Starting phenix.real_space_refine on Fri Mar 6 02:52:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w17_21502/03_2026/6w17_21502.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w17_21502/03_2026/6w17_21502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w17_21502/03_2026/6w17_21502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w17_21502/03_2026/6w17_21502.map" model { file = "/net/cci-nas-00/data/ceres_data/6w17_21502/03_2026/6w17_21502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w17_21502/03_2026/6w17_21502.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 6 5.21 5 S 143 5.16 5 C 17319 2.51 5 N 4684 2.21 5 O 5230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27396 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2979 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 20, 'TRANS': 359} Chain breaks: 4 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2909 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 18, 'TRANS': 345} Chain breaks: 2 Chain: "C" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2589 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2435 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 285} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 861 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 12, 'TRANS': 161} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 736 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'TYR:plan': 8, 'HIS:plan': 3, 'PHE:plan': 12, 'ASP:plan': 8, 'ASN:plan1': 9, 'ARG:plan': 12, 'GLU:plan': 9, 'GLN:plan1': 5, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 328 Chain: "F" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1376 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "G" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1169 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 142} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1063 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 124} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "J" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "K" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "L" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "M" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'G5G:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'G5G:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'G5G:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'G5G:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'G5G:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" 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: "J" 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: "K" 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: "L" 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: 6.20, per 1000 atoms: 0.23 Number of scatterers: 27396 At special positions: 0 Unit cell: (177.556, 143.154, 221.945, 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 6 11.99 O 5230 8.00 N 4684 7.00 C 17319 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.0 seconds 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6606 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 48 sheets defined 45.2% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 159 through 167 removed outlier: 4.233A pdb=" N LEU A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 228 removed outlier: 4.069A pdb=" N THR A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 255 through 261 Processing helix chain 'A' and resid 262 through 265 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 306 through 318 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 341 through 366 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 397 through 403 removed outlier: 4.088A pdb=" N SER A 401 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.828A pdb=" N ALA B 58 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 59 " --> pdb=" O ASP B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 59' Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.930A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 263 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.854A pdb=" N VAL B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.974A pdb=" N LYS B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.839A pdb=" N TYR B 306 " --> pdb=" O SER B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 325 Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 348 through 362 Processing helix chain 'B' and resid 377 through 383 removed outlier: 3.691A pdb=" N ASP B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.982A pdb=" N GLU D 105 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 Processing helix chain 'D' and resid 120 through 139 Processing helix chain 'D' and resid 143 through 152 Processing helix chain 'D' and resid 186 through 202 Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'D' and resid 254 through 299 removed outlier: 5.142A pdb=" N ARG D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 55 Processing helix chain 'E' and resid 64 through 84 removed outlier: 3.721A pdb=" N LEU E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 101 Processing helix chain 'E' and resid 126 through 149 Processing helix chain 'E' and resid 158 through 164 Processing helix chain 'E' and resid 168 through 172 removed outlier: 3.537A pdb=" N LYS E 172 " --> pdb=" O PHE E 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 20 Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 80 through 97 Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 128 through 168 removed outlier: 4.604A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 50 Proline residue: G 41 - end of helix Processing helix chain 'G' and resid 51 through 60 removed outlier: 3.851A pdb=" N GLY G 55 " --> pdb=" O ASN G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 86 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 100 through 116 removed outlier: 3.785A pdb=" N ILE G 104 " --> pdb=" O SER G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 137 Processing helix chain 'G' and resid 138 through 147 removed outlier: 4.405A pdb=" N ILE G 142 " --> pdb=" O GLY G 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 248 Processing helix chain 'H' and resid 252 through 266 removed outlier: 3.748A pdb=" N LEU H 256 " --> pdb=" O ARG H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 292 Processing helix chain 'H' and resid 299 through 309 Processing helix chain 'H' and resid 325 through 338 Processing helix chain 'H' and resid 344 through 359 removed outlier: 3.700A pdb=" N ALA H 348 " --> pdb=" O ASN H 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 61 removed outlier: 3.677A pdb=" N GLN I 59 " --> pdb=" O GLY I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 112 through 127 removed outlier: 3.605A pdb=" N PHE I 127 " --> pdb=" O MET I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 146 Processing helix chain 'I' and resid 172 through 175 Processing helix chain 'I' and resid 181 through 197 Processing helix chain 'I' and resid 202 through 216 Processing helix chain 'I' and resid 222 through 233 Processing helix chain 'I' and resid 252 through 257 Processing helix chain 'I' and resid 258 through 263 Processing helix chain 'I' and resid 273 through 285 removed outlier: 3.544A pdb=" N CYS I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 294 removed outlier: 4.460A pdb=" N ASP I 292 " --> pdb=" O ASP I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 321 Processing helix chain 'I' and resid 337 through 349 Processing helix chain 'I' and resid 351 through 356 removed outlier: 3.897A pdb=" N MET I 355 " --> pdb=" O THR I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 366 removed outlier: 3.775A pdb=" N TYR I 362 " --> pdb=" O THR I 358 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 374 Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.872A pdb=" N GLN J 59 " --> pdb=" O GLY J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 92 Processing helix chain 'J' and resid 97 through 101 removed outlier: 3.846A pdb=" N GLU J 100 " --> pdb=" O ALA J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 126 Processing helix chain 'J' and resid 136 through 146 removed outlier: 3.779A pdb=" N SER J 145 " --> pdb=" O SER J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 197 Processing helix chain 'J' and resid 202 through 216 Processing helix chain 'J' and resid 222 through 233 Processing helix chain 'J' and resid 252 through 263 Proline residue: J 258 - end of helix Processing helix chain 'J' and resid 264 through 267 Processing helix chain 'J' and resid 273 through 285 removed outlier: 3.646A pdb=" N CYS J 285 " --> pdb=" O SER J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 296 removed outlier: 3.633A pdb=" N ALA J 295 " --> pdb=" O LYS J 291 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN J 296 " --> pdb=" O ASP J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 306 removed outlier: 3.633A pdb=" N TYR J 306 " --> pdb=" O THR J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 321 removed outlier: 3.790A pdb=" N ARG J 312 " --> pdb=" O GLY J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 336 No H-bonds generated for 'chain 'J' and resid 334 through 336' Processing helix chain 'J' and resid 337 through 349 Processing helix chain 'J' and resid 350 through 356 Processing helix chain 'J' and resid 359 through 366 Processing helix chain 'J' and resid 368 through 374 removed outlier: 3.972A pdb=" N ARG J 372 " --> pdb=" O SER J 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 61 removed outlier: 3.634A pdb=" N GLN K 59 " --> pdb=" O GLY K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 92 Processing helix chain 'K' and resid 112 through 126 Processing helix chain 'K' and resid 137 through 146 Processing helix chain 'K' and resid 172 through 175 Processing helix chain 'K' and resid 181 through 197 Processing helix chain 'K' and resid 202 through 217 Processing helix chain 'K' and resid 222 through 233 Processing helix chain 'K' and resid 252 through 263 Proline residue: K 258 - end of helix Processing helix chain 'K' and resid 273 through 284 Processing helix chain 'K' and resid 286 through 296 removed outlier: 4.393A pdb=" N LYS K 291 " --> pdb=" O ILE K 287 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASP K 292 " --> pdb=" O ASP K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 302 through 306 removed outlier: 3.963A pdb=" N TYR K 306 " --> pdb=" O THR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 337 through 349 Processing helix chain 'K' and resid 350 through 355 removed outlier: 4.313A pdb=" N GLN K 354 " --> pdb=" O SER K 350 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET K 355 " --> pdb=" O THR K 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 350 through 355' Processing helix chain 'K' and resid 359 through 365 Processing helix chain 'K' and resid 368 through 374 Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 78 through 92 Processing helix chain 'L' and resid 112 through 126 Processing helix chain 'L' and resid 136 through 146 Processing helix chain 'L' and resid 181 through 197 Processing helix chain 'L' and resid 202 through 217 Processing helix chain 'L' and resid 222 through 233 Processing helix chain 'L' and resid 252 through 263 Proline residue: L 258 - end of helix Processing helix chain 'L' and resid 263 through 268 removed outlier: 4.315A pdb=" N ILE L 267 " --> pdb=" O GLN L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 284 Processing helix chain 'L' and resid 286 through 296 removed outlier: 4.430A pdb=" N ASP L 292 " --> pdb=" O ASP L 288 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA L 295 " --> pdb=" O LYS L 291 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN L 296 " --> pdb=" O ASP L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 321 Processing helix chain 'L' and resid 337 through 349 Processing helix chain 'L' and resid 351 through 356 Processing helix chain 'L' and resid 359 through 366 Processing helix chain 'L' and resid 367 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 removed outlier: 6.972A pdb=" N ILE A 8 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR A 129 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N MET A 10 " --> pdb=" O THR A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 209 removed outlier: 6.506A pdb=" N ILE A 330 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.578A pdb=" N GLY B 18 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 7 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE B 6 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 106 through 107 Processing sheet with id=AA8, first strand: chain 'B' and resid 176 through 178 Processing sheet with id=AA9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 8 removed outlier: 6.958A pdb=" N VAL C 372 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ARG C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLY C 367 " --> pdb=" O ARG C 371 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 366 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR C 349 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 26 through 29 removed outlier: 6.522A pdb=" N GLU C 39 " --> pdb=" O HIS C 47 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N HIS C 47 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASP C 41 " --> pdb=" O TRP C 45 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TRP C 45 " --> pdb=" O ASP C 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 58 through 64 removed outlier: 4.595A pdb=" N CYS C 60 " --> pdb=" O CYS C 73 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 103 through 108 removed outlier: 4.499A pdb=" N TRP C 135 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 149 through 153 Processing sheet with id=AB6, first strand: chain 'C' and resid 210 through 213 Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 259 removed outlier: 4.841A pdb=" N LEU C 257 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL C 266 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TRP C 259 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA C 264 " --> pdb=" O TRP C 259 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA C 267 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU C 276 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 30 through 33 Processing sheet with id=AB9, first strand: chain 'D' and resid 157 through 159 Processing sheet with id=AC1, first strand: chain 'E' and resid 16 through 17 Processing sheet with id=AC2, first strand: chain 'F' and resid 51 through 56 removed outlier: 4.594A pdb=" N ARG F 55 " --> pdb=" O GLU F 59 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLU F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 8 through 12 Processing sheet with id=AC4, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'I' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'I' and resid 103 through 104 removed outlier: 6.734A pdb=" N THR I 103 " --> pdb=" O TYR I 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AC8, first strand: chain 'I' and resid 169 through 170 removed outlier: 6.501A pdb=" N ILE I 151 " --> pdb=" O VAL I 298 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER I 300 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU I 153 " --> pdb=" O SER I 300 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 238 through 240 Processing sheet with id=AD1, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AD2, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AD3, first strand: chain 'J' and resid 71 through 72 Processing sheet with id=AD4, first strand: chain 'J' and resid 131 through 132 Processing sheet with id=AD5, first strand: chain 'J' and resid 169 through 170 Processing sheet with id=AD6, first strand: chain 'J' and resid 169 through 170 removed outlier: 6.365A pdb=" N ILE J 151 " --> pdb=" O VAL J 298 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN J 297 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 238 through 241 Processing sheet with id=AD8, first strand: chain 'K' and resid 8 through 11 Processing sheet with id=AD9, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AE1, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AE2, first strand: chain 'K' and resid 105 through 107 removed outlier: 3.765A pdb=" N ALA K 135 " --> pdb=" O LEU K 105 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 131 through 132 Processing sheet with id=AE4, first strand: chain 'K' and resid 169 through 170 Processing sheet with id=AE5, first strand: chain 'K' and resid 169 through 170 removed outlier: 6.052A pdb=" N ILE K 151 " --> pdb=" O VAL K 298 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N SER K 300 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU K 153 " --> pdb=" O SER K 300 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 238 through 241 Processing sheet with id=AE7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE8, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AF1, first strand: chain 'L' and resid 103 through 106 removed outlier: 3.938A pdb=" N THR L 103 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR L 133 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 176 through 178 removed outlier: 6.427A pdb=" N ILE L 151 " --> pdb=" O VAL L 298 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N SER L 300 " --> pdb=" O ILE L 151 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU L 153 " --> pdb=" O SER L 300 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 238 through 241 1322 hydrogen bonds defined for protein. 3657 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: 4.02 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9009 1.34 - 1.46: 6185 1.46 - 1.58: 12521 1.58 - 1.70: 24 1.70 - 1.81: 239 Bond restraints: 27978 Sorted by residual: bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.63e+01 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.53e+01 bond pdb=" C5 ATP A 501 " pdb=" C6 ATP A 501 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.25e+01 bond pdb=" C5 ATP B 501 " pdb=" C6 ATP B 501 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.23e+01 bond pdb=" C8 ATP A 501 " pdb=" N7 ATP A 501 " ideal model delta sigma weight residual 1.310 1.359 -0.049 1.00e-02 1.00e+04 2.37e+01 ... (remaining 27973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 37912 3.96 - 7.92: 106 7.92 - 11.88: 14 11.88 - 15.84: 0 15.84 - 19.80: 4 Bond angle restraints: 38036 Sorted by residual: angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 120.07 19.80 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 120.16 19.71 1.00e+00 1.00e+00 3.89e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 120.26 16.57 1.00e+00 1.00e+00 2.75e+02 angle pdb=" PA ATP B 501 " pdb=" O3A ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 136.83 120.29 16.54 1.00e+00 1.00e+00 2.73e+02 angle pdb=" C5 ATP B 501 " pdb=" C4 ATP B 501 " pdb=" N3 ATP B 501 " ideal model delta sigma weight residual 126.80 118.74 8.06 1.00e+00 1.00e+00 6.49e+01 ... (remaining 38031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.89: 16200 25.89 - 51.78: 583 51.78 - 77.67: 77 77.67 - 103.55: 6 103.55 - 129.44: 1 Dihedral angle restraints: 16867 sinusoidal: 6632 harmonic: 10235 Sorted by residual: dihedral pdb=" O1B ADP L 401 " pdb=" O3A ADP L 401 " pdb=" PB ADP L 401 " pdb=" PA ADP L 401 " ideal model delta sinusoidal sigma weight residual 300.00 170.56 129.44 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" CA VAL L 30 " pdb=" C VAL L 30 " pdb=" N PHE L 31 " pdb=" CA PHE L 31 " ideal model delta harmonic sigma weight residual -180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA VAL I 30 " pdb=" C VAL I 30 " pdb=" N PHE I 31 " pdb=" CA PHE I 31 " ideal model delta harmonic sigma weight residual -180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 16864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3130 0.035 - 0.070: 712 0.070 - 0.105: 303 0.105 - 0.140: 133 0.140 - 0.175: 6 Chirality restraints: 4284 Sorted by residual: chirality pdb=" CB ALO P 6 " pdb=" CA ALO P 6 " pdb=" OG1 ALO P 6 " pdb=" CG2 ALO P 6 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB ALO Q 6 " pdb=" CA ALO Q 6 " pdb=" OG1 ALO Q 6 " pdb=" CG2 ALO Q 6 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CB ALO O 6 " pdb=" CA ALO O 6 " pdb=" OG1 ALO O 6 " pdb=" CG2 ALO O 6 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.52e-01 ... (remaining 4281 not shown) Planarity restraints: 4891 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 5 " 0.017 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" C GLN C 5 " -0.061 2.00e-02 2.50e+03 pdb=" O GLN C 5 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL C 6 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE H 293 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO H 294 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO H 294 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 294 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 257 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO B 258 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " 0.019 5.00e-02 4.00e+02 ... (remaining 4888 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 167 2.50 - 3.10: 21594 3.10 - 3.70: 41288 3.70 - 4.30: 57867 4.30 - 4.90: 95544 Nonbonded interactions: 216460 Sorted by model distance: nonbonded pdb=" O LEU A 19 " pdb=" O SER A 28 " model vdw 1.894 3.040 nonbonded pdb=" O3B ADP I 401 " pdb="MG MG I 402 " model vdw 1.974 2.170 nonbonded pdb=" O1B ADP L 401 " pdb="MG MG L 402 " model vdw 1.974 2.170 nonbonded pdb=" O3B ADP J 401 " pdb="MG MG J 402 " model vdw 1.974 2.170 nonbonded pdb=" O3B ADP K 401 " pdb="MG MG K 402 " model vdw 1.975 2.170 ... (remaining 216455 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 'I' and (resid 5 through 374 or resid 401 through 402)) selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.010 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.520 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 : 0.006 0.897 27984 Z= 0.568 Angle : 0.586 19.797 38036 Z= 0.351 Chirality : 0.040 0.175 4284 Planarity : 0.003 0.039 4891 Dihedral : 13.380 129.442 10261 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.13), residues: 3433 helix: -0.64 (0.13), residues: 1436 sheet: -2.99 (0.18), residues: 590 loop : -3.20 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 318 TYR 0.009 0.000 TYR A 29 PHE 0.009 0.001 PHE C 115 TRP 0.004 0.001 TRP C 375 HIS 0.004 0.000 HIS D 261 Details of bonding type rmsd covalent geometry : bond 0.00299 (27978) covalent geometry : angle 0.58622 (38036) hydrogen bonds : bond 0.10176 ( 1316) hydrogen bonds : angle 5.15260 ( 3657) Misc. bond : bond 0.36637 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 589 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.8972 (mtt90) cc_final: 0.8657 (mtt90) REVERT: B 154 ASP cc_start: 0.8172 (t0) cc_final: 0.7809 (t0) REVERT: B 172 ASN cc_start: 0.8256 (t0) cc_final: 0.7837 (t0) REVERT: B 342 ASP cc_start: 0.8435 (t0) cc_final: 0.7978 (t0) REVERT: C 62 ASP cc_start: 0.8614 (t0) cc_final: 0.8098 (t0) REVERT: C 105 PHE cc_start: 0.7937 (t80) cc_final: 0.7728 (t80) REVERT: C 169 LYS cc_start: 0.9241 (mttt) cc_final: 0.9005 (mttm) REVERT: C 227 SER cc_start: 0.9118 (m) cc_final: 0.8880 (p) REVERT: C 245 ILE cc_start: 0.9301 (mt) cc_final: 0.9058 (tt) REVERT: C 349 THR cc_start: 0.8376 (m) cc_final: 0.8165 (t) REVERT: D 1 MET cc_start: 0.6488 (ptm) cc_final: 0.5931 (ptm) REVERT: F 61 CYS cc_start: 0.7922 (m) cc_final: 0.7604 (m) REVERT: F 64 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7803 (mm-30) REVERT: F 133 ASP cc_start: 0.8799 (m-30) cc_final: 0.8242 (m-30) REVERT: G 131 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8339 (tm-30) REVERT: G 132 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8763 (mmmm) REVERT: H 249 LYS cc_start: 0.8000 (tppt) cc_final: 0.7573 (tppt) REVERT: J 313 MET cc_start: 0.8192 (tpt) cc_final: 0.7833 (tpt) REVERT: J 328 LYS cc_start: 0.8805 (tttt) cc_final: 0.8599 (ttpp) REVERT: K 81 ASP cc_start: 0.8782 (m-30) cc_final: 0.8553 (m-30) REVERT: K 83 GLU cc_start: 0.8849 (tt0) cc_final: 0.8493 (tt0) REVERT: K 103 THR cc_start: 0.9267 (t) cc_final: 0.8913 (p) REVERT: K 118 LYS cc_start: 0.8863 (tppp) cc_final: 0.8585 (mmtt) REVERT: K 169 TYR cc_start: 0.7663 (m-80) cc_final: 0.7149 (t80) REVERT: K 217 CYS cc_start: 0.8531 (m) cc_final: 0.7622 (m) REVERT: L 78 ASN cc_start: 0.7420 (t0) cc_final: 0.6689 (t0) REVERT: L 81 ASP cc_start: 0.8568 (m-30) cc_final: 0.8294 (m-30) REVERT: L 92 ASN cc_start: 0.8452 (m-40) cc_final: 0.8057 (m110) REVERT: L 165 ILE cc_start: 0.8694 (mm) cc_final: 0.8492 (tp) REVERT: L 214 GLU cc_start: 0.7340 (pt0) cc_final: 0.7082 (pt0) REVERT: L 263 GLN cc_start: 0.7418 (mm-40) cc_final: 0.7105 (mt0) REVERT: L 265 SER cc_start: 0.8327 (p) cc_final: 0.8044 (t) REVERT: L 276 GLU cc_start: 0.8547 (tt0) cc_final: 0.8195 (tt0) REVERT: L 305 MET cc_start: 0.8159 (tpt) cc_final: 0.7918 (mmt) REVERT: L 313 MET cc_start: 0.6765 (tpt) cc_final: 0.6317 (tpt) REVERT: L 334 GLU cc_start: 0.7720 (pm20) cc_final: 0.7489 (pm20) outliers start: 0 outliers final: 0 residues processed: 589 average time/residue: 0.1836 time to fit residues: 168.3866 Evaluate side-chains 382 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.0060 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 192 HIS B 227 HIS ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 HIS K 12 ASN K 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.093703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.079096 restraints weight = 81813.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.081278 restraints weight = 41143.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.082750 restraints weight = 24792.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.083716 restraints weight = 16891.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.084370 restraints weight = 12725.562| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27984 Z= 0.135 Angle : 0.621 8.728 38036 Z= 0.307 Chirality : 0.045 0.203 4284 Planarity : 0.004 0.052 4891 Dihedral : 8.310 105.637 4016 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.44 % Allowed : 8.39 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.14), residues: 3433 helix: 0.36 (0.14), residues: 1455 sheet: -2.27 (0.19), residues: 574 loop : -2.45 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 39 TYR 0.023 0.001 TYR D 279 PHE 0.034 0.001 PHE I 262 TRP 0.022 0.001 TRP A 387 HIS 0.009 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00306 (27978) covalent geometry : angle 0.62129 (38036) hydrogen bonds : bond 0.03632 ( 1316) hydrogen bonds : angle 4.51565 ( 3657) Misc. bond : bond 0.00125 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 424 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 ASN cc_start: 0.7801 (m110) cc_final: 0.7331 (m-40) REVERT: A 399 PHE cc_start: 0.7699 (t80) cc_final: 0.7432 (t80) REVERT: B 10 ASN cc_start: 0.8642 (t0) cc_final: 0.8342 (t0) REVERT: B 154 ASP cc_start: 0.8269 (t0) cc_final: 0.7955 (t70) REVERT: B 172 ASN cc_start: 0.8334 (t0) cc_final: 0.8008 (t0) REVERT: B 188 TYR cc_start: 0.8319 (t80) cc_final: 0.8008 (t80) REVERT: B 212 MET cc_start: 0.8190 (ttm) cc_final: 0.7751 (ttp) REVERT: B 342 ASP cc_start: 0.8373 (t0) cc_final: 0.8066 (t0) REVERT: C 62 ASP cc_start: 0.8612 (t0) cc_final: 0.8354 (t0) REVERT: C 245 ILE cc_start: 0.9381 (mt) cc_final: 0.9173 (tt) REVERT: C 256 SER cc_start: 0.8812 (t) cc_final: 0.8345 (t) REVERT: C 346 MET cc_start: 0.8458 (ttt) cc_final: 0.8249 (ttt) REVERT: D 59 TYR cc_start: 0.8886 (t80) cc_final: 0.8645 (t80) REVERT: D 109 MET cc_start: 0.9175 (tpt) cc_final: 0.8972 (tpp) REVERT: F 92 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8298 (tm-30) REVERT: F 133 ASP cc_start: 0.8638 (m-30) cc_final: 0.8355 (m-30) REVERT: G 132 LYS cc_start: 0.9192 (mmmt) cc_final: 0.8979 (mmmm) REVERT: G 151 ASP cc_start: 0.8116 (p0) cc_final: 0.7601 (p0) REVERT: H 326 LYS cc_start: 0.8357 (tptt) cc_final: 0.8138 (tptp) REVERT: H 330 ASP cc_start: 0.8430 (t70) cc_final: 0.7875 (t70) REVERT: H 333 ASN cc_start: 0.8512 (m-40) cc_final: 0.7691 (p0) REVERT: H 349 ARG cc_start: 0.8769 (ttp80) cc_final: 0.8276 (ptm-80) REVERT: I 68 LYS cc_start: 0.8723 (mttt) cc_final: 0.8487 (mtmm) REVERT: I 132 MET cc_start: 0.7824 (tmm) cc_final: 0.7552 (tmm) REVERT: J 132 MET cc_start: 0.8275 (ppp) cc_final: 0.8015 (ppp) REVERT: K 83 GLU cc_start: 0.8683 (tt0) cc_final: 0.8417 (tt0) REVERT: K 103 THR cc_start: 0.9257 (t) cc_final: 0.8878 (p) REVERT: K 118 LYS cc_start: 0.8971 (tppp) cc_final: 0.8698 (tppp) REVERT: K 123 MET cc_start: 0.8320 (tpp) cc_final: 0.8058 (tpp) REVERT: K 136 ILE cc_start: 0.9239 (mm) cc_final: 0.8816 (mm) REVERT: K 169 TYR cc_start: 0.7364 (m-80) cc_final: 0.7016 (t80) REVERT: K 217 CYS cc_start: 0.8512 (m) cc_final: 0.7897 (m) REVERT: K 283 MET cc_start: 0.9056 (mmm) cc_final: 0.8522 (mmm) REVERT: K 316 GLU cc_start: 0.8691 (tp30) cc_final: 0.8309 (tp30) REVERT: L 78 ASN cc_start: 0.7580 (t0) cc_final: 0.6704 (t0) REVERT: L 81 ASP cc_start: 0.8343 (m-30) cc_final: 0.8108 (m-30) REVERT: L 92 ASN cc_start: 0.8577 (m-40) cc_final: 0.8204 (m110) REVERT: L 132 MET cc_start: 0.7986 (ttp) cc_final: 0.7569 (tmm) REVERT: L 210 ARG cc_start: 0.8465 (tmm-80) cc_final: 0.7806 (ttp80) REVERT: L 214 GLU cc_start: 0.7505 (pt0) cc_final: 0.6597 (pt0) REVERT: L 265 SER cc_start: 0.8563 (p) cc_final: 0.8211 (t) REVERT: L 313 MET cc_start: 0.7154 (tpt) cc_final: 0.6635 (tpt) REVERT: L 334 GLU cc_start: 0.7757 (pm20) cc_final: 0.7495 (pm20) outliers start: 41 outliers final: 29 residues processed: 443 average time/residue: 0.1617 time to fit residues: 117.0115 Evaluate side-chains 386 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 357 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 277 ASN Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 288 ARG Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 334 ASN Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 320 LEU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain L residue 217 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 252 optimal weight: 0.7980 chunk 260 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 323 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 14 optimal weight: 0.1980 chunk 237 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 192 HIS A 395 GLN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN C 196 ASN ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.091553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.076811 restraints weight = 81802.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.078974 restraints weight = 41180.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.080408 restraints weight = 24842.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.081372 restraints weight = 16996.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.082025 restraints weight = 12844.713| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27984 Z= 0.131 Angle : 0.597 11.330 38036 Z= 0.295 Chirality : 0.044 0.223 4284 Planarity : 0.004 0.065 4891 Dihedral : 8.229 102.234 4016 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.15 % Allowed : 10.71 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.15), residues: 3433 helix: 0.74 (0.14), residues: 1442 sheet: -1.78 (0.20), residues: 582 loop : -2.05 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 239 TYR 0.019 0.001 TYR F 8 PHE 0.024 0.001 PHE H 265 TRP 0.014 0.001 TRP D 170 HIS 0.010 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00298 (27978) covalent geometry : angle 0.59750 (38036) hydrogen bonds : bond 0.03552 ( 1316) hydrogen bonds : angle 4.48618 ( 3657) Misc. bond : bond 0.00059 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 401 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 PHE cc_start: 0.7716 (t80) cc_final: 0.7453 (t80) REVERT: B 154 ASP cc_start: 0.8191 (t0) cc_final: 0.7911 (t70) REVERT: B 172 ASN cc_start: 0.8346 (t0) cc_final: 0.8145 (t0) REVERT: C 62 ASP cc_start: 0.8604 (t0) cc_final: 0.8346 (t0) REVERT: C 153 ASP cc_start: 0.8639 (t0) cc_final: 0.8353 (t0) REVERT: C 169 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8945 (ptpt) REVERT: C 245 ILE cc_start: 0.9360 (mt) cc_final: 0.9105 (tt) REVERT: C 346 MET cc_start: 0.8572 (ttt) cc_final: 0.8358 (ttt) REVERT: D 59 TYR cc_start: 0.8917 (t80) cc_final: 0.8717 (t80) REVERT: F 92 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8387 (tm-30) REVERT: G 27 GLU cc_start: 0.6210 (mm-30) cc_final: 0.5825 (tp30) REVERT: G 80 PHE cc_start: 0.9333 (t80) cc_final: 0.9040 (t80) REVERT: G 132 LYS cc_start: 0.9303 (mmmt) cc_final: 0.9071 (mmmm) REVERT: G 151 ASP cc_start: 0.8187 (p0) cc_final: 0.7640 (p0) REVERT: H 248 GLU cc_start: 0.7434 (tp30) cc_final: 0.7038 (tp30) REVERT: H 249 LYS cc_start: 0.7714 (tppt) cc_final: 0.7427 (tppt) REVERT: H 318 ARG cc_start: 0.8387 (ptt90) cc_final: 0.7827 (mtm110) REVERT: H 349 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8266 (ptm-80) REVERT: I 68 LYS cc_start: 0.8750 (mttt) cc_final: 0.8547 (mtmm) REVERT: I 313 MET cc_start: 0.8572 (tpp) cc_final: 0.8332 (ttm) REVERT: I 325 MET cc_start: 0.8089 (tpp) cc_final: 0.7742 (mpp) REVERT: J 132 MET cc_start: 0.8329 (ppp) cc_final: 0.8072 (ppp) REVERT: J 313 MET cc_start: 0.8123 (tpp) cc_final: 0.7878 (tpt) REVERT: K 83 GLU cc_start: 0.8769 (tt0) cc_final: 0.8564 (tt0) REVERT: K 103 THR cc_start: 0.9278 (t) cc_final: 0.8822 (p) REVERT: K 118 LYS cc_start: 0.9074 (tppp) cc_final: 0.8769 (tppp) REVERT: K 123 MET cc_start: 0.8393 (tpp) cc_final: 0.8184 (tpp) REVERT: K 132 MET cc_start: 0.8480 (ppp) cc_final: 0.8262 (tmm) REVERT: K 136 ILE cc_start: 0.9188 (mm) cc_final: 0.8889 (mt) REVERT: K 169 TYR cc_start: 0.7309 (m-80) cc_final: 0.6999 (t80) REVERT: K 283 MET cc_start: 0.9118 (mmm) cc_final: 0.8887 (mmm) REVERT: K 316 GLU cc_start: 0.8666 (tp30) cc_final: 0.8406 (tp30) REVERT: L 78 ASN cc_start: 0.7780 (t0) cc_final: 0.6816 (t0) REVERT: L 81 ASP cc_start: 0.8291 (m-30) cc_final: 0.7878 (m-30) REVERT: L 92 ASN cc_start: 0.8580 (m-40) cc_final: 0.8202 (m110) REVERT: L 132 MET cc_start: 0.8050 (ttp) cc_final: 0.7692 (tmm) REVERT: L 208 ILE cc_start: 0.8855 (mt) cc_final: 0.8650 (tp) REVERT: L 210 ARG cc_start: 0.8518 (tmm-80) cc_final: 0.7933 (ttp80) REVERT: L 214 GLU cc_start: 0.7534 (pt0) cc_final: 0.6527 (pt0) REVERT: L 263 GLN cc_start: 0.7933 (mt0) cc_final: 0.6816 (mt0) REVERT: L 265 SER cc_start: 0.8625 (p) cc_final: 0.8285 (t) REVERT: L 313 MET cc_start: 0.6831 (tpt) cc_final: 0.6340 (tpt) REVERT: L 334 GLU cc_start: 0.7735 (pm20) cc_final: 0.7466 (pm20) REVERT: L 360 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7527 (tm-30) outliers start: 61 outliers final: 35 residues processed: 431 average time/residue: 0.1611 time to fit residues: 114.0712 Evaluate side-chains 394 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 358 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 227 MET Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain L residue 217 CYS Chi-restraints excluded: chain L residue 351 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 20 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 226 optimal weight: 2.9990 chunk 319 optimal weight: 0.0170 chunk 182 optimal weight: 4.9990 chunk 143 optimal weight: 20.0000 chunk 307 optimal weight: 0.0980 chunk 93 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A 395 GLN B 10 ASN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.085142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.070519 restraints weight = 81855.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.072663 restraints weight = 41297.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074081 restraints weight = 24867.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075031 restraints weight = 17006.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.075662 restraints weight = 12830.358| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27984 Z= 0.118 Angle : 0.589 10.911 38036 Z= 0.289 Chirality : 0.044 0.206 4284 Planarity : 0.004 0.060 4891 Dihedral : 8.128 96.939 4016 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.43 % Allowed : 12.58 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 3433 helix: 0.94 (0.14), residues: 1435 sheet: -1.49 (0.20), residues: 575 loop : -1.85 (0.17), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 105 TYR 0.022 0.001 TYR C 202 PHE 0.015 0.001 PHE L 352 TRP 0.015 0.001 TRP D 170 HIS 0.007 0.001 HIS H 339 Details of bonding type rmsd covalent geometry : bond 0.00263 (27978) covalent geometry : angle 0.58884 (38036) hydrogen bonds : bond 0.03380 ( 1316) hydrogen bonds : angle 4.44995 ( 3657) Misc. bond : bond 0.00043 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 392 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 PHE cc_start: 0.7704 (t80) cc_final: 0.7429 (t80) REVERT: B 10 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8217 (t0) REVERT: B 154 ASP cc_start: 0.8139 (t0) cc_final: 0.7766 (t70) REVERT: C 153 ASP cc_start: 0.8655 (t0) cc_final: 0.8348 (t0) REVERT: C 169 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8953 (ptpt) REVERT: C 245 ILE cc_start: 0.9378 (mt) cc_final: 0.9076 (tt) REVERT: C 346 MET cc_start: 0.8576 (ttt) cc_final: 0.8372 (ttt) REVERT: D 109 MET cc_start: 0.9124 (tpt) cc_final: 0.8837 (tpp) REVERT: D 157 MET cc_start: 0.6643 (tpp) cc_final: 0.6072 (tpt) REVERT: D 284 MET cc_start: 0.8475 (mmt) cc_final: 0.8203 (mmt) REVERT: F 51 LEU cc_start: 0.8790 (mp) cc_final: 0.8579 (mt) REVERT: F 92 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8399 (tm-30) REVERT: G 80 PHE cc_start: 0.9331 (t80) cc_final: 0.8882 (t80) REVERT: G 131 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8420 (tm-30) REVERT: G 132 LYS cc_start: 0.9329 (mmmt) cc_final: 0.8936 (mmmm) REVERT: H 248 GLU cc_start: 0.7723 (tp30) cc_final: 0.7312 (tp30) REVERT: H 249 LYS cc_start: 0.7717 (tppt) cc_final: 0.7358 (tppt) REVERT: H 299 ASP cc_start: 0.7850 (t0) cc_final: 0.7334 (t0) REVERT: H 349 ARG cc_start: 0.8816 (ttp80) cc_final: 0.8215 (ptm-80) REVERT: H 359 GLU cc_start: 0.8526 (tp30) cc_final: 0.8257 (tp30) REVERT: I 68 LYS cc_start: 0.8768 (mttt) cc_final: 0.8543 (mtmm) REVERT: I 83 GLU cc_start: 0.8243 (pp20) cc_final: 0.7991 (pp20) REVERT: I 123 MET cc_start: 0.8342 (ttm) cc_final: 0.8052 (ttm) REVERT: J 132 MET cc_start: 0.8376 (ppp) cc_final: 0.8104 (ppp) REVERT: K 83 GLU cc_start: 0.8793 (tt0) cc_final: 0.8537 (tt0) REVERT: K 103 THR cc_start: 0.9184 (t) cc_final: 0.8834 (p) REVERT: K 123 MET cc_start: 0.8473 (tpp) cc_final: 0.8240 (tpp) REVERT: K 132 MET cc_start: 0.8505 (ppp) cc_final: 0.8257 (tmm) REVERT: K 136 ILE cc_start: 0.9194 (mm) cc_final: 0.8860 (mt) REVERT: K 169 TYR cc_start: 0.7342 (m-80) cc_final: 0.7006 (t80) REVERT: K 283 MET cc_start: 0.9134 (mmm) cc_final: 0.8865 (mmm) REVERT: L 78 ASN cc_start: 0.7935 (t0) cc_final: 0.7379 (t0) REVERT: L 92 ASN cc_start: 0.8592 (m-40) cc_final: 0.8226 (m-40) REVERT: L 132 MET cc_start: 0.8023 (ttp) cc_final: 0.7780 (tmm) REVERT: L 205 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8478 (pm20) REVERT: L 210 ARG cc_start: 0.8462 (tmm-80) cc_final: 0.7873 (ttp80) REVERT: L 212 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8135 (mt) REVERT: L 214 GLU cc_start: 0.7547 (pt0) cc_final: 0.6470 (pt0) REVERT: L 263 GLN cc_start: 0.7918 (mt0) cc_final: 0.6762 (mt0) REVERT: L 265 SER cc_start: 0.8606 (p) cc_final: 0.8273 (t) REVERT: L 313 MET cc_start: 0.6839 (tpt) cc_final: 0.6476 (tpt) REVERT: L 334 GLU cc_start: 0.7665 (pm20) cc_final: 0.7421 (pm20) REVERT: L 360 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7474 (tm-30) outliers start: 69 outliers final: 39 residues processed: 428 average time/residue: 0.1590 time to fit residues: 112.6094 Evaluate side-chains 395 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 352 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 355 MET Chi-restraints excluded: chain L residue 115 ASN Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 217 CYS Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 213 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 269 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 331 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 251 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 153 optimal weight: 30.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 295 ASN A 316 GLN A 395 GLN B 10 ASN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN C 343 HIS ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN H 277 ASN ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 263 GLN K 88 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.078072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.063088 restraints weight = 83231.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.065078 restraints weight = 42697.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.066419 restraints weight = 26255.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.067330 restraints weight = 18311.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067935 restraints weight = 14034.454| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 27984 Z= 0.273 Angle : 0.712 11.578 38036 Z= 0.359 Chirality : 0.048 0.200 4284 Planarity : 0.005 0.069 4891 Dihedral : 8.383 95.423 4016 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.38 % Allowed : 13.57 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.15), residues: 3433 helix: 0.79 (0.14), residues: 1436 sheet: -1.38 (0.20), residues: 579 loop : -1.84 (0.17), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 297 TYR 0.016 0.002 TYR C 202 PHE 0.021 0.002 PHE B 322 TRP 0.019 0.002 TRP I 79 HIS 0.010 0.001 HIS H 339 Details of bonding type rmsd covalent geometry : bond 0.00628 (27978) covalent geometry : angle 0.71187 (38036) hydrogen bonds : bond 0.04633 ( 1316) hydrogen bonds : angle 4.80973 ( 3657) Misc. bond : bond 0.00095 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 368 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 VAL cc_start: 0.9252 (m) cc_final: 0.8965 (p) REVERT: B 127 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: B 154 ASP cc_start: 0.8469 (t0) cc_final: 0.8201 (t70) REVERT: C 153 ASP cc_start: 0.8786 (t0) cc_final: 0.8410 (t0) REVERT: C 169 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8959 (ptpt) REVERT: C 177 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8737 (t) REVERT: C 245 ILE cc_start: 0.9372 (mt) cc_final: 0.9041 (tt) REVERT: C 346 MET cc_start: 0.8710 (ttt) cc_final: 0.8494 (ttt) REVERT: D 194 LYS cc_start: 0.8996 (ttpt) cc_final: 0.8660 (ttpt) REVERT: F 89 LYS cc_start: 0.8863 (tptp) cc_final: 0.8214 (tppp) REVERT: F 92 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8494 (tm-30) REVERT: G 42 GLN cc_start: 0.8889 (mt0) cc_final: 0.8605 (mt0) REVERT: G 132 LYS cc_start: 0.9391 (mmmt) cc_final: 0.9117 (mmmm) REVERT: G 151 ASP cc_start: 0.8469 (p0) cc_final: 0.7949 (p0) REVERT: H 248 GLU cc_start: 0.7816 (tp30) cc_final: 0.7281 (tp30) REVERT: H 277 ASN cc_start: 0.8626 (m110) cc_final: 0.8405 (m-40) REVERT: H 299 ASP cc_start: 0.7922 (t0) cc_final: 0.7466 (t0) REVERT: H 349 ARG cc_start: 0.8840 (ttp80) cc_final: 0.8109 (ptm-80) REVERT: H 359 GLU cc_start: 0.8695 (tp30) cc_final: 0.8441 (tp30) REVERT: I 270 GLU cc_start: 0.7278 (pm20) cc_final: 0.6790 (pt0) REVERT: J 132 MET cc_start: 0.8433 (ppp) cc_final: 0.8198 (ppp) REVERT: J 255 PHE cc_start: 0.7428 (m-80) cc_final: 0.7156 (m-10) REVERT: J 288 ASP cc_start: 0.7946 (p0) cc_final: 0.7507 (p0) REVERT: K 103 THR cc_start: 0.9262 (t) cc_final: 0.8907 (p) REVERT: K 123 MET cc_start: 0.8543 (tpp) cc_final: 0.8295 (tpp) REVERT: K 169 TYR cc_start: 0.7542 (m-80) cc_final: 0.6931 (t80) REVERT: K 217 CYS cc_start: 0.8666 (m) cc_final: 0.7997 (m) REVERT: K 283 MET cc_start: 0.9062 (mmm) cc_final: 0.8723 (mmm) REVERT: L 78 ASN cc_start: 0.8165 (t0) cc_final: 0.6911 (t0) REVERT: L 81 ASP cc_start: 0.8518 (m-30) cc_final: 0.7991 (m-30) REVERT: L 92 ASN cc_start: 0.8645 (m-40) cc_final: 0.8267 (m-40) REVERT: L 205 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8680 (pm20) REVERT: L 208 ILE cc_start: 0.8970 (mt) cc_final: 0.8745 (tp) REVERT: L 210 ARG cc_start: 0.8629 (tmm-80) cc_final: 0.7967 (ttp80) REVERT: L 214 GLU cc_start: 0.7829 (pt0) cc_final: 0.6878 (pt0) REVERT: L 263 GLN cc_start: 0.8020 (mt0) cc_final: 0.7090 (mt0) REVERT: L 334 GLU cc_start: 0.7790 (pm20) cc_final: 0.7573 (pm20) REVERT: L 360 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7733 (tm-30) outliers start: 96 outliers final: 58 residues processed: 433 average time/residue: 0.1560 time to fit residues: 111.9974 Evaluate side-chains 398 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 336 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 288 ARG Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 305 MET Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 267 ILE Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 227 MET Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 115 ASN Chi-restraints excluded: chain L residue 173 HIS Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 217 CYS Chi-restraints excluded: chain L residue 274 ILE Chi-restraints excluded: chain L residue 351 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 284 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 345 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 HIS ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN I 360 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.075767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.060934 restraints weight = 83614.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.062876 restraints weight = 42781.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.064168 restraints weight = 26265.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.065047 restraints weight = 18260.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.065638 restraints weight = 14002.377| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 27984 Z= 0.279 Angle : 0.726 10.941 38036 Z= 0.366 Chirality : 0.048 0.206 4284 Planarity : 0.005 0.065 4891 Dihedral : 8.489 92.737 4016 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.84 % Allowed : 14.73 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.15), residues: 3433 helix: 0.66 (0.14), residues: 1436 sheet: -1.28 (0.20), residues: 585 loop : -1.82 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 239 TYR 0.017 0.002 TYR L 337 PHE 0.020 0.002 PHE A 31 TRP 0.019 0.002 TRP I 79 HIS 0.011 0.001 HIS H 339 Details of bonding type rmsd covalent geometry : bond 0.00645 (27978) covalent geometry : angle 0.72614 (38036) hydrogen bonds : bond 0.04824 ( 1316) hydrogen bonds : angle 4.92430 ( 3657) Misc. bond : bond 0.00105 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 353 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.9516 (tt) cc_final: 0.9216 (tp) REVERT: B 28 GLN cc_start: 0.8921 (pp30) cc_final: 0.8347 (pp30) REVERT: B 127 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: B 154 ASP cc_start: 0.8516 (t0) cc_final: 0.8221 (t70) REVERT: C 66 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8885 (mppt) REVERT: C 153 ASP cc_start: 0.8743 (t0) cc_final: 0.8410 (t0) REVERT: C 177 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8917 (t) REVERT: C 346 MET cc_start: 0.8776 (ttt) cc_final: 0.8555 (ttt) REVERT: D 109 MET cc_start: 0.9081 (tpt) cc_final: 0.8802 (tpp) REVERT: D 157 MET cc_start: 0.7089 (tpp) cc_final: 0.6661 (tpp) REVERT: F 89 LYS cc_start: 0.8819 (tptp) cc_final: 0.8125 (tppp) REVERT: F 92 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8577 (tm-30) REVERT: G 132 LYS cc_start: 0.9380 (mmmt) cc_final: 0.9122 (mmmm) REVERT: G 151 ASP cc_start: 0.8340 (p0) cc_final: 0.7953 (p0) REVERT: H 248 GLU cc_start: 0.7894 (tp30) cc_final: 0.7687 (tp30) REVERT: H 277 ASN cc_start: 0.8689 (m110) cc_final: 0.8416 (m-40) REVERT: H 299 ASP cc_start: 0.7899 (t0) cc_final: 0.7458 (t0) REVERT: H 359 GLU cc_start: 0.8735 (tp30) cc_final: 0.8494 (tp30) REVERT: I 216 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9154 (pp) REVERT: I 283 MET cc_start: 0.9074 (mmp) cc_final: 0.8628 (mmp) REVERT: J 132 MET cc_start: 0.8374 (ppp) cc_final: 0.8148 (ppp) REVERT: J 165 ILE cc_start: 0.9641 (mt) cc_final: 0.9258 (mm) REVERT: J 288 ASP cc_start: 0.7934 (p0) cc_final: 0.7531 (p0) REVERT: J 325 MET cc_start: 0.8597 (tpp) cc_final: 0.8198 (tpp) REVERT: K 103 THR cc_start: 0.9259 (t) cc_final: 0.8977 (p) REVERT: K 169 TYR cc_start: 0.7661 (m-80) cc_final: 0.7424 (m-80) REVERT: K 217 CYS cc_start: 0.8676 (m) cc_final: 0.7968 (m) REVERT: K 283 MET cc_start: 0.9026 (mmm) cc_final: 0.8685 (mmm) REVERT: L 92 ASN cc_start: 0.8649 (m-40) cc_final: 0.8299 (m-40) REVERT: L 205 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8650 (pm20) REVERT: L 208 ILE cc_start: 0.9019 (mt) cc_final: 0.8806 (tp) REVERT: L 210 ARG cc_start: 0.8678 (tmm-80) cc_final: 0.8468 (ttp80) REVERT: L 263 GLN cc_start: 0.7924 (mt0) cc_final: 0.7072 (mt0) REVERT: L 360 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7955 (tm-30) outliers start: 109 outliers final: 71 residues processed: 427 average time/residue: 0.1553 time to fit residues: 110.8324 Evaluate side-chains 397 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 321 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 73 CYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 305 MET Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 227 MET Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain L residue 115 ASN Chi-restraints excluded: chain L residue 173 HIS Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 217 CYS Chi-restraints excluded: chain L residue 351 THR Chi-restraints excluded: chain L residue 370 VAL Chi-restraints excluded: chain M residue 7 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 176 optimal weight: 3.9990 chunk 328 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 305 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 297 optimal weight: 0.7980 chunk 291 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN B 173 HIS B 319 GLN ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN I 360 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.079395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.064406 restraints weight = 82527.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.066420 restraints weight = 41988.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067798 restraints weight = 25639.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.068715 restraints weight = 17730.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.069299 restraints weight = 13526.935| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27984 Z= 0.143 Angle : 0.651 10.995 38036 Z= 0.322 Chirality : 0.045 0.255 4284 Planarity : 0.004 0.062 4891 Dihedral : 8.317 91.030 4016 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.03 % Allowed : 16.35 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.15), residues: 3433 helix: 0.86 (0.14), residues: 1435 sheet: -1.08 (0.21), residues: 587 loop : -1.66 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 372 TYR 0.017 0.001 TYR L 337 PHE 0.017 0.001 PHE F 93 TRP 0.018 0.001 TRP D 170 HIS 0.008 0.001 HIS H 339 Details of bonding type rmsd covalent geometry : bond 0.00324 (27978) covalent geometry : angle 0.65100 (38036) hydrogen bonds : bond 0.03946 ( 1316) hydrogen bonds : angle 4.63600 ( 3657) Misc. bond : bond 0.00061 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 365 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.8745 (mp10) cc_final: 0.8403 (mp10) REVERT: B 28 GLN cc_start: 0.8935 (pp30) cc_final: 0.8341 (pp30) REVERT: B 127 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: B 154 ASP cc_start: 0.8425 (t0) cc_final: 0.7999 (t70) REVERT: B 219 VAL cc_start: 0.9628 (t) cc_final: 0.9412 (m) REVERT: C 66 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8890 (mppt) REVERT: C 153 ASP cc_start: 0.8747 (t0) cc_final: 0.8388 (t0) REVERT: C 177 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8927 (t) REVERT: C 245 ILE cc_start: 0.9359 (mt) cc_final: 0.9015 (tt) REVERT: C 346 MET cc_start: 0.8691 (ttt) cc_final: 0.8480 (ttt) REVERT: D 109 MET cc_start: 0.9058 (tpt) cc_final: 0.8778 (tpp) REVERT: D 157 MET cc_start: 0.7022 (tpp) cc_final: 0.6239 (tpp) REVERT: F 89 LYS cc_start: 0.8812 (tptp) cc_final: 0.8155 (tppp) REVERT: F 91 MET cc_start: 0.8511 (mmm) cc_final: 0.8288 (mmm) REVERT: F 92 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8570 (tm-30) REVERT: G 80 PHE cc_start: 0.9430 (t80) cc_final: 0.8977 (t80) REVERT: G 132 LYS cc_start: 0.9359 (mmmt) cc_final: 0.9122 (mmmm) REVERT: G 151 ASP cc_start: 0.8318 (p0) cc_final: 0.7891 (p0) REVERT: H 248 GLU cc_start: 0.7734 (tp30) cc_final: 0.7509 (tp30) REVERT: H 277 ASN cc_start: 0.8585 (m110) cc_final: 0.8379 (m-40) REVERT: H 359 GLU cc_start: 0.8675 (tp30) cc_final: 0.8431 (tp30) REVERT: I 270 GLU cc_start: 0.8008 (mp0) cc_final: 0.7802 (mp0) REVERT: J 82 MET cc_start: 0.9028 (tpt) cc_final: 0.8696 (mmm) REVERT: J 132 MET cc_start: 0.8292 (ppp) cc_final: 0.8067 (ppp) REVERT: J 165 ILE cc_start: 0.9656 (mt) cc_final: 0.9449 (mm) REVERT: K 16 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9142 (pp) REVERT: K 103 THR cc_start: 0.9323 (t) cc_final: 0.8981 (p) REVERT: K 123 MET cc_start: 0.8595 (tpp) cc_final: 0.8393 (tpp) REVERT: K 169 TYR cc_start: 0.7500 (m-80) cc_final: 0.6970 (t80) REVERT: K 283 MET cc_start: 0.9031 (mmm) cc_final: 0.8630 (mmm) REVERT: K 316 GLU cc_start: 0.8680 (tp30) cc_final: 0.8390 (tp30) REVERT: L 59 GLN cc_start: 0.8662 (tp40) cc_final: 0.8401 (tp40) REVERT: L 78 ASN cc_start: 0.8124 (t0) cc_final: 0.7652 (t0) REVERT: L 92 ASN cc_start: 0.8635 (m-40) cc_final: 0.8304 (m-40) REVERT: L 132 MET cc_start: 0.8034 (tmm) cc_final: 0.7823 (tmm) REVERT: L 175 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8318 (mt) REVERT: L 205 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8328 (pm20) REVERT: L 208 ILE cc_start: 0.9004 (mt) cc_final: 0.8666 (tp) REVERT: L 263 GLN cc_start: 0.7819 (mt0) cc_final: 0.6921 (mt0) REVERT: L 360 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7885 (tm-30) outliers start: 86 outliers final: 58 residues processed: 425 average time/residue: 0.1547 time to fit residues: 109.6954 Evaluate side-chains 400 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 336 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 288 ARG Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 319 HIS Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 267 ILE Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 227 MET Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain L residue 115 ASN Chi-restraints excluded: chain L residue 173 HIS Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 217 CYS Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 29 optimal weight: 4.9990 chunk 302 optimal weight: 0.8980 chunk 298 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 198 optimal weight: 8.9990 chunk 322 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 ASN G 119 GLN I 137 GLN K 40 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.077351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.062360 restraints weight = 82506.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.064354 restraints weight = 42272.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.065684 restraints weight = 25888.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.066572 restraints weight = 18017.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.067180 restraints weight = 13823.229| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 27984 Z= 0.219 Angle : 0.700 13.197 38036 Z= 0.348 Chirality : 0.046 0.197 4284 Planarity : 0.005 0.059 4891 Dihedral : 8.290 90.452 4016 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.35 % Allowed : 16.81 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.15), residues: 3433 helix: 0.83 (0.14), residues: 1443 sheet: -1.10 (0.21), residues: 585 loop : -1.63 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 380 TYR 0.016 0.001 TYR L 337 PHE 0.020 0.002 PHE A 31 TRP 0.043 0.002 TRP J 340 HIS 0.009 0.001 HIS H 339 Details of bonding type rmsd covalent geometry : bond 0.00508 (27978) covalent geometry : angle 0.70043 (38036) hydrogen bonds : bond 0.04392 ( 1316) hydrogen bonds : angle 4.74596 ( 3657) Misc. bond : bond 0.00080 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 341 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASN cc_start: 0.9118 (t0) cc_final: 0.8766 (t0) REVERT: A 145 ILE cc_start: 0.9547 (tt) cc_final: 0.9255 (tp) REVERT: A 160 GLN cc_start: 0.8579 (mp10) cc_final: 0.8273 (mp10) REVERT: B 28 GLN cc_start: 0.8942 (pp30) cc_final: 0.8369 (pp30) REVERT: B 127 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8183 (m-80) REVERT: B 154 ASP cc_start: 0.8464 (t0) cc_final: 0.8156 (t70) REVERT: C 66 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8874 (mppt) REVERT: C 153 ASP cc_start: 0.8724 (t0) cc_final: 0.8383 (t0) REVERT: C 245 ILE cc_start: 0.9353 (mt) cc_final: 0.9012 (tt) REVERT: C 286 HIS cc_start: 0.9120 (OUTLIER) cc_final: 0.7850 (p-80) REVERT: C 346 MET cc_start: 0.8802 (ttt) cc_final: 0.8590 (ttt) REVERT: D 157 MET cc_start: 0.7122 (tpp) cc_final: 0.6866 (tpp) REVERT: F 89 LYS cc_start: 0.8840 (tptp) cc_final: 0.8204 (tppp) REVERT: F 91 MET cc_start: 0.8500 (mmm) cc_final: 0.8204 (mmm) REVERT: F 92 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8585 (tm-30) REVERT: G 80 PHE cc_start: 0.9460 (t80) cc_final: 0.9060 (t80) REVERT: G 132 LYS cc_start: 0.9373 (mmmt) cc_final: 0.9132 (mmmm) REVERT: G 151 ASP cc_start: 0.8320 (p0) cc_final: 0.7995 (p0) REVERT: H 248 GLU cc_start: 0.7755 (tp30) cc_final: 0.7510 (tp30) REVERT: H 359 GLU cc_start: 0.8737 (tp30) cc_final: 0.8487 (tp30) REVERT: I 270 GLU cc_start: 0.7850 (mp0) cc_final: 0.7645 (mp0) REVERT: I 325 MET cc_start: 0.8728 (mmp) cc_final: 0.8434 (mmm) REVERT: J 82 MET cc_start: 0.9059 (tpt) cc_final: 0.8747 (mmm) REVERT: J 132 MET cc_start: 0.8316 (ppp) cc_final: 0.8114 (ppp) REVERT: J 165 ILE cc_start: 0.9671 (mt) cc_final: 0.9454 (mm) REVERT: J 288 ASP cc_start: 0.7966 (p0) cc_final: 0.7578 (p0) REVERT: K 16 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9115 (pp) REVERT: K 103 THR cc_start: 0.9325 (t) cc_final: 0.9040 (p) REVERT: K 217 CYS cc_start: 0.8594 (m) cc_final: 0.7736 (m) REVERT: K 283 MET cc_start: 0.9036 (mmm) cc_final: 0.8597 (mmm) REVERT: L 59 GLN cc_start: 0.8774 (tp40) cc_final: 0.8441 (tp40) REVERT: L 78 ASN cc_start: 0.8170 (t0) cc_final: 0.7862 (t0) REVERT: L 92 ASN cc_start: 0.8675 (m-40) cc_final: 0.8345 (m-40) REVERT: L 132 MET cc_start: 0.8008 (tmm) cc_final: 0.7802 (tmm) REVERT: L 214 GLU cc_start: 0.7867 (pt0) cc_final: 0.7384 (pt0) REVERT: L 263 GLN cc_start: 0.7967 (mt0) cc_final: 0.7105 (mt0) REVERT: L 360 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7932 (tm-30) outliers start: 95 outliers final: 70 residues processed: 410 average time/residue: 0.1580 time to fit residues: 109.0984 Evaluate side-chains 403 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 329 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 73 CYS Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 288 ARG Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 305 MET Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 267 ILE Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 227 MET Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 115 ASN Chi-restraints excluded: chain L residue 173 HIS Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 217 CYS Chi-restraints excluded: chain L residue 351 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 26 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 269 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 237 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 216 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 ASN ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.079701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.064610 restraints weight = 82544.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.066653 restraints weight = 41671.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.068026 restraints weight = 25375.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.068943 restraints weight = 17554.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.069563 restraints weight = 13409.413| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27984 Z= 0.130 Angle : 0.663 17.245 38036 Z= 0.324 Chirality : 0.044 0.188 4284 Planarity : 0.004 0.060 4891 Dihedral : 8.154 88.883 4016 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.61 % Allowed : 17.86 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3433 helix: 0.92 (0.14), residues: 1440 sheet: -1.00 (0.21), residues: 588 loop : -1.54 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 372 TYR 0.022 0.001 TYR F 8 PHE 0.028 0.001 PHE A 399 TRP 0.039 0.002 TRP J 340 HIS 0.006 0.001 HIS H 339 Details of bonding type rmsd covalent geometry : bond 0.00297 (27978) covalent geometry : angle 0.66267 (38036) hydrogen bonds : bond 0.03775 ( 1316) hydrogen bonds : angle 4.57817 ( 3657) Misc. bond : bond 0.00057 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 364 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASN cc_start: 0.9056 (t0) cc_final: 0.8681 (t0) REVERT: B 28 GLN cc_start: 0.8931 (pp30) cc_final: 0.8341 (pp30) REVERT: B 127 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.8023 (m-80) REVERT: B 154 ASP cc_start: 0.8417 (t0) cc_final: 0.7962 (t70) REVERT: C 66 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8850 (mppt) REVERT: C 153 ASP cc_start: 0.8714 (t0) cc_final: 0.8357 (t0) REVERT: C 207 TRP cc_start: 0.8263 (m100) cc_final: 0.7981 (m100) REVERT: C 346 MET cc_start: 0.8639 (ttt) cc_final: 0.8428 (ttt) REVERT: D 109 MET cc_start: 0.9120 (tpt) cc_final: 0.8700 (tpp) REVERT: D 157 MET cc_start: 0.6971 (tpp) cc_final: 0.6732 (tpp) REVERT: D 173 HIS cc_start: 0.7859 (t70) cc_final: 0.7606 (t70) REVERT: F 89 LYS cc_start: 0.8802 (tptp) cc_final: 0.8176 (tppp) REVERT: F 91 MET cc_start: 0.8449 (mmm) cc_final: 0.8216 (mmm) REVERT: F 92 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8592 (tm-30) REVERT: G 80 PHE cc_start: 0.9397 (t80) cc_final: 0.8942 (t80) REVERT: G 119 GLN cc_start: 0.9222 (pp30) cc_final: 0.8682 (pp30) REVERT: G 132 LYS cc_start: 0.9375 (mmmt) cc_final: 0.9052 (mmmm) REVERT: G 151 ASP cc_start: 0.8308 (p0) cc_final: 0.7952 (p0) REVERT: H 260 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8317 (mm-40) REVERT: H 359 GLU cc_start: 0.8707 (tp30) cc_final: 0.8442 (tp30) REVERT: I 325 MET cc_start: 0.8715 (mmp) cc_final: 0.8467 (mmm) REVERT: J 132 MET cc_start: 0.8254 (ppp) cc_final: 0.8047 (ppp) REVERT: J 325 MET cc_start: 0.8507 (tpp) cc_final: 0.8111 (tpp) REVERT: K 16 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9117 (pp) REVERT: K 103 THR cc_start: 0.9323 (t) cc_final: 0.9068 (p) REVERT: K 123 MET cc_start: 0.8589 (tpp) cc_final: 0.8330 (tpp) REVERT: K 169 TYR cc_start: 0.7551 (m-80) cc_final: 0.6932 (t80) REVERT: L 59 GLN cc_start: 0.8681 (tp40) cc_final: 0.8400 (tp40) REVERT: L 78 ASN cc_start: 0.8077 (t0) cc_final: 0.7227 (t0) REVERT: L 92 ASN cc_start: 0.8660 (m-40) cc_final: 0.8345 (m-40) REVERT: L 208 ILE cc_start: 0.8885 (mt) cc_final: 0.8613 (tp) REVERT: L 214 GLU cc_start: 0.7743 (pt0) cc_final: 0.7247 (pt0) REVERT: L 263 GLN cc_start: 0.7867 (mt0) cc_final: 0.6999 (mt0) REVERT: L 360 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7851 (tm-30) outliers start: 74 outliers final: 62 residues processed: 414 average time/residue: 0.1573 time to fit residues: 108.4222 Evaluate side-chains 403 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 338 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 73 CYS Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 288 ARG Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 227 MET Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 115 ASN Chi-restraints excluded: chain L residue 173 HIS Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 217 CYS Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 298 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 240 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.077865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.062812 restraints weight = 82702.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.064808 restraints weight = 42136.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.066148 restraints weight = 25806.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.067019 restraints weight = 17986.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.067643 restraints weight = 13843.726| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 27984 Z= 0.214 Angle : 0.713 14.017 38036 Z= 0.353 Chirality : 0.047 0.331 4284 Planarity : 0.005 0.058 4891 Dihedral : 8.172 88.894 4016 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.75 % Allowed : 17.90 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 3433 helix: 0.85 (0.14), residues: 1442 sheet: -1.01 (0.21), residues: 585 loop : -1.52 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 210 TYR 0.025 0.002 TYR F 8 PHE 0.033 0.002 PHE A 287 TRP 0.035 0.002 TRP J 340 HIS 0.007 0.001 HIS H 339 Details of bonding type rmsd covalent geometry : bond 0.00500 (27978) covalent geometry : angle 0.71330 (38036) hydrogen bonds : bond 0.04372 ( 1316) hydrogen bonds : angle 4.73522 ( 3657) Misc. bond : bond 0.00073 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 347 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASN cc_start: 0.9041 (t0) cc_final: 0.8746 (t0) REVERT: A 145 ILE cc_start: 0.9551 (tt) cc_final: 0.9176 (tp) REVERT: B 28 GLN cc_start: 0.8926 (pp30) cc_final: 0.8372 (pp30) REVERT: B 127 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: B 154 ASP cc_start: 0.8454 (t0) cc_final: 0.8023 (t70) REVERT: C 66 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8872 (mppt) REVERT: C 153 ASP cc_start: 0.8708 (t0) cc_final: 0.8377 (t0) REVERT: C 207 TRP cc_start: 0.8252 (m100) cc_final: 0.8010 (m100) REVERT: C 346 MET cc_start: 0.8763 (ttt) cc_final: 0.8561 (ttt) REVERT: D 109 MET cc_start: 0.9104 (tpt) cc_final: 0.8717 (tpp) REVERT: D 157 MET cc_start: 0.6991 (tpp) cc_final: 0.6648 (tpp) REVERT: F 89 LYS cc_start: 0.8888 (tptp) cc_final: 0.8370 (tppp) REVERT: F 91 MET cc_start: 0.8506 (mmm) cc_final: 0.8282 (mmm) REVERT: F 92 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8908 (tm-30) REVERT: F 143 ASP cc_start: 0.7435 (t70) cc_final: 0.7161 (t0) REVERT: G 80 PHE cc_start: 0.9448 (t80) cc_final: 0.8987 (t80) REVERT: G 119 GLN cc_start: 0.9296 (pp30) cc_final: 0.8930 (pp30) REVERT: G 132 LYS cc_start: 0.9346 (mmmt) cc_final: 0.9108 (mmmm) REVERT: G 151 ASP cc_start: 0.8312 (p0) cc_final: 0.8055 (p0) REVERT: H 248 GLU cc_start: 0.7005 (tp30) cc_final: 0.6793 (tm-30) REVERT: H 260 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8338 (mm-40) REVERT: H 359 GLU cc_start: 0.8649 (tp30) cc_final: 0.8402 (tp30) REVERT: I 325 MET cc_start: 0.8733 (mmp) cc_final: 0.8490 (mmm) REVERT: J 325 MET cc_start: 0.8536 (tpp) cc_final: 0.8133 (tpp) REVERT: K 16 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9114 (pp) REVERT: K 103 THR cc_start: 0.9289 (t) cc_final: 0.9082 (p) REVERT: K 169 TYR cc_start: 0.7619 (m-80) cc_final: 0.6910 (t80) REVERT: K 283 MET cc_start: 0.8958 (mmm) cc_final: 0.8638 (mmm) REVERT: L 59 GLN cc_start: 0.8731 (tp40) cc_final: 0.8431 (tp40) REVERT: L 78 ASN cc_start: 0.7995 (t0) cc_final: 0.7514 (t0) REVERT: L 81 ASP cc_start: 0.8994 (p0) cc_final: 0.8553 (p0) REVERT: L 92 ASN cc_start: 0.8628 (m-40) cc_final: 0.8293 (m-40) REVERT: L 208 ILE cc_start: 0.8945 (mt) cc_final: 0.8663 (tp) REVERT: L 214 GLU cc_start: 0.7823 (pt0) cc_final: 0.7256 (pt0) REVERT: L 263 GLN cc_start: 0.7941 (mt0) cc_final: 0.7086 (mt0) REVERT: L 360 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7916 (tm-30) outliers start: 78 outliers final: 64 residues processed: 402 average time/residue: 0.1518 time to fit residues: 102.5125 Evaluate side-chains 401 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 334 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 73 CYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 227 MET Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 115 ASN Chi-restraints excluded: chain L residue 173 HIS Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 217 CYS Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 246 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 282 optimal weight: 0.1980 chunk 220 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 279 optimal weight: 1.9990 chunk 289 optimal weight: 0.9990 chunk 143 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.080411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.065305 restraints weight = 81648.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.067367 restraints weight = 41033.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.068715 restraints weight = 24878.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.069661 restraints weight = 17255.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.070291 restraints weight = 13123.751| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27984 Z= 0.126 Angle : 0.675 12.125 38036 Z= 0.329 Chirality : 0.045 0.242 4284 Planarity : 0.004 0.060 4891 Dihedral : 8.030 88.941 4016 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.57 % Allowed : 18.25 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.15), residues: 3433 helix: 0.93 (0.14), residues: 1430 sheet: -0.90 (0.21), residues: 590 loop : -1.45 (0.17), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 372 TYR 0.030 0.001 TYR F 8 PHE 0.030 0.001 PHE A 287 TRP 0.034 0.002 TRP J 340 HIS 0.005 0.001 HIS H 339 Details of bonding type rmsd covalent geometry : bond 0.00284 (27978) covalent geometry : angle 0.67457 (38036) hydrogen bonds : bond 0.03652 ( 1316) hydrogen bonds : angle 4.59334 ( 3657) Misc. bond : bond 0.00053 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4456.75 seconds wall clock time: 77 minutes 44.31 seconds (4664.31 seconds total)