Starting phenix.real_space_refine on Fri Aug 7 10:03:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9skj_54966/08_2026/9skj_54966.cif Found real_map, /net/cci-nas-00/data/ceres_data/9skj_54966/08_2026/9skj_54966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9skj_54966/08_2026/9skj_54966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9skj_54966/08_2026/9skj_54966.map" model { file = "/net/cci-nas-00/data/ceres_data/9skj_54966/08_2026/9skj_54966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9skj_54966/08_2026/9skj_54966.cif" } resolution = 3.1 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= 0.011 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 13004 2.51 5 N 3367 2.21 5 O 3873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20288 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2451 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "C" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "D" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "E" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "F" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "G" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "H" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2243 Classifications: {'peptide': 280} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 266} Time building chain proxies: 3.97, per 1000 atoms: 0.20 Number of scatterers: 20288 At special positions: 0 Unit cell: (132.48, 139.104, 178.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 3873 8.00 N 3367 7.00 C 13004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 625.1 milliseconds 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4946 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 8 sheets defined 67.2% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 27 through 39 removed outlier: 3.599A pdb=" N ASN A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 61 removed outlier: 3.533A pdb=" N LEU A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU A 56 " --> pdb=" O CYS A 52 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 78 Processing helix chain 'A' and resid 79 through 92 removed outlier: 5.094A pdb=" N LYS A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 126 through 134 removed outlier: 3.559A pdb=" N GLN A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 150 removed outlier: 4.450A pdb=" N ARG A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 161 Processing helix chain 'A' and resid 180 through 251 removed outlier: 4.284A pdb=" N ALA A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 289 through 294 removed outlier: 6.963A pdb=" N ALA A 292 " --> pdb=" O THR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.556A pdb=" N ARG A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 356 removed outlier: 4.532A pdb=" N LEU A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 42 through 61 Processing helix chain 'B' and resid 75 through 78 Processing helix chain 'B' and resid 79 through 91 removed outlier: 4.440A pdb=" N LYS B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 91 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 124 through 135 removed outlier: 3.731A pdb=" N MET B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 139 No H-bonds generated for 'chain 'B' and resid 137 through 139' Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'B' and resid 180 through 251 Processing helix chain 'B' and resid 277 through 287 Processing helix chain 'B' and resid 290 through 294 removed outlier: 3.572A pdb=" N LEU B 294 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 311 Processing helix chain 'B' and resid 337 through 356 removed outlier: 3.539A pdb=" N GLY B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 44 through 61 Processing helix chain 'C' and resid 75 through 78 Processing helix chain 'C' and resid 79 through 91 removed outlier: 4.843A pdb=" N LYS C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 124 through 135 Processing helix chain 'C' and resid 139 through 150 removed outlier: 4.140A pdb=" N ARG C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 180 through 251 Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.762A pdb=" N LEU C 294 " --> pdb=" O VAL C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 311 Processing helix chain 'C' and resid 337 through 356 removed outlier: 3.564A pdb=" N ILE C 341 " --> pdb=" O GLY C 337 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY C 355 " --> pdb=" O MET C 351 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 356 " --> pdb=" O VAL C 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 40 removed outlier: 4.064A pdb=" N VAL D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TRP D 37 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 59 removed outlier: 4.122A pdb=" N MET D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 85 removed outlier: 3.637A pdb=" N SER D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 140 through 150 Processing helix chain 'D' and resid 180 through 251 removed outlier: 3.518A pdb=" N VAL D 207 " --> pdb=" O SER D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 286 Processing helix chain 'D' and resid 295 through 310 Processing helix chain 'D' and resid 337 through 354 Processing helix chain 'E' and resid 28 through 39 Processing helix chain 'E' and resid 39 through 59 removed outlier: 3.502A pdb=" N VAL E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 86 Processing helix chain 'E' and resid 86 through 92 removed outlier: 3.761A pdb=" N LEU E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 112 Processing helix chain 'E' and resid 113 through 123 Processing helix chain 'E' and resid 124 through 134 Processing helix chain 'E' and resid 140 through 150 Processing helix chain 'E' and resid 160 through 164 Processing helix chain 'E' and resid 180 through 250 removed outlier: 3.991A pdb=" N ALA E 184 " --> pdb=" O THR E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 287 removed outlier: 4.373A pdb=" N GLY E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE E 278 " --> pdb=" O GLY E 274 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 311 removed outlier: 3.501A pdb=" N ARG E 299 " --> pdb=" O ASN E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 350 Processing helix chain 'F' and resid 28 through 39 removed outlier: 4.424A pdb=" N LEU F 32 " --> pdb=" O ASP F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 61 removed outlier: 3.731A pdb=" N VAL F 46 " --> pdb=" O THR F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 85 Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 99 through 112 Processing helix chain 'F' and resid 113 through 124 Processing helix chain 'F' and resid 124 through 134 Processing helix chain 'F' and resid 137 through 150 removed outlier: 4.319A pdb=" N HIS F 142 " --> pdb=" O GLU F 138 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 250 removed outlier: 3.508A pdb=" N VAL F 207 " --> pdb=" O SER F 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA F 250 " --> pdb=" O ILE F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 260 removed outlier: 3.828A pdb=" N SER F 258 " --> pdb=" O PRO F 255 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY F 260 " --> pdb=" O TYR F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 287 removed outlier: 3.563A pdb=" N ALA F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 311 Processing helix chain 'F' and resid 337 through 356 removed outlier: 3.532A pdb=" N VAL F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY F 356 " --> pdb=" O VAL F 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 40 removed outlier: 3.720A pdb=" N ALA G 39 " --> pdb=" O VAL G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 53 removed outlier: 4.214A pdb=" N ALA G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL G 46 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA G 53 " --> pdb=" O ALA G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 61 Processing helix chain 'G' and resid 82 through 85 Processing helix chain 'G' and resid 86 through 91 Processing helix chain 'G' and resid 99 through 112 Processing helix chain 'G' and resid 113 through 124 removed outlier: 3.878A pdb=" N LEU G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 134 Processing helix chain 'G' and resid 140 through 150 removed outlier: 3.557A pdb=" N GLU G 150 " --> pdb=" O VAL G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 162 removed outlier: 3.540A pdb=" N LYS G 162 " --> pdb=" O ASN G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 250 removed outlier: 3.739A pdb=" N GLN G 185 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS G 219 " --> pdb=" O THR G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 260 removed outlier: 4.162A pdb=" N SER G 258 " --> pdb=" O PRO G 255 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY G 260 " --> pdb=" O TYR G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 286 removed outlier: 3.597A pdb=" N ARG G 280 " --> pdb=" O ASP G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 311 removed outlier: 3.745A pdb=" N LYS G 310 " --> pdb=" O GLU G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 356 removed outlier: 3.734A pdb=" N ILE G 343 " --> pdb=" O ALA G 339 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU G 344 " --> pdb=" O ILE G 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 78 Processing helix chain 'H' and resid 79 through 92 removed outlier: 4.498A pdb=" N LYS H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 112 Processing helix chain 'H' and resid 113 through 122 Processing helix chain 'H' and resid 124 through 134 removed outlier: 3.963A pdb=" N MET H 128 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN H 130 " --> pdb=" O TYR H 126 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU H 131 " --> pdb=" O VAL H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 150 removed outlier: 4.394A pdb=" N ALA H 144 " --> pdb=" O ASP H 140 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU H 150 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 161 removed outlier: 3.543A pdb=" N LYS H 161 " --> pdb=" O ASP H 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 157 through 161' Processing helix chain 'H' and resid 180 through 250 removed outlier: 4.104A pdb=" N ALA H 249 " --> pdb=" O ASP H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 288 removed outlier: 3.778A pdb=" N GLY H 277 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL H 288 " --> pdb=" O ILE H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 294 Processing helix chain 'H' and resid 295 through 311 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 156 removed outlier: 3.718A pdb=" N VAL A 71 " --> pdb=" O TRP A 172 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 67 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL A 70 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 153 through 156 removed outlier: 6.113A pdb=" N VAL B 70 " --> pdb=" O GLN B 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 153 through 156 removed outlier: 6.085A pdb=" N VAL C 70 " --> pdb=" O GLN C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 153 through 156 removed outlier: 5.997A pdb=" N VAL D 70 " --> pdb=" O GLN D 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 153 through 156 removed outlier: 6.280A pdb=" N VAL E 70 " --> pdb=" O GLN E 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 153 through 156 removed outlier: 6.215A pdb=" N VAL F 70 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 153 through 156 removed outlier: 3.640A pdb=" N VAL G 155 " --> pdb=" O THR G 173 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL G 70 " --> pdb=" O GLN G 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 153 through 156 removed outlier: 7.615A pdb=" N THR H 66 " --> pdb=" O SER H 328 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N SER H 328 " --> pdb=" O THR H 66 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA H 68 " --> pdb=" O SER H 326 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER H 326 " --> pdb=" O ALA H 68 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL H 70 " --> pdb=" O GLN H 324 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN H 324 " --> pdb=" O VAL H 70 " (cutoff:3.500A) 1341 hydrogen bonds defined for protein. 3891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6558 1.35 - 1.46: 4261 1.46 - 1.58: 9730 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 20623 Sorted by residual: bond pdb=" CB LYS C 135 " pdb=" CG LYS C 135 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.29e+00 bond pdb=" CB LYS B 132 " pdb=" CG LYS B 132 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.70e+00 bond pdb=" CB ASP A 315 " pdb=" CG ASP A 315 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.66e+00 bond pdb=" CG LYS B 132 " pdb=" CD LYS B 132 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" CB GLU E 297 " pdb=" CG GLU E 297 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.10e+00 ... (remaining 20618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 27679 2.38 - 4.75: 190 4.75 - 7.13: 21 7.13 - 9.51: 8 9.51 - 11.88: 4 Bond angle restraints: 27902 Sorted by residual: angle pdb=" CB LYS B 132 " pdb=" CG LYS B 132 " pdb=" CD LYS B 132 " ideal model delta sigma weight residual 111.30 120.15 -8.85 2.30e+00 1.89e-01 1.48e+01 angle pdb=" CB LYS C 135 " pdb=" CG LYS C 135 " pdb=" CD LYS C 135 " ideal model delta sigma weight residual 111.30 119.70 -8.40 2.30e+00 1.89e-01 1.34e+01 angle pdb=" CB MET H 152 " pdb=" CG MET H 152 " pdb=" SD MET H 152 " ideal model delta sigma weight residual 112.70 123.16 -10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CA LEU A 36 " pdb=" CB LEU A 36 " pdb=" CG LEU A 36 " ideal model delta sigma weight residual 116.30 128.18 -11.88 3.50e+00 8.16e-02 1.15e+01 angle pdb=" CB MET E 351 " pdb=" CG MET E 351 " pdb=" SD MET E 351 " ideal model delta sigma weight residual 112.70 121.99 -9.29 3.00e+00 1.11e-01 9.59e+00 ... (remaining 27897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10988 17.94 - 35.88: 1346 35.88 - 53.82: 301 53.82 - 71.76: 82 71.76 - 89.70: 40 Dihedral angle restraints: 12757 sinusoidal: 5178 harmonic: 7579 Sorted by residual: dihedral pdb=" CA ASP B 137 " pdb=" CB ASP B 137 " pdb=" CG ASP B 137 " pdb=" OD1 ASP B 137 " ideal model delta sinusoidal sigma weight residual -30.00 -88.42 58.42 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CB GLU H 293 " pdb=" CG GLU H 293 " pdb=" CD GLU H 293 " pdb=" OE1 GLU H 293 " ideal model delta sinusoidal sigma weight residual 0.00 89.56 -89.56 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU F 83 " pdb=" CG GLU F 83 " pdb=" CD GLU F 83 " pdb=" OE1 GLU F 83 " ideal model delta sinusoidal sigma weight residual 0.00 88.85 -88.85 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 12754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2836 0.053 - 0.106: 414 0.106 - 0.159: 28 0.159 - 0.212: 1 0.212 - 0.265: 1 Chirality restraints: 3280 Sorted by residual: chirality pdb=" CG LEU B 56 " pdb=" CB LEU B 56 " pdb=" CD1 LEU B 56 " pdb=" CD2 LEU B 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.26 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE F 252 " pdb=" CA ILE F 252 " pdb=" CG1 ILE F 252 " pdb=" CG2 ILE F 252 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CB ILE B 271 " pdb=" CA ILE B 271 " pdb=" CG1 ILE B 271 " pdb=" CG2 ILE B 271 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 3277 not shown) Planarity restraints: 3531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 315 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C ASP A 315 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP A 315 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A 316 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 37 " 0.011 2.00e-02 2.50e+03 1.29e-02 4.19e+00 pdb=" CG TRP G 37 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP G 37 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP G 37 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 37 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 37 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 37 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 37 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 37 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP G 37 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 297 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" CD GLU B 297 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU B 297 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 297 " -0.011 2.00e-02 2.50e+03 ... (remaining 3528 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 8950 2.95 - 3.44: 21952 3.44 - 3.93: 32999 3.93 - 4.41: 36156 4.41 - 4.90: 58974 Nonbonded interactions: 159031 Sorted by model distance: nonbonded pdb=" O ASP A 315 " pdb=" OD1 ASP A 315 " model vdw 2.464 3.040 nonbonded pdb=" O SER G 113 " pdb=" OG SER G 113 " model vdw 2.532 3.040 nonbonded pdb=" N GLU F 297 " pdb=" OE1 GLU F 297 " model vdw 2.597 3.120 nonbonded pdb=" C SER E 149 " pdb=" OG SER E 149 " model vdw 2.612 2.616 nonbonded pdb=" N VAL G 256 " pdb=" N TYR G 257 " model vdw 2.615 2.560 ... (remaining 159026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 252 or resid 272 through 356)) selection = (chain 'C' and (resid 27 through 252 or resid 272 through 356)) selection = (chain 'D' and (resid 27 through 252 or resid 272 through 356)) selection = (chain 'E' and (resid 27 through 252 or resid 272 through 356)) selection = (chain 'F' and (resid 27 through 252 or resid 272 through 356)) selection = (chain 'G' and (resid 27 through 252 or resid 272 through 356)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.130 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 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 : 0.002 0.045 20623 Z= 0.103 Angle : 0.494 11.883 27902 Z= 0.247 Chirality : 0.035 0.265 3280 Planarity : 0.003 0.052 3531 Dihedral : 17.166 89.695 7811 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.93 % Allowed : 24.53 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: 2.75 (0.18), residues: 2553 helix: 3.05 (0.13), residues: 1642 sheet: 1.83 (0.40), residues: 190 loop : -1.30 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 280 TYR 0.015 0.001 TYR H 120 PHE 0.017 0.001 PHE H 104 TRP 0.035 0.001 TRP G 37 HIS 0.001 0.000 HIS H 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (20623) covalent geometry : angle 0.49366 / 0.25 (27902) hydrogen bonds : bond 0.11019 / 7.20 ( 1341) hydrogen bonds : angle 3.97076 / 2.87 ( 3891) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 ASP cc_start: 0.9015 (p0) cc_final: 0.8686 (m-30) REVERT: B 93 ASP cc_start: 0.9140 (t0) cc_final: 0.8848 (t0) REVERT: B 174 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8700 (mt) REVERT: C 351 MET cc_start: 0.8685 (tmm) cc_final: 0.8135 (tmm) REVERT: D 44 MET cc_start: 0.6316 (ptp) cc_final: 0.5842 (tmm) REVERT: D 59 PHE cc_start: 0.8907 (m-80) cc_final: 0.8462 (m-80) REVERT: D 126 TYR cc_start: 0.8733 (t80) cc_final: 0.8396 (t80) REVERT: D 334 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8894 (m-30) REVERT: E 202 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8280 (tm-30) REVERT: F 37 TRP cc_start: 0.6015 (m100) cc_final: 0.5663 (t60) REVERT: F 102 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8348 (mp0) REVERT: F 174 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9019 (mt) REVERT: F 351 MET cc_start: 0.7739 (ppp) cc_final: 0.7154 (ttt) REVERT: G 56 LEU cc_start: 0.9405 (tp) cc_final: 0.9195 (pp) REVERT: G 152 MET cc_start: 0.8518 (ttm) cc_final: 0.8265 (mtp) REVERT: G 168 LEU cc_start: 0.9321 (mp) cc_final: 0.8809 (mm) REVERT: H 122 ARG cc_start: 0.8910 (mtt90) cc_final: 0.8366 (mtt90) REVERT: H 128 MET cc_start: 0.9292 (pmm) cc_final: 0.9061 (pmm) REVERT: H 323 TYR cc_start: 0.7793 (m-80) cc_final: 0.7498 (m-80) outliers start: 21 outliers final: 16 residues processed: 127 average time/residue: 0.1215 time to fit residues: 24.9936 Evaluate side-chains 123 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain H residue 126 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0470 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.1980 chunk 71 optimal weight: 0.0870 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 324 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.106261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.065666 restraints weight = 51126.527| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.60 r_work: 0.2872 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.0589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20623 Z= 0.088 Angle : 0.430 9.331 27902 Z= 0.220 Chirality : 0.034 0.166 3280 Planarity : 0.003 0.043 3531 Dihedral : 4.144 54.330 2753 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.73 % Allowed : 23.65 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: 2.95 (0.18), residues: 2553 helix: 3.18 (0.13), residues: 1647 sheet: 1.93 (0.40), residues: 190 loop : -1.19 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 280 TYR 0.017 0.001 TYR A 126 PHE 0.006 0.001 PHE H 107 TRP 0.020 0.001 TRP H 172 HIS 0.001 0.000 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00178 / 0.09 (20623) covalent geometry : angle 0.43000 / 0.22 (27902) hydrogen bonds : bond 0.03359 / 2.22 ( 1341) hydrogen bonds : angle 3.17070 / 2.28 ( 3891) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 ASP cc_start: 0.9122 (t0) cc_final: 0.8840 (t0) REVERT: B 126 TYR cc_start: 0.7674 (t80) cc_final: 0.7333 (t80) REVERT: C 150 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8390 (pm20) REVERT: C 351 MET cc_start: 0.8684 (tmm) cc_final: 0.8163 (tmm) REVERT: D 37 TRP cc_start: 0.8967 (m-90) cc_final: 0.8766 (p90) REVERT: D 44 MET cc_start: 0.6336 (ptp) cc_final: 0.5904 (tmm) REVERT: D 59 PHE cc_start: 0.8889 (m-80) cc_final: 0.8428 (m-80) REVERT: D 126 TYR cc_start: 0.8724 (t80) cc_final: 0.8419 (t80) REVERT: E 202 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8279 (tm-30) REVERT: F 37 TRP cc_start: 0.6101 (m100) cc_final: 0.5775 (t60) REVERT: F 351 MET cc_start: 0.7696 (ppp) cc_final: 0.7183 (ttt) REVERT: G 44 MET cc_start: 0.5257 (tmm) cc_final: 0.3645 (ptt) REVERT: G 168 LEU cc_start: 0.9315 (mp) cc_final: 0.8576 (mt) REVERT: H 122 ARG cc_start: 0.8856 (mtt90) cc_final: 0.8227 (mtt90) REVERT: H 128 MET cc_start: 0.9314 (pmm) cc_final: 0.9097 (pmm) REVERT: H 141 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8568 (mt) REVERT: H 323 TYR cc_start: 0.7797 (m-80) cc_final: 0.7492 (m-80) outliers start: 39 outliers final: 25 residues processed: 153 average time/residue: 0.1328 time to fit residues: 32.1976 Evaluate side-chains 130 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 324 GLN Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 36 optimal weight: 0.9980 chunk 233 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 174 optimal weight: 0.0050 chunk 125 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 204 optimal weight: 0.0020 chunk 142 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 167 optimal weight: 0.3980 chunk 190 optimal weight: 2.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.106265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.065654 restraints weight = 51118.691| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.59 r_work: 0.2868 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20623 Z= 0.087 Angle : 0.429 10.962 27902 Z= 0.217 Chirality : 0.034 0.167 3280 Planarity : 0.003 0.040 3531 Dihedral : 3.791 55.731 2734 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.73 % Allowed : 23.69 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: 3.03 (0.17), residues: 2553 helix: 3.23 (0.13), residues: 1645 sheet: 1.98 (0.38), residues: 190 loop : -1.13 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 280 TYR 0.018 0.001 TYR A 126 PHE 0.007 0.001 PHE H 104 TRP 0.018 0.001 TRP G 37 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.09 (20623) covalent geometry : angle 0.42851 / 0.22 (27902) hydrogen bonds : bond 0.03195 / 2.12 ( 1341) hydrogen bonds : angle 3.02884 / 2.18 ( 3891) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 ASP cc_start: 0.9111 (t0) cc_final: 0.8833 (t0) REVERT: B 126 TYR cc_start: 0.7673 (t80) cc_final: 0.7348 (t80) REVERT: C 150 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8388 (pm20) REVERT: C 351 MET cc_start: 0.8665 (tmm) cc_final: 0.8142 (tmm) REVERT: D 37 TRP cc_start: 0.8964 (m-90) cc_final: 0.8733 (p90) REVERT: D 44 MET cc_start: 0.6337 (ptp) cc_final: 0.5904 (tmm) REVERT: D 59 PHE cc_start: 0.8875 (m-80) cc_final: 0.8373 (m-80) REVERT: D 126 TYR cc_start: 0.8799 (t80) cc_final: 0.8490 (t80) REVERT: E 202 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8238 (tm-30) REVERT: F 37 TRP cc_start: 0.6042 (m100) cc_final: 0.5713 (t60) REVERT: F 102 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8357 (mp0) REVERT: F 351 MET cc_start: 0.7721 (ppp) cc_final: 0.7230 (ttt) REVERT: G 44 MET cc_start: 0.5440 (tmm) cc_final: 0.3890 (ptt) REVERT: G 168 LEU cc_start: 0.9306 (mp) cc_final: 0.8607 (mt) REVERT: H 122 ARG cc_start: 0.8873 (mtt90) cc_final: 0.8280 (mtt90) REVERT: H 128 MET cc_start: 0.9299 (pmm) cc_final: 0.9096 (pmm) REVERT: H 141 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8599 (mt) REVERT: H 323 TYR cc_start: 0.7763 (m-80) cc_final: 0.7452 (m-80) outliers start: 39 outliers final: 26 residues processed: 149 average time/residue: 0.1263 time to fit residues: 30.2051 Evaluate side-chains 133 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 128 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 220 optimal weight: 0.4980 chunk 233 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 216 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.119919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.080658 restraints weight = 53377.865| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.46 r_work: 0.2854 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20623 Z= 0.101 Angle : 0.438 10.389 27902 Z= 0.222 Chirality : 0.035 0.169 3280 Planarity : 0.003 0.040 3531 Dihedral : 3.819 58.779 2734 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.95 % Allowed : 24.05 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: 3.06 (0.17), residues: 2553 helix: 3.26 (0.13), residues: 1644 sheet: 1.98 (0.37), residues: 190 loop : -1.11 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 280 TYR 0.019 0.001 TYR A 126 PHE 0.009 0.001 PHE H 104 TRP 0.021 0.001 TRP G 37 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (20623) covalent geometry : angle 0.43789 / 0.22 (27902) hydrogen bonds : bond 0.03265 / 2.16 ( 1341) hydrogen bonds : angle 2.97798 / 2.14 ( 3891) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 110 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 ASP cc_start: 0.9129 (t0) cc_final: 0.8843 (t0) REVERT: B 126 TYR cc_start: 0.7745 (t80) cc_final: 0.7423 (t80) REVERT: C 150 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8397 (pm20) REVERT: C 351 MET cc_start: 0.8667 (tmm) cc_final: 0.8144 (tmm) REVERT: D 37 TRP cc_start: 0.8980 (m-90) cc_final: 0.8731 (p90) REVERT: D 44 MET cc_start: 0.6339 (ptp) cc_final: 0.5908 (tmm) REVERT: D 59 PHE cc_start: 0.8884 (m-80) cc_final: 0.8608 (m-80) REVERT: D 126 TYR cc_start: 0.8842 (t80) cc_final: 0.8563 (t80) REVERT: E 202 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8273 (tm-30) REVERT: F 37 TRP cc_start: 0.6081 (m100) cc_final: 0.5774 (t60) REVERT: F 351 MET cc_start: 0.7723 (ppp) cc_final: 0.7225 (ttt) REVERT: G 44 MET cc_start: 0.5601 (tmm) cc_final: 0.4114 (ptt) REVERT: G 168 LEU cc_start: 0.9298 (mp) cc_final: 0.8607 (mt) REVERT: H 128 MET cc_start: 0.9275 (pmm) cc_final: 0.9062 (pmm) REVERT: H 299 ARG cc_start: 0.8809 (mmp-170) cc_final: 0.8301 (mmp80) REVERT: H 323 TYR cc_start: 0.7810 (m-80) cc_final: 0.7471 (m-80) outliers start: 44 outliers final: 32 residues processed: 151 average time/residue: 0.1432 time to fit residues: 33.9489 Evaluate side-chains 136 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain H residue 126 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 135 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 194 optimal weight: 0.5980 chunk 240 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 219 optimal weight: 0.4980 chunk 107 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.111253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.070825 restraints weight = 48155.574| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.50 r_work: 0.2900 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20623 Z= 0.090 Angle : 0.435 10.856 27902 Z= 0.220 Chirality : 0.034 0.168 3280 Planarity : 0.003 0.040 3531 Dihedral : 3.779 57.175 2734 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.73 % Allowed : 24.14 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: 3.10 (0.17), residues: 2553 helix: 3.28 (0.13), residues: 1644 sheet: 2.03 (0.36), residues: 190 loop : -1.10 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 280 TYR 0.019 0.001 TYR A 126 PHE 0.010 0.001 PHE H 104 TRP 0.022 0.001 TRP G 37 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (20623) covalent geometry : angle 0.43484 / 0.22 (27902) hydrogen bonds : bond 0.03150 / 2.08 ( 1341) hydrogen bonds : angle 2.91507 / 2.10 ( 3891) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 ASP cc_start: 0.9101 (t0) cc_final: 0.8810 (t0) REVERT: B 126 TYR cc_start: 0.7689 (t80) cc_final: 0.7366 (t80) REVERT: C 150 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: C 351 MET cc_start: 0.8696 (tmm) cc_final: 0.8182 (tmm) REVERT: D 37 TRP cc_start: 0.8883 (m-90) cc_final: 0.8650 (p90) REVERT: D 44 MET cc_start: 0.6371 (ptp) cc_final: 0.5961 (tmm) REVERT: D 59 PHE cc_start: 0.8889 (m-80) cc_final: 0.8584 (m-80) REVERT: D 126 TYR cc_start: 0.8834 (t80) cc_final: 0.8536 (t80) REVERT: E 202 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8300 (tm-30) REVERT: F 37 TRP cc_start: 0.6096 (m100) cc_final: 0.5779 (t60) REVERT: F 102 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8355 (mp0) REVERT: F 351 MET cc_start: 0.7747 (ppp) cc_final: 0.7230 (ttt) REVERT: G 44 MET cc_start: 0.5820 (tmm) cc_final: 0.4183 (ptt) REVERT: G 56 LEU cc_start: 0.9400 (tp) cc_final: 0.9189 (tt) REVERT: G 168 LEU cc_start: 0.9283 (mp) cc_final: 0.8574 (mt) REVERT: H 122 ARG cc_start: 0.8875 (mtt90) cc_final: 0.8417 (mtm-85) REVERT: H 128 MET cc_start: 0.9255 (pmm) cc_final: 0.9027 (pmm) REVERT: H 193 ASP cc_start: 0.9401 (OUTLIER) cc_final: 0.9107 (m-30) REVERT: H 299 ARG cc_start: 0.8833 (mmp-170) cc_final: 0.8465 (mmp80) REVERT: H 323 TYR cc_start: 0.7780 (m-80) cc_final: 0.7463 (m-80) outliers start: 39 outliers final: 27 residues processed: 146 average time/residue: 0.1262 time to fit residues: 29.5077 Evaluate side-chains 133 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain H residue 193 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 47 optimal weight: 1.9990 chunk 252 optimal weight: 0.0370 chunk 211 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.106765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.066090 restraints weight = 49958.656| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.55 r_work: 0.2845 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20623 Z= 0.110 Angle : 0.450 10.950 27902 Z= 0.227 Chirality : 0.035 0.171 3280 Planarity : 0.003 0.040 3531 Dihedral : 3.619 51.894 2730 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.95 % Allowed : 23.91 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: 3.09 (0.17), residues: 2553 helix: 3.27 (0.13), residues: 1646 sheet: 2.03 (0.36), residues: 190 loop : -1.09 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 280 TYR 0.020 0.001 TYR A 126 PHE 0.012 0.001 PHE G 321 TRP 0.026 0.001 TRP G 37 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (20623) covalent geometry : angle 0.44961 / 0.23 (27902) hydrogen bonds : bond 0.03339 / 2.21 ( 1341) hydrogen bonds : angle 2.94461 / 2.12 ( 3891) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 ASP cc_start: 0.9136 (t0) cc_final: 0.8844 (t0) REVERT: B 126 TYR cc_start: 0.7795 (t80) cc_final: 0.7457 (t80) REVERT: C 150 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8418 (pm20) REVERT: C 351 MET cc_start: 0.8680 (tmm) cc_final: 0.8174 (tmm) REVERT: D 44 MET cc_start: 0.6249 (ptp) cc_final: 0.5796 (tmm) REVERT: D 59 PHE cc_start: 0.8899 (m-80) cc_final: 0.8597 (m-80) REVERT: D 126 TYR cc_start: 0.8876 (t80) cc_final: 0.8579 (t80) REVERT: D 266 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8587 (t0) REVERT: E 202 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8307 (tm-30) REVERT: F 37 TRP cc_start: 0.6107 (m100) cc_final: 0.5797 (t60) REVERT: F 351 MET cc_start: 0.7710 (ppp) cc_final: 0.7235 (ttt) REVERT: G 44 MET cc_start: 0.5807 (tmm) cc_final: 0.4379 (ptt) REVERT: G 168 LEU cc_start: 0.9281 (mp) cc_final: 0.8592 (mt) REVERT: H 128 MET cc_start: 0.9277 (pmm) cc_final: 0.9062 (pmm) REVERT: H 299 ARG cc_start: 0.8835 (mmp-170) cc_final: 0.8532 (mmp80) REVERT: H 323 TYR cc_start: 0.7815 (m-80) cc_final: 0.7458 (m-80) outliers start: 44 outliers final: 32 residues processed: 146 average time/residue: 0.1181 time to fit residues: 27.4160 Evaluate side-chains 135 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain H residue 193 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 134 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 217 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 30.0000 chunk 76 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.118943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.079609 restraints weight = 53020.209| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.45 r_work: 0.2852 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20623 Z= 0.100 Angle : 0.451 11.552 27902 Z= 0.226 Chirality : 0.035 0.169 3280 Planarity : 0.003 0.040 3531 Dihedral : 3.578 46.560 2730 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.73 % Allowed : 24.22 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: 3.11 (0.17), residues: 2553 helix: 3.28 (0.13), residues: 1646 sheet: 2.05 (0.36), residues: 189 loop : -1.06 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 280 TYR 0.019 0.001 TYR A 126 PHE 0.012 0.001 PHE G 321 TRP 0.028 0.001 TRP G 37 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (20623) covalent geometry : angle 0.45102 / 0.23 (27902) hydrogen bonds : bond 0.03256 / 2.15 ( 1341) hydrogen bonds : angle 2.90763 / 2.09 ( 3891) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 ASP cc_start: 0.9132 (t0) cc_final: 0.8840 (t0) REVERT: B 126 TYR cc_start: 0.7733 (t80) cc_final: 0.7383 (t80) REVERT: C 150 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8409 (pm20) REVERT: C 351 MET cc_start: 0.8696 (tmm) cc_final: 0.8206 (tmm) REVERT: D 37 TRP cc_start: 0.8979 (m-90) cc_final: 0.8727 (p90) REVERT: D 44 MET cc_start: 0.6309 (ptp) cc_final: 0.5842 (tmm) REVERT: D 59 PHE cc_start: 0.8882 (m-80) cc_final: 0.8578 (m-80) REVERT: D 126 TYR cc_start: 0.8864 (t80) cc_final: 0.8564 (t80) REVERT: D 266 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8565 (t0) REVERT: D 297 GLU cc_start: 0.8612 (tp30) cc_final: 0.8075 (tp30) REVERT: E 202 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8277 (tm-30) REVERT: F 37 TRP cc_start: 0.6115 (m100) cc_final: 0.5797 (t60) REVERT: F 102 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8323 (mp0) REVERT: F 174 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8917 (mt) REVERT: F 351 MET cc_start: 0.7698 (ppp) cc_final: 0.7227 (ttt) REVERT: G 44 MET cc_start: 0.6044 (tmm) cc_final: 0.4599 (ptt) REVERT: G 168 LEU cc_start: 0.9295 (mp) cc_final: 0.8585 (mt) REVERT: H 128 MET cc_start: 0.9292 (pmm) cc_final: 0.9068 (pmm) REVERT: H 299 ARG cc_start: 0.8828 (mmp-170) cc_final: 0.8571 (mmp80) REVERT: H 323 TYR cc_start: 0.7773 (m-80) cc_final: 0.7425 (m-80) outliers start: 39 outliers final: 30 residues processed: 143 average time/residue: 0.1329 time to fit residues: 30.4670 Evaluate side-chains 137 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 193 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 107 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 156 optimal weight: 0.4980 chunk 87 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.118060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.078558 restraints weight = 53225.572| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.47 r_work: 0.2849 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20623 Z= 0.103 Angle : 0.458 11.624 27902 Z= 0.229 Chirality : 0.035 0.170 3280 Planarity : 0.004 0.049 3531 Dihedral : 3.491 42.930 2728 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.64 % Allowed : 24.18 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: 3.10 (0.17), residues: 2553 helix: 3.27 (0.13), residues: 1646 sheet: 2.08 (0.36), residues: 189 loop : -1.07 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 280 TYR 0.018 0.001 TYR A 126 PHE 0.014 0.001 PHE G 321 TRP 0.030 0.001 TRP G 37 HIS 0.001 0.000 HIS H 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (20623) covalent geometry : angle 0.45815 / 0.23 (27902) hydrogen bonds : bond 0.03272 / 2.17 ( 1341) hydrogen bonds : angle 2.90482 / 2.09 ( 3891) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 ASP cc_start: 0.9138 (t0) cc_final: 0.8860 (t0) REVERT: B 126 TYR cc_start: 0.7755 (t80) cc_final: 0.7404 (t80) REVERT: C 150 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8425 (pm20) REVERT: C 351 MET cc_start: 0.8689 (tmm) cc_final: 0.8198 (tmm) REVERT: D 37 TRP cc_start: 0.9019 (m-90) cc_final: 0.8768 (p90) REVERT: D 44 MET cc_start: 0.6314 (ptp) cc_final: 0.5846 (tmm) REVERT: D 59 PHE cc_start: 0.8889 (m-80) cc_final: 0.8579 (m-80) REVERT: D 126 TYR cc_start: 0.8903 (t80) cc_final: 0.8606 (t80) REVERT: D 266 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8574 (t0) REVERT: D 297 GLU cc_start: 0.8633 (tp30) cc_final: 0.8101 (tp30) REVERT: E 202 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8293 (tm-30) REVERT: F 37 TRP cc_start: 0.6165 (m100) cc_final: 0.5846 (t60) REVERT: F 102 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8377 (mp0) REVERT: F 174 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8962 (mt) REVERT: F 351 MET cc_start: 0.7652 (ppp) cc_final: 0.7205 (ttt) REVERT: G 44 MET cc_start: 0.6271 (tmm) cc_final: 0.4905 (ptt) REVERT: G 168 LEU cc_start: 0.9300 (mp) cc_final: 0.8668 (mt) REVERT: H 79 TRP cc_start: 0.7727 (m100) cc_final: 0.6933 (m100) REVERT: H 122 ARG cc_start: 0.8803 (ttm110) cc_final: 0.8133 (mtm110) REVERT: H 128 MET cc_start: 0.9283 (pmm) cc_final: 0.9054 (pmm) REVERT: H 299 ARG cc_start: 0.8838 (mmp-170) cc_final: 0.8597 (mmp80) REVERT: H 323 TYR cc_start: 0.7779 (m-80) cc_final: 0.7424 (m-80) outliers start: 37 outliers final: 31 residues processed: 140 average time/residue: 0.1320 time to fit residues: 29.7132 Evaluate side-chains 139 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 193 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 186 optimal weight: 10.0000 chunk 192 optimal weight: 0.2980 chunk 174 optimal weight: 0.9990 chunk 131 optimal weight: 40.0000 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.110426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069526 restraints weight = 48011.551| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.59 r_work: 0.2883 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20623 Z= 0.113 Angle : 0.469 11.848 27902 Z= 0.235 Chirality : 0.035 0.172 3280 Planarity : 0.003 0.053 3531 Dihedral : 3.470 43.279 2728 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.68 % Allowed : 24.14 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: 3.09 (0.17), residues: 2553 helix: 3.26 (0.13), residues: 1646 sheet: 2.06 (0.36), residues: 189 loop : -1.08 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 280 TYR 0.019 0.001 TYR A 126 PHE 0.015 0.001 PHE G 321 TRP 0.032 0.001 TRP G 37 HIS 0.001 0.000 HIS H 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (20623) covalent geometry : angle 0.46851 / 0.23 (27902) hydrogen bonds : bond 0.03377 / 2.24 ( 1341) hydrogen bonds : angle 2.92930 / 2.11 ( 3891) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.9116 (mmt) cc_final: 0.8873 (mmt) REVERT: A 315 ASP cc_start: 0.8964 (p0) cc_final: 0.8705 (m-30) REVERT: B 93 ASP cc_start: 0.9139 (t0) cc_final: 0.8857 (t0) REVERT: B 126 TYR cc_start: 0.7744 (t80) cc_final: 0.7353 (t80) REVERT: C 150 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8434 (pm20) REVERT: C 297 GLU cc_start: 0.8551 (tp30) cc_final: 0.8171 (tp30) REVERT: C 351 MET cc_start: 0.8683 (tmm) cc_final: 0.8191 (tmm) REVERT: D 37 TRP cc_start: 0.8936 (m-90) cc_final: 0.8699 (p90) REVERT: D 44 MET cc_start: 0.6341 (ptp) cc_final: 0.5890 (tmm) REVERT: D 59 PHE cc_start: 0.8877 (m-80) cc_final: 0.8557 (m-80) REVERT: D 126 TYR cc_start: 0.8897 (t80) cc_final: 0.8605 (t80) REVERT: D 266 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8483 (t0) REVERT: E 202 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8276 (tm-30) REVERT: E 297 GLU cc_start: 0.8519 (tp30) cc_final: 0.8306 (tp30) REVERT: F 37 TRP cc_start: 0.6182 (m100) cc_final: 0.5854 (t60) REVERT: F 102 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8351 (mp0) REVERT: F 174 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8941 (mt) REVERT: G 44 MET cc_start: 0.6388 (tmm) cc_final: 0.4845 (ptt) REVERT: G 128 MET cc_start: 0.8834 (mmp) cc_final: 0.8521 (mmp) REVERT: G 168 LEU cc_start: 0.9324 (mp) cc_final: 0.8668 (mt) REVERT: H 79 TRP cc_start: 0.7738 (m100) cc_final: 0.6946 (m100) REVERT: H 122 ARG cc_start: 0.8802 (ttm110) cc_final: 0.8132 (mtm110) REVERT: H 128 MET cc_start: 0.9272 (pmm) cc_final: 0.9036 (pmm) REVERT: H 323 TYR cc_start: 0.7824 (m-80) cc_final: 0.7409 (m-80) outliers start: 38 outliers final: 30 residues processed: 142 average time/residue: 0.1270 time to fit residues: 29.3641 Evaluate side-chains 139 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 113 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 246 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 249 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 125 optimal weight: 0.0770 chunk 230 optimal weight: 9.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.119163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.080028 restraints weight = 52752.677| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.43 r_work: 0.2835 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20623 Z= 0.114 Angle : 0.478 11.825 27902 Z= 0.240 Chirality : 0.035 0.172 3280 Planarity : 0.004 0.052 3531 Dihedral : 3.384 43.204 2726 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.46 % Allowed : 24.31 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: 3.07 (0.17), residues: 2553 helix: 3.25 (0.13), residues: 1645 sheet: 2.08 (0.36), residues: 189 loop : -1.09 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 280 TYR 0.020 0.001 TYR H 120 PHE 0.013 0.001 PHE G 321 TRP 0.032 0.001 TRP G 37 HIS 0.001 0.000 HIS H 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (20623) covalent geometry : angle 0.47821 / 0.24 (27902) hydrogen bonds : bond 0.03382 / 2.24 ( 1341) hydrogen bonds : angle 2.92441 / 2.10 ( 3891) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.9065 (mmt) cc_final: 0.8857 (mmt) REVERT: B 93 ASP cc_start: 0.9150 (t0) cc_final: 0.8869 (t0) REVERT: B 126 TYR cc_start: 0.7707 (t80) cc_final: 0.7303 (t80) REVERT: C 150 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8422 (pm20) REVERT: C 297 GLU cc_start: 0.8569 (tp30) cc_final: 0.8195 (tp30) REVERT: C 351 MET cc_start: 0.8690 (tmm) cc_final: 0.8187 (tmm) REVERT: D 37 TRP cc_start: 0.9040 (m-90) cc_final: 0.8787 (p90) REVERT: D 44 MET cc_start: 0.6312 (ptp) cc_final: 0.5849 (tmm) REVERT: D 59 PHE cc_start: 0.8894 (m-80) cc_final: 0.8584 (m-80) REVERT: D 126 TYR cc_start: 0.8885 (t80) cc_final: 0.8592 (t80) REVERT: D 266 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8478 (t0) REVERT: E 202 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8281 (tm-30) REVERT: E 297 GLU cc_start: 0.8530 (tp30) cc_final: 0.8313 (tp30) REVERT: F 37 TRP cc_start: 0.6201 (m100) cc_final: 0.5879 (t60) REVERT: F 102 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8344 (mp0) REVERT: F 174 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8937 (mt) REVERT: F 351 MET cc_start: 0.7553 (ppp) cc_final: 0.6900 (ttt) REVERT: G 168 LEU cc_start: 0.9321 (mp) cc_final: 0.8716 (mt) REVERT: H 79 TRP cc_start: 0.7708 (m100) cc_final: 0.6904 (m100) REVERT: H 128 MET cc_start: 0.9270 (pmm) cc_final: 0.9029 (pmm) REVERT: H 143 ARG cc_start: 0.9614 (ptp-110) cc_final: 0.9298 (ptp90) REVERT: H 323 TYR cc_start: 0.7819 (m-80) cc_final: 0.7372 (m-80) outliers start: 33 outliers final: 30 residues processed: 140 average time/residue: 0.1283 time to fit residues: 28.7671 Evaluate side-chains 139 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 107 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 255 optimal weight: 0.0670 chunk 198 optimal weight: 30.0000 chunk 231 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 97 optimal weight: 50.0000 chunk 41 optimal weight: 0.0030 chunk 230 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.118178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.078846 restraints weight = 53199.339| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.48 r_work: 0.2833 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20623 Z= 0.118 Angle : 0.492 11.874 27902 Z= 0.245 Chirality : 0.036 0.294 3280 Planarity : 0.004 0.069 3531 Dihedral : 3.402 43.259 2726 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.51 % Allowed : 24.40 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: 3.05 (0.17), residues: 2553 helix: 3.23 (0.13), residues: 1645 sheet: 2.09 (0.36), residues: 189 loop : -1.11 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 280 TYR 0.021 0.001 TYR H 120 PHE 0.011 0.001 PHE G 321 TRP 0.033 0.001 TRP G 37 HIS 0.001 0.000 HIS H 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (20623) covalent geometry : angle 0.49211 / 0.25 (27902) hydrogen bonds : bond 0.03422 / 2.27 ( 1341) hydrogen bonds : angle 2.93981 / 2.11 ( 3891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4644.64 seconds wall clock time: 80 minutes 16.17 seconds (4816.17 seconds total)