.138 Angle : 0.666 11.340 28254 Z= 0.314 Chirality : 0.046 0.191 3141 Planarity : 0.005 0.068 3609 Dihedral : 9.200 151.893 2923 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.72 % Allowed : 21.71 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2540 helix: 0.40 (0.16), residues: 1110 sheet: 0.59 (0.24), residues: 473 loop : 0.55 (0.22), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 86 HIS 0.005 0.001 HIS C 161 PHE 0.018 0.001 PHE A 255 TYR 0.023 0.001 TYR A 198 ARG 0.012 0.001 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 991) hydrogen bonds : angle 4.49634 ( 2619) covalent geometry : bond 0.00327 (20815) covalent geometry : angle 0.66570 (28254) ********************** 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 673 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 592 time to evaluate : 2.408 Fit side-chains REVERT: A 61 LYS cc_start: 0.8301 (pttp) cc_final: 0.7872 (pttp) REVERT: A 82 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7368 (tpp) REVERT: A 154 ASP cc_start: 0.7842 (t70) cc_final: 0.7593 (t0) REVERT: A 157 ASP cc_start: 0.7280 (t0) cc_final: 0.6946 (t0) REVERT: A 226 GLU cc_start: 0.8215 (tp30) cc_final: 0.7850 (mm-30) REVERT: A 265 SER cc_start: 0.8762 (m) cc_final: 0.8424 (t) REVERT: A 299 MET cc_start: 0.8387 (mtp) cc_final: 0.8159 (mtm) REVERT: A 316 GLU cc_start: 0.8614 (tp30) cc_final: 0.8278 (tp30) REVERT: A 354 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6740 (pm20) REVERT: A 361 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6986 (mt-10) REVERT: B 6 THR cc_start: 0.7766 (OUTLIER) cc_final: 0.7541 (p) REVERT: B 21 PHE cc_start: 0.8647 (m-80) cc_final: 0.8280 (m-80) REVERT: B 61 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7917 (mmtp) REVERT: B 89 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8227 (t) REVERT: B 117 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7054 (mm-30) REVERT: B 118 LYS cc_start: 0.8031 (tptt) cc_final: 0.7746 (tptt) REVERT: B 205 GLU cc_start: 0.7527 (mp0) cc_final: 0.7157 (mp0) REVERT: B 211 ASP cc_start: 0.8038 (t0) cc_final: 0.7742 (t0) REVERT: B 241 GLU cc_start: 0.7438 (tp30) cc_final: 0.6880 (tp30) REVERT: C 72 GLU cc_start: 0.8000 (tt0) cc_final: 0.7688 (tp30) REVERT: C 99 GLU cc_start: 0.7599 (pm20) cc_final: 0.7271 (pm20) REVERT: C 113 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8117 (mtmm) REVERT: C 118 LYS cc_start: 0.8412 (mtpp) cc_final: 0.8177 (mttm) REVERT: C 297 ASN cc_start: 0.8405 (m110) cc_final: 0.8140 (m110) REVERT: C 334 GLU cc_start: 0.7838 (pm20) cc_final: 0.7574 (pm20) REVERT: D 51 ASP cc_start: 0.7931 (p0) cc_final: 0.7719 (p0) REVERT: D 90 PHE cc_start: 0.8421 (m-80) cc_final: 0.7882 (m-80) REVERT: D 132 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7872 (ppp) REVERT: D 211 ASP cc_start: 0.8188 (t0) cc_final: 0.7986 (t0) REVERT: D 284 LYS cc_start: 0.8744 (mttp) cc_final: 0.8401 (mttp) REVERT: E 47 MET cc_start: 0.6009 (OUTLIER) cc_final: 0.5652 (ppp) REVERT: E 59 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8302 (tp40) REVERT: E 99 GLU cc_start: 0.7687 (pm20) cc_final: 0.7457 (pp20) REVERT: E 202 THR cc_start: 0.8554 (p) cc_final: 0.8166 (p) REVERT: E 288 ASP cc_start: 0.7660 (m-30) cc_final: 0.7334 (m-30) REVERT: F 28 ARG cc_start: 0.8320 (ttm170) cc_final: 0.8031 (ttm-80) REVERT: F 59 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8134 (tp40) REVERT: F 99 GLU cc_start: 0.7775 (mp0) cc_final: 0.7413 (mp0) REVERT: F 113 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7833 (mmtp) REVERT: F 210 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8283 (ttm110) REVERT: F 241 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: F 314 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: G 47 MET cc_start: 0.6516 (pmm) cc_final: 0.6289 (pmm) REVERT: G 99 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: G 125 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7622 (mm-30) REVERT: G 147 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8307 (ptm160) REVERT: G 270 GLU cc_start: 0.6355 (mp0) cc_final: 0.4851 (tt0) REVERT: G 276 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8168 (mt-10) outliers start: 81 outliers final: 53 residues processed: 629 average time/residue: 1.6620 time to fit residues: 1162.6109 Evaluate side-chains 674 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 605 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 180 LEU 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 A residue 354 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 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 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 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 122 ILE 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 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 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain F residue 59 GLN 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 G residue 17 VAL Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 126 THR 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 338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 187 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN A 115 ASN B 12 ASN B 111 ASN B 297 ASN C 137 GLN C 353 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN G 225 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.108278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.093026 restraints weight = 30072.562| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.63 r_work: 0.3011 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 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 = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.236 20815 Z= 0.224 Angle : 0.957 59.200 28254 Z= 0.521 Chirality : 0.048 0.273 3141 Planarity : 0.005 0.067 3609 Dihedral : 9.203 151.950 2923 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.63 % Allowed : 21.98 % Favored : 74.39 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.17), residues: 2540 helix: 0.37 (0.16), residues: 1110 sheet: 0.60 (0.24), residues: 473 loop : 0.55 (0.22), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 86 HIS 0.005 0.001 HIS B 275 PHE 0.018 0.001 PHE A 255 TYR 0.024 0.001 TYR A 198 ARG 0.012 0.001 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 991) hydrogen bonds : angle 4.49622 ( 2619) covalent geometry : bond 0.00514 (20815) covalent geometry : angle 0.95681 (28254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22453.68 seconds wall clock time: 393 minutes 19.87 seconds (23599.87 seconds total)